Existence in vivo of the loop E motif in potato spindle tuber viroid RNA

In vitro experiments have previously identified in potato spindle tuber viroid (PSTVd), the type member of the nuclear viroids, an element of local tertiary structure termed loop E. Here, by direct UV irradiation of PSTVd-infected tomato tissue and subsequent RNA analysis by denaturing polyacrylamide gel electrophoresis, northern blot hybridization and primer extension, we report that PSTVd (+) RNA also forms the loop E in vivo. These results provide strong support for the physiological relevance of this structural motif, which is involved in a wide range of functions including replication, host specificity and pathogenesis.