title: Mining antimicrobial peptides from small open reading frames in Ciona intestinalis.
abstract: Though being able to encode various kinds of bioactive peptides, small open reading frames (sORFs) are poorly annotated in many genomic data. The present study was conducted to evaluate the potential of sORFs in encoding antimicrobial peptides (AMPs) in the basal chordate model Ciona intestinalis. About 4.8 m genomic sequence was first retrieved for sORFs mining by the program sORF finder, then the sORFs were translated into amino acid sequences for AMP prediction via CAMP server, and thereafter, ten putative AMPs were selected for expression and antimicrobial activity validation. In total, over 180 peptides deduced from the sORFs were predicted to be AMPs. Among the ten tested peptides, six were found to have significant expressed sequence tag matches, providing strong evidence for gene expression; five were proved to be active against the bacterial strains. These results indicate that many sORFs in C. intestinalis genome contain AMP information. This work can serve as an important initial step to investigate the role of sORFs in the innate defense of C. intestinalis.
authors.affiliation: Biology Department, Qingdao University of Science and Technology, Qingdao, 266042, China.
authors.forename: Yongzhong
authors.initials: Y
authors.lastname: Lu
authors.forename: Yu
authors.initials: Y
authors.lastname: Zhuang
authors.forename: Jie
authors.initials: J
authors.lastname: Liu
mesh_terms: D000595:Amino Acid Sequence; D000818:Animals; D000900:Anti-Bacterial Agents / Q000138:chemical synthesis / Q000494:pharmacology; D000935:Antifungal Agents / Q000138:chemical synthesis / Q000494:pharmacology; D023181:Antimicrobial Cationic Peptides / Q000138:chemical synthesis / Q000235:genetics* / Q000494:pharmacology; D001483:Base Sequence; D002176:Candida albicans / Q000187:drug effects; D002938:Ciona intestinalis / Q000235:genetics*; D019295:Computational Biology; D004926:Escherichia coli / Q000187:drug effects; D020224:Expressed Sequence Tags; D008826:Microbial Sensitivity Tests; D008969:Molecular Sequence Data; D016366:Open Reading Frames; D012689:Sequence Homology, Nucleic Acid
chemical_list: D000900:Anti-Bacterial Agents; D000935:Antifungal Agents; D023181:Antimicrobial Cationic Peptides
keywords: antimicrobial activity; bioinformatics; gene annotation; genomic sequence; secondary structure