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. 2021 Oct 28;11(1):21291.
doi: 10.1038/s41598-021-00797-3.

Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point

Tapan Kumar Mohanta #  1 , Awdhesh Kumar Mishra #  2 , Yugal Kishore Mohanta  3 , Ahmed Al-Harrasi  4
Affiliations

Virtual 2D mapping of the viral proteome reveals host-specific modality distribution of molecular weight and isoelectric point

Tapan Kumar Mohanta et al. Sci Rep. .

Abstract

A proteome-wide study of the virus kingdom based on 1.713 million protein sequences from 19,128 virus proteomes was conducted to construct an overall proteome map of the virus kingdom. Viral proteomes encode an average of 386.214 amino acids per protein with the variation in the number of protein-coding sequences being host-specific. The proteomes of viruses of fungi hosts (882.464) encoded the greatest number of amino acids, while the viral proteome of bacterial host (210.912) encoded the smallest number of amino acids. Viral proteomes were found to have a host-specific amino acid composition. Leu (8.556%) was the most abundant and Trp (1.274%) the least abundant amino acid in the collective proteome of viruses. Viruses were found to exhibit a host-dependent molecular weight and isoelectric point of encoded proteins. The isoelectric point (pI) of viral proteins was found in the acidic range, having an average pI of 6.89. However, the pI of viral proteins of algal (pI 7.08) and vertebrate (pI 7.09) hosts was in the basic range. The virtual 2D map of the viral proteome from different hosts exhibited host-dependent modalities. The virus proteome from algal hosts and archaea exhibited a bimodal distribution of molecular weight and pI, while the virus proteome of bacterial host exhibited a trimodal distribution, and the virus proteome of fungal, human, land plants, invertebrate, protozoa, and vertebrate hosts exhibited a unimodal distribution.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Individual amino acid composition of the virus proteome. Ala (A) amino acid was found to be highest in viruses of bacteria and fungi and lowest in the human host. Similarly, Ile (I) amino acid was found highest in the virus proteome of the protozoan host. The letters in the X-axis represent the initials of 20 essential amino acids. The graph was generated using Microsoft excel version 2016.
Figure 2
Figure 2
Host-specific amino acid composition of the virus proteome. It was found that Leu (8.556%) was highest and Trp (1.274%) was the lowest abundant amino acid of the virus kingdom. The stacked chart represents the amino acid composition percentage share of virus proteome originated from different hosts. The graphs were generated using GraphPad Prism version 6.
Figure 3
Figure 3
(A) Heatmap and (B) network plot of the amino acid composition of the virus proteome originated from different hosts. Heatmap shows, maximum of the virus protein shows a positive correlation on its amino acid composition. The highest positive correlation was found between the virus proteome of bacteria and archaea (0.978) whereas the lowest correlation was found between virus proteome originated from fungi and protozoa (0.718). The dark blue mark indicates the highest and the red mark indicates the lowest correlation. Pearson’s correlation study was conducted to construct the correlation plot (p < 0.05).
Figure 4
Figure 4
Correlation heat map of the composition of viral amino acid originated from different hosts. The maximum of the amino acids showed a negative correlation (red) whereas only a few amino acids showed a positive correlation (blue). The protein sequences of the virus originated from host land plants showed a positive correlation coefficient (0.9916) whereas protein sequences of the virus originated from bacteria showed a negative correlation (− 2.03E04). Pearson’s correlation study was conducted to construct the correlation plot (p < 0.05).
Figure 5
Figure 5
Molecular weight-based correlation analysis of virus proteome. (A) Heatmap (B) correlation (Pearson’s r) plot. The results show the molecular weight of the virus proteins originated from different hosts. The molecular weight of virus proteins originated from algae, archaea, and bacteria showed a negative correlation with the virus proteins originated from fungi, humans, and land plants; virus proteome of bacteria showed a negative correlation with land plants. However, the virus proteins originated from host fungi showed a positive correlation with virus protein in humans, invertebrates, land, plants, protozoa, and vertebrate; invertebrates with fungi, humans, land plants, protozoa, and vertebrates.
Figure 6
Figure 6
Virtual 2D map of virus proteome. (A) The molecular weight and isoelectric point of the virus proteome showed a bimodal distribution. Host-dependent modal distribution of virus proteome can be seen from the figure. Few encode unimodal [(D) fungi, (F) human, (H) invertebrate, (J) plants, (E) protozoa, and (G) vertebrate], a few bimodal [(B) algae, (C) archaea] and (I) bacteria showed trimodal distribution of molecular weight and isoelectric point of virus proteome. The colour opacity represents the acidity and alkalinity of the virus proteome. Green hues tend toward acidity, whereas blue hues tend toward alkalinity. The scatter plots were generated using “scatter plot online” server (https://scatterplot.online/).
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