MicroRNAs (miRNAs) in eukaryotes guide post-transcriptional regulation by means of targeted RNA degradation and translational arrest1. They are released by a Dicer nuclease as a 21–24-nucleotide RNA duplex from a precursor in which an imperfectly matched inverted repeat forms a partly double-stranded region. One of the two strands is then recruited by an Argonaute nuclease that is the effector protein of the silencing mechanism. Short interfering RNAs (siRNAs), which are similar to miRNAs, are also produced by Dicer but the precursors are perfectly double-stranded RNA. These siRNAs guide post-transcriptional regulation, as with miRNAs, and epigenetic genome modification. Diverse eukaryotes including fungi, plants, protozoans and metazoans produce siRNAs2,3,4,5 but, until now, miRNAs have not been described in unicellular organisms and it has been suggested that they evolved together with multicellularity in separate plant and animal lineages6. Here we show that the unicellular alga Chlamydomonas reinhardtii contains miRNAs, putative evolutionary precursors of miRNAs and species of siRNAs resembling those in higher plants. The common features of miRNAs and siRNAs in an alga and in higher plants indicate that complex RNA-silencing systems evolved before multicellularity and were a feature of primitive eukaryotic cells.
Subscribe to Journal
Get full journal access for 1 year
only $3.90 per issue
All prices are NET prices.
VAT will be added later in the checkout.
Tax calculation will be finalised during checkout.
Rent or Buy article
Get time limited or full article access on ReadCube.
All prices are NET prices.
Bartel, D. P. MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116, 281–297 (2004)
Reinhart, B. J. & Bartel, D. P. Small RNAs correspond to centromere heterochromatic repeats. Science 297, 1831 (2002)
Llave, C., Kasschau, K. D., Rector, M. A. & Carrington, J. C. Endogenous and silencing-associated small RNAs in plants. Plant Cell 14, 1605–1619 (2002)
Djikeng, A., Shi, H. F., Tschudi, C. & Ullu, E. RNA interference in Trypanosoma brucei: Cloning of small interfering RNAs provides evidence for retroposon-derived 24- 26-nucleotide RNAs. RNA 7, 1522–1530 (2001)
Ambros, V., Lee, R. C., Lavanway, A., Williams, P. T. & Jewell, D. MicroRNAs and other tiny endogenous RNAs in C. elegans. Curr. Biol. 13, 807–818 (2003)
Allen, E. et al. Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana. Nature Genet. 36, 1282–1290 (2004)
Cerutti, H. & Casas-Mollano, J. A. On the origin and functions of RNA-mediated silencing: from protists to man. Curr. Genet. 50, 81–99 (2006)
Lu, C. et al. MicroRNAs and other small RNAs enriched in the Arabidopsis RNA-dependent RNA polymerase-2 mutant. Genome Res. 16, 1276–1288 (2006)
Schwarz, D. S. et al. Asymmetry in the assembly of the RNAi enzyme complex. Cell 115, 199–208 (2003)
Khvorova, A., Reynolds, A. & Jayasena, S. D. Functional siRNAs and miRNAs exhibit strand bias. Cell 115, 209–216 (2003)
Vazquez, F. et al. Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs. Mol. Cell 16, 69–79 (2004)
Borsani, O., Zhu, J., Verslues, P. E., Sunkar, R. & Zhu, J.-K. Endogenous siRNAs derived from a pair of natural cis-antisense transcripts regulate salt tolerance in Arabidopsis. Cell 123, 1279–1291 (2005)
Peragine, A., Yoshikawa, M., Wu, G., Albrecht, H. L. & Poethig, R. S. SGS3 and SGS2/SDE1/RDR6 are required for juvenile development and the production of trans-acting siRNAs in Arabidopsis. Genes Dev. 18, 2368–2379 (2004)
Han, J. et al. Molecular basis for the recognition of primary micro-RNAs by the Drosha–DGCR8 complex. Cell 125, 887–901 (2006)
Llave, C., Xie, Z., Kasschau, K. D. & Carrington, J. C. Cleavage of Scarecrow-like mRNA targets directed by a class of Arabidopsis miRNA. Science 297, 2053–2056 (2002)
Schwab, R. et al. Specific effects of microRNAs on the plant transcriptome. Dev. Cell 8, 517–527 (2005)
Pazour, G. J., Agrin, N., Leszyk, J. & Witman, G. B. Proteomic analysis of a eukaryotic cilium. J. Cell Biol. 170, 103–113 (2005)
Yu, B. et al. Methylation as a crucial step in plant microRNA biogenesis. Science 307, 932–935 (2005)
Yang, Z., Ebright, Y. W., Yu, B. & Chen, X. HEN1 recognizes 21–24 nt small RNA duplexes and deposits a methyl group onto the 2′ OH of the 3′ terminal nucleotide. Nucleic Acids Res. 34, 667–675 (2006)
Li, J., Yang, Z., Yu, B., Liu, J. & Chen, X. Methylation protects miRNAs and siRNAs from a 3′-end uridylation activity in Arabidopsis. Curr. Biol. 15, 1501–1507 (2005)
Floyd, S. K. & Bowman, J. L. Ancient microRNA target sequences in plants. Nature 428, 485–486 (2004)
Arazi, T. et al. Cloning and characterization of micro-RNAs from moss. Plant J. 43, 837–848 (2005)
Baulcombe, D. RNA silencing in plants. Nature 431, 356–363 (2004)
Wegener, D., Treier, U. & Beck, C. F. Procedures for the generation of mature Chlamydomonas reinhardtii zygotes for molecular and biochemical analyses. Plant Physiol. 90, 512–515 (1989)
Chappell, L., Baulcombe, D. & Molnar, A. in Current Protocols in Microbiology (eds Coico, R. et al.) 16H.2.1–16H.2.17 (Wiley, Hoboken, NJ, 2005)
Baumberger, N. & Baulcombe, D. C. Arabidopsis ARGONAUTE1 is an RNA Slicer that selectively recruits micro RNAs and short interfering RNAs. Proc. Natl Acad. Sci. USA 102, 11928–11933 (2005)
Margulies, M. et al. Genome sequencing in microfabricated high-density picolitre reactors. Nature 437, 376–380 (2005)
Edgar, R. C. MUSCLE: a multiple sequence alignment method with reduced time and space complexity. BMC Bioinformatics 5, 1–19 (2004)
Hofacker, I. L. et al. Fast folding and comparison of RNA secondary structures. Monatsh. Chem. 125, 167–188 (1994)
Bonnet, E., Wuyts, J., Rouze, P. & Van de Peer, Y. Evidence that microRNA precursors, unlike other non-coding RNAs, have lower folding free energies than random sequences. Bioinformatics 20, 2911–2917 (2004)
We thank S. Purton for helpful discussions and technical advice, and E. Havecker and R. A. Mosher for critical comments on the manuscript. This work was supported by the Gatsby Charitable Foundation. A.M. was a recipient of a long-term EMBO fellowship. F.S. was supported in part by a BBSRC grant and E.C.T. was supported by a Marie Curie Early Stage Training Fellowship. The Chlamydomonas genome sequence data were produced by the US Department of Energy Joint Genome Institute (http://www.jgi.doe.gov/) and are provided for use in this publication only.
Author Contributions A.M. and D.C.B. designed research. A.M. and E.C.T. performed the experiments. F.S. and D.J.S. developed the sRNA pipeline and performed the computational analyses. A.M., F.S., D.J.S. and D.C.B. analysed the data. A.M., F.S. and D.C.B. wrote the paper.
The small RNA sequences have been deposited in GEO with the accession number GSE7575.
Reprints and permissions information is available at www.nature.com/reprints. The authors declare no competing financial interests.
About this article
Cite this article
Molnár, A., Schwach, F., Studholme, D. et al. miRNAs control gene expression in the single-cell alga Chlamydomonas reinhardtii. Nature 447, 1126–1129 (2007). https://doi.org/10.1038/nature05903
Genome-wide analyses across Viridiplantae reveal the origin and diversification of small RNA pathway-related genes
Communications Biology (2021)
Nature Reviews Genetics (2020)
Distinct roles of Argonaute in the green alga Chlamydomonas reveal evolutionary conserved mode of miRNA-mediated gene expression
Scientific Reports (2019)
Improved photobio-H2 production regulated by artificial miRNA targeting psbA in green microalga Chlamydomonas reinhardtii
Biotechnology for Biofuels (2018)