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. 2021 Mar 23;11(1):6676.
doi: 10.1038/s41598-021-86201-6.

Virtual 2-D map of the fungal proteome

Tapan Kumar Mohanta #  1 , Awdhesh Kumar Mishra #  2 , Adil Khan  3 , Abeer Hashem  4   5 , Elsayed Fathi Abd-Allah  6 , Ahmed Al-Harrasi  7
Affiliations

Virtual 2-D map of the fungal proteome

Tapan Kumar Mohanta et al. Sci Rep. .

Abstract

The molecular weight and isoelectric point (pI) of the proteins plays important role in the cell. Depending upon the shape, size, and charge, protein provides its functional role in different parts of the cell. Therefore, understanding to the knowledge of their molecular weight and charges is (pI) is very important. Therefore, we conducted a proteome-wide analysis of protein sequences of 689 fungal species (7.15 million protein sequences) and construct a virtual 2-D map of the fungal proteome. The analysis of the constructed map revealed the presence of a bimodal distribution of fungal proteomes. The molecular mass of individual fungal proteins ranged from 0.202 to 2546.166 kDa and the predicted isoelectric point (pI) ranged from 1.85 to 13.759 while average molecular weight of fungal proteome was 50.98 kDa. A non-ribosomal peptide synthase (RFU80400.1) found in Trichoderma arundinaceum was identified as the largest protein in the fungal kingdom. The collective fungal proteome is dominated by the presence of acidic rather than basic pI proteins and Leu is the most abundant amino acid while Cys is the least abundant amino acid. Aspergillus ustus encodes the highest percentage (76.62%) of acidic pI proteins while Nosema ceranae was found to encode the highest percentage (66.15%) of basic pI proteins. Selenocysteine and pyrrolysine amino acids were not found in any of the analysed fungal proteomes. Although the molecular weight and pI of the protein are of enormous important to understand their functional roles, the amino acid compositions of the fungal protein will enable us to understand the synonymous codon usage in the fungal kingdom. The small peptides identified during the study can provide additional biotechnological implication.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
Principal component analysis (PCA) of acidic pI proteins in the fungal proteome. The figure illustrates the relationship between the acidic pI of Ascomycota, Basidiomycota, Microsporidia, Zoopagomycota, Chytridiomycota, and Opthisthokonta. The acidic pI of Chytridiomycota and Opthisthokonta cluster independently from the other phyla. Within the figure (a) scores: reflects the similarities in sample grouping, (b) loading: represents the relative position of a variable and how it relates a sample to different variables, (c) influence plot: represents the Q- or F-residuals vs Leverage or Hotelling T2 statistics that shows the residual statistics on the ordinate axis of sample distance to model and (d) variance: represent the variation in the data of different components. Total residual variance is calculated as a sum of the square of residuals for all the variables, divided by the number of degrees of freedom. The green colour indicates the calibration and the red indicates the validation.
Figure 2
Figure 2
Principal component analysis (PCA) of basic pI proteins in the fungal proteome. The figure illustrates the relationship between the basic pI of Ascomycota, Basidiomycota, Microsporidia, Zoopagomycota, Chytridiomycota, and Opthisthokonta. The basic pI of Chytridiomycota, Opthisthokonta, and Zoopagomyota cluster independently from the other fungal phyla. In the figure (a) scores: reflects the similarities in sample grouping, (b) loading: represents the relative position of a variable and how it relates a sample to different variables, (c) influence plot: represents the Q- or F-residuals vs Leverage or Hotelling T2 statistics that shows the residual statistics on the ordinate axis of sample distance to model, and (d) variance: represent the variation in the data by different components. Total residual variance is calculated as a sum of square of residuals for all the variables, divided by the number of degrees of freedom. The green color indicates the calibration and the red indicates the validation. The collective fungal proteome was found to contain an average of 17.449 (0.172%) neutral pI proteins (Fig. 1F). The pI of the entire plant kingdom has been reported to range from 1.99 to 13.96. The lowest pI found for fungal proteins was less than the lowest plant protein pI. In contrast, the highest pI found for a fungal protein was lower than the highest pI found for a plant protein.
Figure 3
Figure 3
Principal component analysis (PCA) of percentage (%) of occurrence of neutral pI proteins in the fungal proteome. The figure illustrates the relationship between the percentage of neutral pI proteins in the Ascomycota, Basidiomycota, Microsporidia, Zoopagomycota, Chytridiomycota, and Opthisthokonta.
Figure 4
Figure 4
Virtual 2D map of the fungal proteome. The virtual map reveals the bimodal distribution of molecular mass (kDa) and isoelectric point (pI) in the collective fungal proteome. The X-axis represents the isoelectric point and Y-axis represents the molecular mass of the fungal proteins.
Figure 5
Figure 5
PCA analysis of amino acid composition in fungal proteomes. Analysis revealed that Pro, Gly, and Arg; Val, Ser, Met, Cys, Gln, Trp, Thr, His, and Ala cluster together while Leu, Ile, Phe, Tyr, Asn, Asp, Glu, and Lys group independently from the other amino acids.
Figure 6
Figure 6
Average number of amino acids per protein in the fungi. The protein sequences of species within the Ascomycota possess a higher number of amino acids than was found in the species of other phyla. Protein sequences of species within the Microsporidia possess a lower number of amino acids.
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