Dark Proteome of Newly Emerged SARS-CoV-2 in Comparison with Human and Bat Coronaviruses

Rajanish Giri; Taniya Bhardwaj; Meenakshi Shegane; Bhuvaneshwari R. Gehi; Prateek Kumar; Kundlik Gadhave

MSA analysis among all three coronaviruses demonstrates that S protein of SARS-CoV-2 has a 77.71% sequence identity with Bat CoV and 77.14% identity with Human SARS (Supplementary Figure S1A) . All three S proteins are found to have a conserved C-terminal region. However, the N-terminal regions of S proteins display noticeable differences. Given that there is significant sequence variation RBD located at the N-terminal region of S protein, this might be the reason behind variation in its virulence and its receptor-mediated binding and entry into the host cell. According to our intrinsic disorder propensity analysis, S protein from all three CoVs analysed in this study are highly structured, as their predicted disorder propensity lies below 10% ( Table 1 ). In fact, the mean PPID scores of SARS-CoV-2, Human SARS CoV, and Bat CoV are calculated to be 1.41%, 1.12%, and 1.85%, respectively. Figures 3B, 3C , and 3D represent the intrinsic disorder profiles of S proteins from SARS-CoV-2, Human SARS and Bat CoV obtained from six disorder predictors. Finally, Figure 3E shows aligned disorder profiles of S proteins from these CoVs and illustrates remarkable similarity in their disorder propensity, especially in the C-terminal region. It is of interest to map known functional regions of S proteins to their corresponding disorder profiles. The maturation of S protein requires specific posttranslational modification (PTM), proteolytic cleavage that happens at two stages. First, host cell furin or another cellular protease nicks the S precursor to generate S1 and S2 proteins, whereas the second cleavage that takes place after the viral attachment to host cell receptors leads to the release of a fusion peptide generating the S2' subunit. In Human SARS CoV, the first and second cleavage site is located at residues R 667 and R 797 , respectively, whereas in Bat CoV, the corresponding cleavage sites are residues R 654 and R 784 . As it follows from Figure 3 , these cleavage sites are located within the IDPRs. In Human SARS CoV S protein, fusion peptide (residues 770-788) is located within a flexible region, is characterized by the mean disorder score of 0.232±0.053. Similarly, in Bat CoV S protein, fusion peptide (residues 757-775) has a mean disorder score of 0.320±0.046. S protein contains two heptad repeat regions that form coiledcoil structure during viral and target cell membrane fusion, assuming a trimer-of-hairpins structure needed for the functional positioning of the fusion peptide. In Human SARS CoV S protein, heptad repeat regions are formed by residues 902-952 and 1145-1184, which have mean disorder scores of 0.458±0.067 and 0.353±0.062, respectively. The analogous situation is observed for the S protein from Bat CoV, where these heptad repeat regions are positioned at residues 889-939 (0.44±0.11) and 1132-1171 (0.353±0.062). Another functional region found in S proteins is the receptor-binding domain (residues 306-527 and 310-514 in Human SARS CoV and Bat CoV, respectively) containing a receptor-binding motif responsible for interaction with human ACE2. In human S protein of Human SARS CoV this motif (residues 424-494) is not only characterized by structural flexibility, possessing a mean disorder score author/funder. All rights reserved. No reuse allowed without permission.