Mutations that alter a repeated ACCA element located at the 5′ end of the Potato virus X genome affect RNA accumulation

The repeated ACCA or AC-rich sequence and structural (SL1) elements in the 5′ non-translated region (NTR) of the Potato virus X (PVX) RNA play vital roles in the PVX life cycle by controlling translation, RNA replication, movement, and assembly. It has already been shown that the repeated ACCA or AC-rich sequence affect both gRNA and sgRNA accumulation, while not affecting minus-strand RNA accumulation, and are also required for host protein binding. The functional significance of the repeated ACCA sequence elements in the 5′ NTR region was investigated by analyzing the effects of deletion and site-directed mutations on PVX replication in Nicotiana benthamiana plants and NT1 protoplasts. Substitution (ACCA into AAAA or UUUU) mutations introduced in the first (nt 10–13) element in the 5′ NTR of the PVX RNA significantly affected viral replication, while mutations introduced in the second (nt 17–20) and third (nt 20–23) elements did not. The fourth (nt 29–32) ACCA element weakly affected virus replication, whereas mutations in the fifth (nt 38–41) significantly reduced virus replication due to the structure disruption of SL1 by AAAA and/or UUUU substitutions. Further characterization of the first ACCA element indicated that duplication of ACCA at nt 10–13 (nt 10–17, ACCAACCA) caused severe symptom development as compared to that of wild type, while deletion of the single element (nt 10–13), ΔACCA) or tripling of this element caused reduced symptom development. Single- and double-nucleotide substitutions introduced into the first ACCA element revealed the importance of CC located at nt positions 11 and 12. Altogether, these results indicate that the first ACCA element is important for PVX replication.