Genetic Variation And Structural Function Of Viroid

Viroids are the smallest pathogens infecting plants known today.They do not encode any protein and replicate depending completely on host factors.Up to now,more than 30 viroids have been reported.Coleus blumei viroids(CbVds)and Potato spindle tuber viroid(PSTVd),members of family Pospiviroidae,provide unique models to investigate genetic variations and structural functions of viroids.Coleus blumei(coleus)is an ornamental plant grown worldwide,and six main viroids infecting coleus have been identified:Coleus blumei viroid-1?6(CbVd-1?6);however,information of the coleus viroids are limited until now.In this study,infectious clones of CbVd-1,CbVd-3,CbVd-5 and CbVd-6 were used as inoculum sources and their biological properties were investigated.Biological assay showed that the first detected time for these four viroids were different,ranging from 45 days post inoculation(dpi)to 300 dpi.Molecular characterization of their progenies demonstrated that progeny sequences of all the four CbVds followed the quasispecies model and the population diversity of CbVds is dependent on both host species and viroids themselves.In addition,a circular RNA,sharing no sequence similarity to any of the known viroids,was hypothesized as a new viroid based on its molecular characteristic in this study.Our study provided more information about viroids in coleus and would be helpful to clarify the pathogenicity mechanism of coleus viroids.Various RNAs including most of the plant viruses and viroids spread throughout their hosts by cell-to-cell and long-distance trafficking.Cell-to-cell trafficking by passing through different cellular layers is a key process for RNA traffic inside a host,but its regulatory mechanism is still not fully elucidated and good models for investigating it is also important.Here,we report a simple RNA motif,termed as loopl9,in Potato spindle tuber viroid(PSTVd).Loop 19 centers on a symmetric A/C bulge in the PSTVd secondary structure.Analyses using northern blot,RT-PCR and in situ hybridization demonstrated that PSTVd loop 19 plays a decisive role in mediating RNA trafficking from palisade to spongy mesophyll in Nicotiana benthamiana leaves.Our findings have broad implications for studying the RNA motifs mediating trafficking of RNAs across specific cellular boundaries in other biological processes.