Ohtsuka Y and Inagaki H (2020), In silico identification and functional validat...

XB-ART-57217

Sci Rep 2020 Jul 28;101:12619. doi: 10.1038/s41598-020-69485-y.

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

Ohtsuka Y , Inagaki H .

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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.

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Species referenced: Xenopus tropicalis

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References [+] :

Almagro Armenteros, DeepLoc: prediction of protein subcellular localization using deep learning. 2017, Pubmed

	Figure 1. Multiple sequence alignment of the signal peptide and identity matrix in LCAMP families. Sequences of the predicted signal peptides in Ci-MAM (A) and novel (B) families were aligned using ClustalW. Percentage identity values for pairwise comparisons of the sequences without signal peptides of these family genes are shown.
	Figure 2. Effect of salt on the antimicrobial activity of Ciona LCAMPs. Antimicrobial activity of KH.C1.640, KH.C7.94, KH.S1531.4, KH.S908.1, and KH.S921.1 peptides against E. coli was assessed in the presence of 100, 200, 300, and 500 mM NaCl. Peptide concentrations were 3.12, 6.25, and 12.5 μM. Error bars show the standard deviation (n = 3) from a single experiment.
	Figure 3. LCAMP mRNA expression in Ciona hemocytes stimulated with LPS. The expression of LCAMP genes in Ciona hemocytes treated (+) or untreated (−) with 0.1 mg/mL LPS for 1 h was analyzed by RT-PCR. EF1α and PPIA were used as internal controls.