title: Avian reovirus L2 genome segment sequences and predicted structure/function of the encoded RNA-dependent RNA polymerase protein.
abstract: BACKGROUND
  The orthoreoviruses are infectious agents that possess a genome comprised of 10 double-stranded RNA segments encased in two concentric protein capsids. Like virtually all RNA viruses, an RNA-dependent RNA polymerase (RdRp) enzyme is required for viral propagation. RdRp sequences have been determined for the prototype mammalian orthoreoviruses and for several other closely-related reoviruses, including aquareoviruses, but have not yet been reported for any avian orthoreoviruses.
  
  
  RESULTS
  We determined the L2 genome segment nucleotide sequences, which encode the RdRp proteins, of two different avian reoviruses, strains ARV138 and ARV176 in order to define conserved and variable regions within reovirus RdRp proteins and to better delineate structure/function of this important enzyme. The ARV138 L2 genome segment was 3829 base pairs long, whereas the ARV176 L2 segment was 3830 nucleotides long. Both segments were predicted to encode lambdaB RdRp proteins 1259 amino acids in length. Alignments of these newly-determined ARV genome segments, and their corresponding proteins, were performed with all currently available homologous mammalian reovirus (MRV) and aquareovirus (AqRV) genome segment and protein sequences. There was approximately 55% amino acid identity between ARV lambdaB and MRV lambda3 proteins, making the RdRp protein the most highly conserved of currently known orthoreovirus proteins, and there was approximately 28% identity between ARV lambdaB and homologous MRV and AqRV RdRp proteins. Predictive structure/function mapping of identical and conserved residues within the known MRV lambda3 atomic structure indicated most identical amino acids and conservative substitutions were located near and within predicted catalytic domains and lining RdRp channels, whereas non-identical amino acids were generally located on the molecule's surfaces.
  
  
  CONCLUSIONS
  The ARV lambdaB and MRV lambda3 proteins showed the highest ARV:MRV identity values (approximately 55%) amongst all currently known ARV and MRV proteins. This implies significant evolutionary constraints are placed on dsRNA RdRp molecules, particularly in regions comprising the canonical polymerase motifs and residues thought to interact directly with template and nascent mRNA. This may point the way to improved design of anti-viral agents specifically targeting this enzyme.
authors.affiliation: Department of Medical Microbiology and Infectious Diseases, University of Manitoba, Manitoba, Canada. wanhongxu@hotmail.com
authors.forename: Wanhong
authors.initials: W
authors.lastname: Xu
authors.forename: Kevin M
authors.initials: KM
authors.lastname: Coombs
mesh_terms: D000595:Amino Acid Sequence; D016679:Genome, Viral; D008969:Molecular Sequence Data; D030101:Orthoreovirus, Avian / Q000145:classification / Q000201:enzymology* / Q000235:genetics; D010802:Phylogeny; D012324:RNA-Dependent RNA Polymerase / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*; D016415:Sequence Alignment; D014764:Viral Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism*
chemical_list: D014764:Viral Proteins; D012324:RNA-Dependent RNA Polymerase