The Basic and Secondary Structures of IRES in Foot-and-Mouth Disease Virus Strain China/99 and Alignment with That of Reference Strains
The sequence of internal ribosome entry site(IRES)in a virulent foot-and-mouth disease virus(FMDV)strain China/99 RNA from infected bovine tongue epithelium was determined by cloning of cDNA fragments obtained by RT-PCR The cDNA fragments were inserted into pGEM-T vectors and transformed into JM109,then the recombinant plasmids were identified by electrophoresis,EcoR I cleavage and PCR The nucleotide sequence of FMDV strain China/99 IRES was compared with that of seven other reference strains and their secondary structures were drawn by the software RNA draw The IRES sequence alignment showed that there was no obvious difference in all the strains,but showed that this region was more conservative The analysis of secondary structures showed that FMDV IRES at least had the three types of secondary structure:five domains in the first type were in agreement with Pilipenko′s;six domains in second type and 9-11 domains in third type were different from Pilipenko′s However, the differences of the secondary structures of FMDV IRES were that,the most of motifs or nucleotide stretches were the same,such as AACUCC,GAAA,CUUU,AGG,AACC,GUAA,etc The nucleotides on stem shoud be factors contributing to the maintenance of the IRES folding pattern,on the other hand,the nucleotides on loop contributed to the maintenance of the IRES functions,for examples,the motif GAAA is a part of three-dimensional structure and CUUU is a binding site for polypyrimidine tract-binding protein