Comparative Nucleotide and Amino Acid Sequence Analysis of the Sequence-Specific RNA-Binding Rotavirus Nonstructural Protein NSP3

Abstract

NSP3, an acidic nonstructural protein, encoded by gene 7 has been implicated as the key player in the assembly of the 11 viral plus-strand RNAs into the early replication intermediates during rotavirus morphogenesis. To date, the sequence of NSP3 from only three animal rotaviruses (SA11, SA114F, and bovine UK) has been determined and that from a human strain has not been reported. To determine the genetic diversity among gene 7 alleles from group A rotaviruses, the nucleotide sequence of the NSP3 gene from 13 strains belonging to nine different G serotypes, from both humans and animals, has been determined. Based on the amino acid sequence identity as well as phylogenetic analysis, NSP3 from group A rotaviruses falls into three evolutionarily related groups, i.e., the SA11 group, the Wa group, and the S2 group. The SA11/SA114F gene appears to have a distant ancestral origin from that of the others and codes for a polypeptide of 315 amino acids (aa) in length. NSP3 from all other group A rotaviruses is only 313 aa in length because of a 2-amino-acid deletion near the carboxy-terminus. While the SA114F gene has the longest 3' untranslated region (UTR) of 132 nucleotides, that from other strains suffered deletions of varying lengths at two positions downstream of the translational termination codon. In spite of the divergence of the nucleotide (nt) sequence in the protein coding region, a stretch of about 80 nt in the 3' UTR is highly conserved in the NSP3 gene from all the strains. This conserved sequence in the 3' UTR might play an important role in the regulation of expression of the NSP3 gene.

Analysis of genetic diversity and molecular evolution of human group B rotaviruses based on whole genome segments

“…The RNA polymerase domain in VP1 and N-terminal RNA-binding domain in NSP3 are evidently conserved compared with other regions in individual proteins, as also found in cognate proteins of GAR (Rao et al, 1995;Heiman et al, 2008;McDonald et al, 2009). In these domains, some amino acids/motifs are commonly found among GAR, GBR and GCR, despite high sequence diversity among them.…”

Full Genomic Analysis of Human Rotavirus Strain B4106 and Lapine Rotavirus Strain 30/96 Provides Evidence for Interspecies Transmission

“…The NSP2 RNA-binding domain and four cysteines at residues 6, 8, 85, and 285, suggested to be involved in disulfide bonds (83), were also conserved. In NSP3, the consensus sequence (I/L)xxM(I/ L)(S/T)xxG (73), also present in the RNA-binding proteins of orbiviruses (NS2) and reoviruses (NS), and a hydrophobic heptad repeat region, involved in the oligomer forming properties of NSP3 (50,87,95), were also conserved. However, the proposed leucine zipper domain, with five leucines at amino acid residues 275, 281, 288, 295, and 302 (73), were absent in the NSP3 of both B4106 and 30/96 strains.…”

Efficient Translation of Rotavirus mRNA Requires Simultaneous Interaction of NSP3 with the Eukaryotic Translation Initiation Factor eIF4G and the mRNA 3′ End

“…The RNA-binding domain of NSP3 has been mapped to the N-terminal half of the protein (22). Two mutations were introduced into this domain: a conserved tryptophan (29) at position 87 was changed to alanine to give NSP3 W/A:87 , and a deletion of 11 amino acids was introduced at positions 65 to 75 to give NSP3⌬ [65][66][67][68][69][70][71][72][73][74][75] . Figure 7A depicts an example of the purified NSP3 used in the experiments described below.…”