Whole genome protein domain analysis using a new method for domain clustering

Area of Science:

• Genomics
• Proteomics
• Bioinformatics

Background:

• Protein domains are fundamental units of protein function and evolution.
• Understanding domain shuffling is key to deciphering genome evolution and protein complexity.
• Previous analyses lacked comprehensive domain delineation across diverse microbial life.

Purpose of the Study:

• To systematically analyze protein domain shuffling in 17 microbial genomes.
• To identify conserved and unique protein domain building blocks across Bacteria, Archaea, and yeast.
• To investigate the prevalence and characteristics of multi-domain proteins in selected organisms.

Main Methods:

• Utilized MKDOM Version 2, a novel domain clustering program employing PSI-BLAST recursive homology searches.
• Analyzed protein domain arrangements in 17 completed microbial genomes.
• Developed a WWW graphical interface for interactive browsing of domain data.

Main Results:

• Delineated frequent protein domain building blocks, distinguishing species-specific from shared domains.
• Identified domains shared across Bacteria, Archaea, and yeast as potential fundamental building blocks of cellular life.
• Observed a high number of large multi-domain proteins in organisms like Bacillus subtilis and Mycobacterium tuberculosis.
• Provided examples of highly shuffled and circularly permuted domains.

Conclusions:

• Protein domain shuffling is a significant evolutionary mechanism shaping microbial proteomes.
• Shared protein domains represent core evolutionary innovations underlying diverse cellular life.
• Specific microbial genomes exhibit unique patterns of protein domain organization, suggesting distinct evolutionary trajectories.