Evolution of PAS domains and PAS-containing genes in eukaryotes

Area of Science:

• Evolutionary biology
• Molecular biology
• Biochemistry

Background:

• PAS domains are widespread signaling modules in proteins across all life kingdoms.
• They are integral to photoreceptors and transcriptional regulators in eukaryotic circadian clocks, including bHLH-PAS, PER, PHY, ZTL, WC-1, WC-2, and VVD proteins.
• PAS domains primarily mediate protein-protein interactions and light-sensing functions.

Purpose of the Study:

• To conduct evolutionary analyses of the PAS superfamily.
• To investigate the evolutionary pressures and structural conservation of PAS domains.
• To infer the evolutionary origins of key PAS-containing genes in relation to geological eras and environmental changes.

Main Methods:

• Phylogenetic analysis of the PAS superfamily.
• Selection pressure analysis (dN/dS ratios).
• Structural analysis of PAS domains.
• Dating of gene family origins using molecular clock methods.

Main Results:

• The PAS superfamily predominantly evolved under strong purifying selection (average ω: 0.0030–0.1164).
• Evidence of episodic positive selection was detected in specific lineages during evolution.
• Despite sequence and length variations, PAS domains exhibit a highly conserved 3D structure determined by only eight residues.
• Origin of WC-1, WC-2, bHLH-PAS, and PER genes likely occurred in the Neoproterozoic Era (1000–542 Mya).
• Plant PHY and ZTL genes evolved in the Paleozoic Era (541–252 Mya).

Conclusions:

• PAS domains have maintained functional constraints throughout evolution, evidenced by conserved structure and purifying selection.
• Episodic positive selection suggests adaptation to specific environmental pressures during certain evolutionary periods.
• The timing of gene family origins correlates with significant global climate and light regime shifts, indicating adaptation.
• PAS domains are fundamental to eukaryotic circadian clock mechanisms and have undergone significant evolutionary history.