iLIR database: A web resource for LIR motif-containing proteins in eukaryotes

Area of Science:

• Cell Biology
• Molecular Biology
• Biochemistry

Background:

• Atg8-family proteins are central to the core autophagic machinery, essential for autophagosome biogenesis and selective autophagy.
• These proteins mediate substrate targeting by interacting with specific autophagy receptors and other cellular components.
• Atg8-interacting proteins (LIRCPs) contain a conserved motif (LIR/LRS/AIM) crucial for their binding to Atg8-family proteins.

Purpose of the Study:

• To develop a comprehensive resource for identifying Atg8-interacting proteins (LIRCPs) across various organisms.
• To facilitate research into the roles of LIRCPs in autophagy and other cellular processes.
• To identify novel LIRCPs, particularly in mammals, through computational and text-mining approaches.

Main Methods:

• In silico identification of canonical LIRCPs in the proteomes of 8 model organisms using the iLIR server.
• Gene Ontology (GO) term analysis to functionally annotate identified LIRCPs.
• Curated text-mining analysis of scientific literature to discover novel mammalian LIRCPs.

Main Results:

• The iLIR database (https://ilir.warwick.ac.uk) was established as a freely available web resource.
• The database lists putative canonical LIRCPs identified computationally across 8 model organisms.
• Novel putative LIRCPs in mammals, not previously linked to autophagy, were identified through literature analysis.

Conclusions:

• The iLIR database provides a valuable resource for autophagy research by cataloging LIRCPs.
• Computational and text-mining strategies are effective for identifying LIRCPs across diverse species.
• Further characterization of identified LIRCPs will enhance our understanding of selective autophagy mechanisms.