hfAIM

hfAIM identifies genome-wide autophagy-associated Atg8 interacting motifs (AIMs) by scanning proteomes for the degenerate F/W/Y-X-X-L/I/V motif and applying additional sequence constraints to predict functional AIMs.

Key Features:

• Genome-wide scanning: Performs in silico, proteome-wide identification and prediction of Atg8 interacting motifs (AIMs).
• AIM consensus motif: Targets the degenerate consensus sequence F/W/Y-X-X-L/I/V commonly associated with Atg8 interaction.
• Additional sequence constraints: Requires presence of acidic amino acids and absence of positively charged amino acids at specified motif positions.
• Improved prediction fidelity: Incorporates the additional charge-based constraints to increase accuracy of AIM prediction across diverse proteomes.
• Proteome application: Applied to the Arabidopsis thaliana proteome, identifying potential AIMs including nine peroxisomal PEX proteins such as AtPEX1, AtPEX6, and AtPEX10.
• Conserved motif detection: Identifies evolutionarily conserved AIMs within protein families.
• Experimental validation linkage: Predicted AIMs were experimentally validated to interact with Atg8 via bimolecular fluorescence complementation (BiFC) assays in planta.
• Phenotypic association: Links mutations within or near identified hfAIM motifs in PEX1, PEX6, and PEX10 to defects in growth and development.

Scientific Applications:

• Selective autophagy target discovery: Enables genome-wide screens to identify proteins potentially regulated by selective autophagy via Atg8 interaction.
• Evolutionary and functional analysis: Facilitates identification of conserved AIMs for evolutionary comparisons and functional studies of protein families.
• Experimental prioritization: Provides candidate AIMs to guide experimental validation such as BiFC and investigations of mutation-associated phenotypes.

Methodology:

In silico proteome-wide scanning for the degenerate F/W/Y-X-X-L/I/V motif combined with filtering by required acidic residues and exclusion of positively charged residues at specified motif positions to predict AIMs.