[Comparative analysis of primary structure of nucleocapsid protein from Western equine encephalomyelitis virus and other alphaviruses].
Part of WEE virus (strain 16310-5614) genome coding for the nucleocapsid (C) protein was cloned and sequenced in two independent clones. The C gene of WEE virus is composed of 77 nucleotides, both for the BFS and 16310 strains, and is 48, 24, 33, 15, 3, and 3 nucleotides shorter than that of Venezuelan equine encephalomyelitis (VEE), Semliki Forest, Ross River, Sindbis, O'Nyong-Nyong, and Eastern equine encephalomyelitis (EEE) viruses, respectively. It contains 16 nucleotide changes in comparison with the BFS-1703 strain, four of which are significant: Ser57(BFS)-->Ala(16310), Gly63-->Cys, Lys74-->Glu, Gly97-->Trp. Amino acid composition, charges, hydropathic profiles, and location of potential functional sites in C proteins of the heretofore studied alphaviruses have been compared. High positively charged N-domain of the nucleocapsid is the most variable in all alphaviruses and is characterized by an irregular secondary structure due to high Pro content (25.5%). Positively charged Lys (10.8% of total) and Arg (6.9% of total) are presented 18 and 11 times, respectively, in the N-domain of WEE virus (16310) protein, and clusters thereof possibly form the initial sites for interaction with RNA. Only Sindbis virus (HRSP and Ock) nucleocapsids do not contain Cys, while others do contain several residues. This part of C protein includes overlapping nuclear transport signals predicted for several cellular proteins and repeated 4, 7, and 2 times in WEE, EEE, and Sindbis viruses, respectively. There is a highly conservative region (96-113 as residues) in the C protein structure of all studied alphaviruses, which potentially binds to a large ribosomal subunit as it was shown for Sindbis virus by Wengler et al. (1992), and a consensus motif K/R95-P-X-K/R-X-R-M could be a main part of the nucleoprotein ribosome binding site. The W186HHGAVQ (WEE virus) is absolutely conservative for all alphaviruses and with the invariant Asn222 could have a common function, including C protein lateral interaction (Choi et al., 1991). The origination of WEE virus C protein from EEE virus is confirmed by very high (92.7%) similarity of this protein's C domain in the WEE/EEE pair and low (64.8%) in the WEE/Sindbis pair. Determination of C gene and protein type in the Sindbis/WEE virus serocomplex might be useful in the differential identification of this virus group.
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D000524:Alphavirus / Q000235:genetics*; D000595:Amino Acid Sequence; D004667:Encephalitis Virus, Western Equine / Q000235:genetics*; D008969:Molecular Sequence Data; D019251:Nucleocapsid / Q000235:genetics*