RNA polymerase V (Pol V), previously known as RNA polymerase IVb, is a multisubunit plant specific

RNA polymerase In molecular biology, RNA polymerase (abbreviated RNAP or RNApol), or more specifically DNA-directed/dependent RNA polymerase (DdRP), is an enzyme that synthesizes RNA from a DNA template. Using the enzyme helicase, RNAP locally opens the ...

. It is required for normal function and biogenesis of small interfering

RNA Ribonucleic acid (RNA) is a polymeric molecule essential in various biological roles in coding, decoding, regulation and expression of genes. RNA and deoxyribonucleic acid ( DNA) are nucleic acids. Along with lipids, proteins, and carbohydra ...

(

siRNA Small interfering RNA (siRNA), sometimes known as short interfering RNA or silencing RNA, is a class of double-stranded RNA at first non-coding RNA molecules, typically 20-24 (normally 21) base pairs in length, similar to miRNA, and operating ...

). Together with

RNA polymerase IV RNA polymerase IV (RNAP IV) is an enzyme that synthesizes small interfering RNA (siRNA) in plants, which silence gene expression. RNAP IV belongs to a family of enzymes that catalyze the process of transcription known as RNA Polymerases, which syn ...

(Pol IV), Pol V is involved in an siRNA-dependent epigenetic pathway known as

RNA-directed DNA methylation RNA-directed DNA methylation (RdDM) is a biological process in which non-coding RNA molecules direct the addition of DNA methylation to specific DNA sequences. The RdDM pathway is unique to plants, although other mechanisms of RNA-directed chromati ...

(RdDM), which establishes and maintains heterochromatic silencing in plants.

Structure

RNA polymerase V is composed of 12 subunits that are paralogous to

RNA polymerase II RNA polymerase II (RNAP II and Pol II) is a multiprotein complex that transcribes DNA into precursors of messenger RNA (mRNA) and most small nuclear RNA (snRNA) and microRNA. It is one of the three RNAP enzymes found in the nucleus of eukary ...

(Pol II) subunits. Approximately half of these subunits are shared among Pol II, IV, and V. Its two largest subunits, together forming the catalytic site, make up the most conserved region sharing similarity with eukaryotic and bacterial polymerases. The subunits unique to only Pol IV and V are believed to have arisen from gene duplication events that occurred prior to the evolution of land plants. The structure of Pol V has been studied in a variety of plants, including ''

Arabidopsis thaliana ''Arabidopsis thaliana'', the thale cress, mouse-ear cress or arabidopsis, is a small flowering plant native to Eurasia and Africa. ''A. thaliana'' is considered a weed; it is found along the shoulders of roads and in disturbed land. A winter ...

'',

maize Maize ( ; ''Zea mays'' subsp. ''mays'', from es, maíz after tnq, mahiz), also known as corn ( North American and Australian English), is a cereal grain first domesticated by indigenous peoples in southern Mexico about 10,000 years ago. ...

, and

cauliflower Cauliflower is one of several vegetables in the species '' Brassica oleracea'' in the genus ''Brassica'', which is in the Brassicaceae (or mustard) family. It is an annual plant that reproduces by seed. Typically, only the head is eaten – t ...

. Affinity purification has shown significant differences in Pol V composition among these different species. In ''Arabidopsis'', the largest subunit is known as NRPE1. This subunit contains a GW-rich AGO-hook motif that provides the ability to interact with the

argonaute The Argonaute protein family, first discovered for its evolutionarily conserved stem cell function, plays a central role in RNA silencing processes as essential components of the RNA-induced silencing complex (RISC). RISC is responsible for the g ...

protein AGO4, as well as targeting of

DNA methylation DNA methylation is a biological process by which methyl groups are added to the DNA molecule. Methylation can change the activity of a DNA segment without changing the sequence. When located in a gene promoter, DNA methylation typically acts ...

. While the subunit is unique to Pol V, it does contain a conserved domain common with the largest subunit of Pol IV known as Defective Chloroplasts and Leaves (DeCL), which provides an unknown function. The second largest subunit of Pol V, NRPD/E2, is shared with Pol IV. Aside from its catalytic site, ''Arabidopsis'' Pol V contains 10 smaller, noncatalytic subunits. Of these, 6 are shared with Pol II and 8 are shared with Pol IV. The fourth and seventh subunits form what is known as the "Stalk" subcomplex, while the fifth and ninth subunits form the "Jaw" subcomplex.

Function

Pol V transcribes one of the two types of non-coding RNA involved in RdDM. In canonical RdDM, Pol V transcribes a scaffold RNA which base pairs with a 24-nt siRNA bound to AGO4. The AGO-hook motif in Pol V's largest subunit recruits this AGO4 to the site. Pol V transcripts are also necessary for the recruitment of chromatin remodelers to the target site. One such protein is Domains Rearranged Methyltransferase 2 (DRM2), which is believed to be recruited when the AGO4-bound siRNA base pairs with the scaffold. Once proteins are bound to this scaffold RNA, histone modification and DNA methylation may proceed.

References

{{Kinases Enzymes RNA