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Mining Amphibian and Insect Transcriptomes for Antimicrobial Peptide Sequences with rAMPage
Diana Lin1, Darcy Sutherland1,2,3, Sambina Islam Aninta1
1Canada's Michael Smith Genome Sciences Centre at BC Cancer, Vancouver, BC V5Z 4S6, Canada.
Antibiotics (Basel, Switzerland)
|July 27, 2022
Summary
Researchers developed rAMPage, a bioinformatics tool to find antimicrobial peptides (AMPs) from RNA sequencing data. This platform identified novel AMPs with potential to combat antibiotic resistance.
Area of Science:
- Bioinformatics
- Genomics
- Drug Discovery
Background:
- Antibiotic resistance is a growing global health threat.
- Novel antimicrobial therapeutics are urgently needed.
- Antimicrobial peptides (AMPs) show promise as alternatives to traditional antibiotics.
Purpose of the Study:
- To present rAMPage, a scalable bioinformatics platform for discovering AMPs from RNA sequencing (RNA-seq) data.
- To demonstrate the utility and scalability of rAMPage in identifying novel AMPs.
Main Methods:
- rAMPage was applied to 84 RNA-seq datasets from 75 amphibian and insect species.
- Identified putative AMP sequences were compared against public databases for novelty.
- Selected novel AMP candidates underwent antimicrobial susceptibility testing.
Main Results:
- rAMPage identified 1137 putative AMPs, with 1024 novel sequences.
- Seven of the 21 tested AMP candidates exhibited high antimicrobial activity.
- The platform demonstrated scalability and efficiency in AMP discovery.
Conclusions:
- rAMPage enables rapid and efficient in silico discovery of novel antimicrobial peptides.
- This approach facilitates early-stage drug development for combating antibiotic resistance.
- Bioinformatics platforms are crucial for identifying new antimicrobial agents.
