An antagonistic function for Arabidopsis DCL2 in development and a new function for DCL4 in generating viral siRNAs

Plants contain more DICER‐LIKE (DCL) enzymes and double‐stranded RNA binding (DRB) proteins than other eukaryotes, resulting in increased small RNA network complexities. Analyses of single, double, triple and quadruple dcl mutants exposed DCL1 as a sophisticated enzyme capable of producing both microRNAs (miRNAs) and siRNAs, unlike the three other DCLs, which only produce siRNAs. Depletion of siRNA‐specific DCLs results in unbalanced small RNA levels, indicating a redeployment of DCL/DRB complexes. In particular, DCL2 antagonizes the production of miRNAs and siRNAs by DCL1 in certain circumstances and affects development deleteriously in dcl1 dcl4 and dcl1 dcl3 dcl4 mutant plants, whereas dcl1 dcl2 dcl3 dcl4 quadruple mutant plants are viable. We also show that viral siRNAs are produced by DCL4, and that DCL2 can substitute for DCL4 when this latter activity is reduced or inhibited by viruses, pointing to the competitiveness of DCL2. Given the complexity of the small RNA repertoire in plants, the implication of each DCL, in particular DCL2, in the production of small RNAs that have no known function will constitute one of the next challenges.

[1]  I. Henderson,et al.  Dissecting Arabidopsis thaliana DICER function in small RNA processing, gene silencing and DNA methylation patterning , 2006, Nature Genetics.

[2]  Olivier Voinnet,et al.  DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal , 2005, Nature Genetics.

[3]  A. Mallory,et al.  Ectopic DICER-LIKE1 Expression in P1/HC-Pro Arabidopsis Rescues Phenotypic Anomalies but Not Defects in MicroRNA and Silencing Pathways , 2005, The Plant Cell Online.

[4]  Valerian V Dolja,et al.  Viral RNA silencing suppressors inhibit the microRNA pathway at an intermediate step. , 2004, Genes & development.

[5]  D. Bartel,et al.  MicroRNAS and their regulatory roles in plants. , 2006, Annual review of plant biology.

[6]  Scott A. Givan,et al.  ASRP: the Arabidopsis Small RNA Project Database , 2004, Nucleic Acids Res..

[7]  K. Mise,et al.  A plant RNA virus suppresses RNA silencing through viral RNA replication , 2005, The EMBO journal.

[8]  Yuichiro Watanabe,et al.  Arabidopsis micro-RNA biogenesis through Dicer-like 1 protein functions. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[9]  D. Xie,et al.  Viral Virulence Protein Suppresses RNA Silencing–Mediated Defense but Upregulates the Role of MicroRNA in Host Gene Expression , 2004, The Plant Cell Online.

[10]  Edwards Allen,et al.  DICER-LIKE 4 functions in trans-acting small interfering RNA biogenesis and vegetative phase change in Arabidopsis thaliana. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[11]  P. Waterhouse,et al.  A Branched Pathway for Transgene-Induced RNA Silencing in Plants , 2002, Current Biology.

[12]  B. Reinhart,et al.  MicroRNAs in plants. , 2002, Genes & development.

[13]  S. Jacobsen,et al.  Disruption of an RNA helicase/RNAse III gene in Arabidopsis causes unregulated cell division in floral meristems. , 1999, Development.

[14]  David P. Kreil,et al.  Atypical RNA polymerase subunits required for RNA-directed DNA methylation , 2005, Nature Genetics.

[15]  Kazuo Shinozaki,et al.  Specific interactions between Dicer-like proteins and HYL1/DRB- family dsRNA-binding proteins in Arabidopsis thaliana , 2004, Plant Molecular Biology.

[16]  W. Gruissem,et al.  Molecular characterization of geminivirus-derived small RNAs in different plant species , 2006, Nucleic Acids Research.

[17]  R. MacDiarmid.  RNA silencing in productive virus infections. , 2005, Annual review of phytopathology.

[18]  C. Fauquet,et al.  MicroRNA-binding viral protein interferes with Arabidopsis development. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[19]  N. Fedoroff,et al.  The Arabidopsis double-stranded RNA-binding protein HYL1 plays a role in microRNA-mediated gene regulation. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[20]  Animesh Ray,et al.  DICER-LIKE1: blind men and elephants in Arabidopsis development. , 2002, Trends in plant science.

[21]  Jinsong Bao,et al.  Hierarchical Action and Inhibition of Plant Dicer-Like Proteins in Antiviral Defense , 2006, Science.

[22]  G. Macino,et al.  Redundancy of the Two Dicer Genes in Transgene-Induced Posttranscriptional Gene Silencing in Neurospora crassa , 2004, Molecular and Cellular Biology.

[23]  H. Vaucheret.  Post-transcriptional small RNA pathways in plants: mechanisms and regulations. , 2006, Genes & development.

[24]  F. Qu,et al.  The Coat Protein of Turnip Crinkle Virus Suppresses Posttranscriptional Gene Silencing at an Early Initiation Step , 2003, Journal of Virology.

[25]  B. Reinhart,et al.  A viral suppressor of RNA silencing differentially regulates the accumulation of short interfering RNAs and micro-RNAs in tobacco , 2002, Proceedings of the National Academy of Sciences of the United States of America.

[26]  V. Ambros,et al.  Interacting endogenous and exogenous RNAi pathways in Caenorhabditis elegans. , 2006, RNA.

[27]  Philippe Mourrain,et al.  Arabidopsis SGS2 and SGS3 Genes Are Required for Posttranscriptional Gene Silencing and Natural Virus Resistance , 2000, Cell.

[28]  O. Borsani,et al.  Endogenous siRNAs Derived from a Pair of Natural cis-Antisense Transcripts Regulate Salt Tolerance in Arabidopsis , 2005, Cell.

[29]  S. Lerbs-Mache,et al.  Reinforcement of silencing at transposons and highly repeated sequences requires the concerted action of two distinct RNA polymerases IV in Arabidopsis. , 2005, Genes & development.

[30]  C. Mello,et al.  The dsRNA Binding Protein RDE-4 Interacts with RDE-1, DCR-1, and a DExH-Box Helicase to Direct RNAi in C. elegans , 2002, Cell.

[31]  E. Sontheimer,et al.  Distinct Roles for Drosophila Dicer-1 and Dicer-2 in the siRNA/miRNA Silencing Pathways , 2004, Cell.

[32]  H. Vaucheret,et al.  The Nuclear dsRNA Binding Protein HYL1 Is Required for MicroRNA Accumulation and Plant Development, but Not Posttranscriptional Transgene Silencing , 2004, Current Biology.

[33]  David P. Bartel,et al.  Partially Redundant Functions of Arabidopsis DICER-like Enzymes and a Role for DCL4 in Producing trans-Acting siRNAs , 2005, Current Biology.

[34]  H. Vaucheret,et al.  Arabidopsis HEN1 A Genetic Link between Endogenous miRNA Controlling Development and siRNA Controlling Transgene Silencing and Virus Resistance , 2003, Current Biology.

[35]  Adam M. Gustafson,et al.  Genetic and Functional Diversification of Small RNA Pathways in Plants , 2004, PLoS biology.

[36]  G. Ruvkun,et al.  Functional Proteomics Reveals the Biochemical Niche of C. elegans DCR-1 in Multiple Small-RNA-Mediated Pathways , 2006, Cell.

[37]  R. Poethig,et al.  A pathway for the biogenesis of trans-acting siRNAs in Arabidopsis. , 2005, Genes & development.

[38]  Shivakundan Singh Tej,et al.  Elucidation of the Small RNA Component of the Transcriptome , 2005, Science.

[39]  J. Messing,et al.  CARPEL FACTORY, a Dicer Homolog, and HEN1, a Novel Protein, Act in microRNA Metabolism in Arabidopsis thaliana , 2002, Current Biology.

[40]  Philippe Mourrain,et al.  Fertile Hypomorphic ARGONAUTE (ago1) Mutants Impaired in Post-Transcriptional Gene Silencing and Virus Resistance , 2002, The Plant Cell Online.

[41]  J. Birchler,et al.  RNA silencing in Drosophila , 2005, FEBS letters.

[42]  Nicolas Bouché,et al.  DRB4-Dependent TAS3 trans-Acting siRNAs Control Leaf Morphology through AGO7 , 2006, Current Biology.

[43]  D. Bartel,et al.  AGO1 homeostasis entails coexpression of MIR168 and AGO1 and preferential stabilization of miR168 by AGO1. , 2006, Molecular cell.