In silico identification and functional validation of linear cationic \u03b1-helical antimicrobial peptides in the ascidian Ciona intestinalis

Yukio Ohtsuka,Hidetoshi Inagaki

doi:10.1038/s41598-020-69485-y

Yukio Ohtsuka, Hidetoshi Inagaki

Open Access

https://doi.org/10.1038/s41598-020-69485-y

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Abstract

We developed a computing method to identify linear cationic α-helical antimicrobial peptides (LCAMPs) in the genome of Ciona intestinalis based on its structural and physicochemical features. Using this method, 22 candidates of Ciona LCAMPs, including well-known antimicrobial peptides, were identified from 21,975 non-redundant amino acid sequences in Ciona genome database, Ghost database. We also experimentally confirmed the antimicrobial activities of five LCAMP candidates, and three of them were found to be active in the presence of 500 mM NaCl, nearly equivalent to the salt concentration of seawater. Membrane topology prediction suggested that salt resistance of Ciona LCAMPs might be influenced by hydrophobic interactions between the peptide and membrane. Further, we applied our method to Xenopus tropicalis genome and found 11 LCAMP candidates. Thus, our method may serve as an effective and powerful tool for searching LCAMPs that are difficult to find using conventional homology-based methods.

Highlights

We developed a computing method to identify linear cationic α-helical antimicrobial peptides (LCAMPs) in the genome of Ciona intestinalis based on its structural and physicochemical features
We developed a computing method for the detection of LCAMPs in the Ciona genome based on the structural and physicochemical features of known LCAMP precursors: short length, secretory peptide, and cationic amphipathic α-helix of mature peptide
Using DeepLoc-1.0 server, 22 genes were identified as LCAMP candidates (Table 1)

Summary

Introduction

We developed a computing method to identify linear cationic α-helical antimicrobial peptides (LCAMPs) in the genome of Ciona intestinalis based on its structural and physicochemical features. Using this method, 22 candidates of Ciona LCAMPs, including well-known antimicrobial peptides, were identified from 21,975 non-redundant amino acid sequences in Ciona genome database, Ghost database. LCAMPs are known for their broad-spectrum activities including the ability to rapidly kill or neutralize bacteria, fungi, viruses, parasites, and even cancer cells[6,7] They are considered promising lead candidates for the development of new peptide a ntibiotics[8]. To effectively and accurately identify novel antimicrobial peptides, there is a need to develop additional bioinformatics tools to survey protein sequence databases without use of sequence homology

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Conclusion