Characterization of the RNA motif responsible for the specific interaction of potato spindle tuber viroid RNA (PSTVd) and the tomato protein Virp1.

ABSTRACT: Viroids are small non-coding parasitic RNAs that are able to infect their host plants systemically. This circular naked RNA makes use of host proteins to accomplish its proliferation. Here we analyze the specific binding of the tomato protein Virp1 to the terminal right domain of potato spindle tuber viroid RNA (PSTVd). We find that two asymmetric internal loops within the PSTVd (+) RNA, each composed of the sequence elements 5'-ACAGG and CUCUUCC-5', are responsible for the specific RNA-protein interaction. In view of the nucleotide composition we call this structural element an 'RY motif'. The RY motif located close to the terminal right hairpin loop of the PSTVd secondary structure has an approximately 5-fold stronger binding affinity than the more centrally located RY motif. Simultaneou

SUBMITTER: Gozmanova M 

PROVIDER: S-EPMC206474 | biostudies-literature | 2003 Oct

REPOSITORIES: biostudies-literature