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Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing

Nature Reviews Molecular Cell Biology volume 12, pages 483–492 (2011)Cite this article

Subjects

Key Points

  • RNA polymerase IV (Pol IV) and Pol V are plant-specific RNA polymerases that have non-redundant activities that evolved as specialized forms of Pol II. Although non-essential for viability under laboratory conditions, they have important roles in plant development and genome defence.

  • In the RNA-directed DNA methylation (RdDM) pathway, Pol IV acts in conjunction with RNA-DEPENDENT RNA POLYMERASE 2 (RDR2) and DICER-LIKE 3 (DCL3) to generate 24-nucleotide small interfering RNAs (siRNAs) that associate primarily with ARGONAUTE 4 (AGO4). AGO4–siRNA complexes bind to Pol V transcripts at target loci, facilitating the recruitment of chromatin modifying activities, including the de novo cytosine methyltransferase DOMAINS REARRANGED METHYLTRANSFERASE 2 (DRM2).

  • Pol IV and Pol V orchestrate a variety of other non-coding RNA-mediated gene silencing processes, including heterochromatin organization, paramutation, short- and long-range spreading of silencing signals, and biotic and abiotic stress responses. Many of these pathways use additional components of the RdDM pathway or related silencing pathways.

  • Arabidopsis thaliana Pol IV and Pol V are differentiated by variation within their largest, fifth and seventh subunits, with additional isoforms of Pol V containing alternative third and ninth subunits. Unique subunit usage may confer functional diversification on these enzymes through mechanisms that are either inherent to the subunits themselves or through the protein–protein or protein–nucleic acid interactions they may mediate.

  • Pol V transcripts that are detected in vivo require key amino acids that are conserved at all RNA polymerase active sites. Pol IV transcripts have not been defined in vivo, but biological functions of Pol IV are also abolished by mutation of the active site.

  • Pol IV or Pol V transcription has not yet been recapitulated in vitro, precluding detailed analyses of their templates or properties as enzymes.

Abstract

In all eukaryotes, nuclear DNA-dependent RNA polymerases I, II and III synthesize the myriad RNAs that are essential for life. Remarkably, plants have evolved two additional multisubunit RNA polymerases, RNA polymerases IV and V, which orchestrate non-coding RNA-mediated gene silencing processes affecting development, transposon taming, antiviral defence and allelic crosstalk. Biochemical details concerning the templates and products of RNA polymerases IV and V are lacking. However, their subunit compositions reveal that they evolved as specialized forms of RNA polymerase II, which provides the unique opportunity to study the functional diversification of a eukaryotic RNA polymerase family.

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Figure 1: Domain structures of the largest subunit of the five Arabidopsis thaliana nuclear multisubunit RNA polymerases.
Figure 2: Model for the RNA-directed DNA methylation pathway in Arabidopsis thaliana.
Figure 3: Interactions among proteins of the RNA-directed DNA methylation pathway.
Figure 4: Summary of Arabidopsis thaliana Pol II, Pol IV and Pol V subunit compositions.

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Acknowledgements

Our studies of RNA polymerases IV and V are supported by grants from the US National Institutes of Health (GM077590) and the Monsanto Company. All opinions expressed are those of the authors and do not necessarily reflect the views of our sponsors. We apologize to our many colleagues whose work was not cited owing to limitations on the numbers of references.

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Authors and Affiliations

  1. Department of Biology and Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, 47405, Indiana, USA

    Jeremy R. Haag & Craig S. Pikaard

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  1. Jeremy R. Haag
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  2. Craig S. Pikaard
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Correspondence to Craig S. Pikaard.

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Glossary

Short interspersed nuclear elements

(SINES). Retrotransposable elements in eukaryotic genomes that are ancestrally related to tRNAs.

Retrotransposons

Transposons that replicate through RNA intermediates and can induce mutations by inserting near or within genes.

Inverted repeats

Nucleotide sequences that contain regions of self-complementarity, such that they are capable of folding back on themselves to generate double-stranded RNA hairpin structures.

Companion cells

Specialized parenchyma cells that are located in the phloem of flowering plants and carry out the loading and unloading of molecules into associated phloem sieve-tubes.

Chromocenters

Sites of heterochromatin association in the nucleus, typically involving pericentromeric repeats and other repeats.

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Haag, J., Pikaard, C. Multisubunit RNA polymerases IV and V: purveyors of non-coding RNA for plant gene silencing. Nat Rev Mol Cell Biol 12, 483–492 (2011). https://doi.org/10.1038/nrm3152

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