Author's School

Graduate School of Arts & Sciences

Author's Department/Program

Biology and Biomedical Sciences: Plant and Microbial Biosciences


English (en)

Date of Award


Degree Type


Degree Name

Doctor of Philosophy (PhD)

Chair and Committee

Craig Pikaard


RNA Polymerases IV and V: Pol IV and Pol V) are plant-specific enzyme complexes with subunit homology to RNA Polymerase II: Pol II). The largest subunits in Pol IV and Pol V, NRPD1 and NRPE1 respectively, share a second largest subunit, NRPD2/NRPE2. The evolutionarily conserved Metal A and Metal B binding sites are required for Pol IV and V in vivo function fitting the prediction that these are functional polymerases. The Defective Chloroplast and Leaves-like: DeCL) domain at the C-terminus of both NRPD1 and NRPE1 is also required for complementation but other domains in the NRPE1 CTD are largely dispensable. Biochemical analysis reveals Pol IV to be a DNA-dependent RNA Polymerase capable of producing RNA from a tripartite template that mimics an open transcription bubble. The Metal A binding site is required for Pol IV in vitro transcription while the enzyme is resistant to alpha-amanitin, a potent Pol II inhibitor. Pol IV has also been found to physically associate with RNA DEPENDENT RNA POLYMERASE 2: RDR2) in vivo providing an explanation for how Pol IV RNA products are channeled specifically to RDR2 for the production of double-stranded RNA and eventual dicing. Biochemical analysis has also revealed that RDR2 is capable of transcribing both single-stranded RNA and DNA in vitro, consistent with previously analyzed RNA-dependent RNA polymerases from plants and other organisms.


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