Protein-protein interaction network module changes associated with the vertebrate fin-to-limb transition

Area of Science:

• Evolutionary developmental biology
• Systems biology
• Comparative genomics

Background:

• Evolutionary phenotypic transitions, like fin-to-limb, involve protein network modifications.
• Understanding these protein network changes is vital for evolutionary insights.
• Previous studies lacked comparative analyses of protein-protein interaction (PPI) networks across evolutionary transitions.

Purpose of the Study:

• To develop a network-based platform for investigating the fin-to-limb transition.
• To compare protein modules between fish fins and mammal limbs.
• To identify and validate novel protein candidates involved in this transition.

Main Methods:

• Constructed quality-enhanced protein networks by integrating PPI data with anatomy ontology.
• Compared protein modules of zebrafish paired fins (pectoral, pelvic) with mouse paired limbs (forelimb, hindlimb).
• Utilized enrichment and homology analyses for novel protein candidate validation.

Main Results:

• Identified hub proteins, such as shh and bmp4, critical for module stability.
• Examined the changing roles of these hub proteins during the fin-to-limb transition.
• Found that proteins with preserved roles were more likely to be hub proteins.

Conclusions:

• The study provides a novel network-based framework for studying evolutionary transitions.
• Preserved hub proteins play a significant role in maintaining functions during the fin-to-limb transition.
• This approach aids in understanding the molecular basis of major evolutionary changes.