Bioinformatic prediction of polymerase elements in the rotavirus VP1 protein.
Rotaviruses are the major cause of acute gastroenteritis in infants world-wide. The genome consists of eleven double stranded RNA segments. The major segment encodes the structural protein VP1, the viral RNA-dependent RNA polymerase (RdRp), which is a minor component of the viral inner core. This study is a detailed bioinformatic assessment of the VP1 sequence. Using various methods we have identified canonical motifs within the VP1 sequence which correspond to motifs previously identified within RdRps of other positive strand, double-strand RNA viruses. The study also predicts an overall structural conservation in the middle region that may correspond to the palm subdomain and part of the fingers and thumb subdomains, which comprise the polymerase core of the protein. Based on this analysis, we suggest that the rotavirus replicase has the minimal elements to function as an RNA-dependent RNA polymerase. VP1, besides having common RdRp features, also contains large unique regions that might be responsible for characteristic features observed in the Reoviridae family.
Vásquez-del Carpió
Rodrigo
R
Laboratorio de Virología, Facultad de Química y Biología, Universidad de Santiago de Chile, Santiago, Chile.
Morales
Jaime L
JL
Barro
Mario
M
Ricardo
Alba
A
Spencer
Eugenio
E
D000818:Animals; D002460:Cell Line; D019295:Computational Biology / Q000379:methods; D008253:Macaca mulatta; D008969:Molecular Sequence Data; D012324:RNA-Dependent RNA Polymerase / Q000235:genetics*; D012401:Rotavirus / Q000235:genetics*; D016415:Sequence Alignment; D014758:Viral Core Proteins / Q000235:genetics*
C069187:VP1 protein, Rotavirus; D014758:Viral Core Proteins; D012324:RNA-Dependent RNA Polymerase