Potato spindle tuber viroid (PSTVd) is a small, single-stranded, circular, 
non-coding RNA pathogen. Host DNA-dependent RNA polymerase II (RNAP II) was 
proposed to be critical for its replication, but no interaction site for RNAP II 
on the PSTVd RNA genome was identified. Using a co-immunoprecipitation strategy 
involving a mAb specific for the conserved heptapeptide (i.e. YSPTSPS) located 
at the carboxy-terminal domain of the largest subunit of RNAP II, we established 
the interaction of tomato RNAP II with PSTVd RNA and showed that RNAP II 
associates with the left terminal domain of PSTVd (+) RNA. RNAP II did not 
interact with any of several PSTVd (-) RNAs tested. Deletion and site-directed 
mutagenesis of a shortened model PSTVd (+) RNA fragment were used to identify 
the role of specific nucleotides and structural motifs in this interaction. Our 
results provide evidence for the interaction of a RNAP II complex from a natural 
host with the rod-like conformation of the left terminal domain of PSTVd (+) 
RNA.