Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides
Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides
Abstract The ever-growing global health threat of antibiotic resistance is compelling researchers to explore alternatives to conventional antibiotics. Antimicrobial peptides (AMPs) are emerging as a promising solution to fill this need. Naturally occurring AMPs are produced by all forms of life as part of the innate immune system. High-throughput bioinformatics tools have enabled fast and large-scale discovery of AMPs from genomic, transcriptomic, and proteomic resources of selected organisms. Public protein sequence databases, comprising over 200 million records and growing, serve as comprehensive compendia of sequences from a broad range of source organisms. Yet, large-scale in silico probing of those databases for novel AMPs has never been reported. In the present study, we propose an AMP mining workflow to predict novel AMPs from the UniProtKB/Swiss-Prot database using the AMP prediction tool, AMPlify, as its discovery engine. Using this workflow, we identified 8,008 novel putative AMPs from all eukaryotic sequences in the database. Focusing on the practical use of AMPs as suitable antimicrobial agents with applications in the poultry industry, we prioritized 40 of those AMPs based on their similarities to known chicken AMPs in predicted structures. In our tests, 13 out of the 38 successfully synthesized peptides showed antimicrobial activity against Escherichia coli and/or Staphylococcus aureus.
Sutherland Darcy、Hoang Linda M.N.、Ebrahimikondori Hossein、Birol Inanc、Coombe Lauren、Aninta Sambina Islam、Li Chenkai、Warren Ren¨| L.、Salehi Ali、Lin Diana、Richter Amelia、Yanai Anat、Helbing Caren C.、Kotkoff Monica
Canada?ˉs Michael Smith Genome Sciences Centre||Public Health Laboratory, British Columbia Centre for Disease Control||Department of Pathology and Laboratory Medicine, University of British ColumbiaPublic Health Laboratory, British Columbia Centre for Disease Control||Department of Pathology and Laboratory Medicine, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences Centre||Public Health Laboratory, British Columbia Centre for Disease Control||Department of Pathology and Laboratory Medicine, University of British Columbia||Department of Medical Genetics, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences Centre||Bioinformatics Graduate Program, University of British ColumbiaCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences Centre||Public Health Laboratory, British Columbia Centre for Disease ControlCanada?ˉs Michael Smith Genome Sciences CentreCanada?ˉs Michael Smith Genome Sciences Centre||Public Health Laboratory, British Columbia Centre for Disease ControlCanada?ˉs Michael Smith Genome Sciences Centre||Public Health Laboratory, British Columbia Centre for Disease ControlDepartment of Biochemistry and Microbiology, University of VictoriaCanada?ˉs Michael Smith Genome Sciences Centre
医学研究方法生物科学研究方法、生物科学研究技术微生物学
Sutherland Darcy,Hoang Linda M.N.,Ebrahimikondori Hossein,Birol Inanc,Coombe Lauren,Aninta Sambina Islam,Li Chenkai,Warren Ren¨| L.,Salehi Ali,Lin Diana,Richter Amelia,Yanai Anat,Helbing Caren C.,Kotkoff Monica.Mining the UniProtKB/Swiss-Prot database for antimicrobial peptides[EB/OL].(2025-03-28)[2025-05-16].https://www.biorxiv.org/content/10.1101/2024.05.24.595811.点此复制
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