Prediction of proteinase cleavage sites in polyproteins of coronaviruses and its applications in analyzing SARS-CoV genomes

Abstract

Recently, we have developed a coronavirus-specific gene-finding system, ZCURVE_CoV 1.0. In this paper, the system is further improved by taking the prediction of cleavage sites of viral proteinases in polyproteins into account. The cleavage sites of the 3C-like proteinase and papain-like proteinase are highly conserved. Based on the method of traditional positional weight matrix trained by the peptides around cleavage sites, the present method also sufficiently considers the length conservation of non-structural proteins cleaved by the 3C-like proteinase and papain-like proteinase to reduce the false positive prediction rate. The improved system, ZCURVE_CoV 2.0, has been run for each of the 24 completely sequenced coronavirus genomes in GenBank. Consequently, all the non-structural proteins in the 24 genomes are accurately predicted. Compared with known annotations, the performance of the present method is satisfactory. The software ZCURVE_CoV 2.0 is freely available at http://tubic.tju.edu.cn/sars/.

Fig. 1

Comparison between the N-terminal sequences of the polyprotein 1abs in MHV and BCoV is shown schematically. The additional cleavage site in the annotated PCP CP3 predicted by the present method for MHV is situated at the corresponding position where the PCP CP3 and PCP CP4 are cleaved in BCoV. Cleavage sites that have been annotated by NCBI are indicated by black arrows, while the cleavage site predicted by the present method is indicated by an open arrow.

Fig. 2

Conservation of the sites cleaved by coronavirus proteinases. Two separate multiple, gap-free alignments around the P1|P1′ positions of the sites cleaved by the 3C-like proteinase (A) and papain-like proteinase (B) in the training set are converted to logo presentations in which the size of an amino acid is proportional to its conservation at the specific position and the sampling size. The amino acid conservation is measured in bits of information plotted on a vertical axis whose upper limit is determined by the natural diversity of amino acids (20) expressed as a logarithm of 2 . Seventy-seven sites cleaved by the 3C-like proteinase were used to generate the logo in A, and 17 sites cleaved by the papain-like proteinase were used to generate the logo in B.