Phosphorylation Mechanism Switching in Histidine Kinases Is a Tool for Fast Protein Evolution: Insights From...

Area of Science:

• Bacterial signaling and two-component systems
• Protein structure and function
• Evolutionary biology

Background:

• Histidine kinases (HKs) are crucial for bacteria to sense and respond to environmental changes.
• HKs are multidomain proteins that function as homodimers, utilizing cis or trans autophosphorylation mechanisms for pathway specificity.
• The structural and evolutionary basis for these distinct phosphorylation mechanisms remains unclear.

Purpose of the Study:

• To investigate the structural determinants of cis versus trans autophosphorylation in HKs using computational modeling.
• To analyze the evolutionary prevalence and history of cis and trans phosphorylation mechanisms in HKs.
• To explore how variations in HK structure influence phosphorylation mechanism and system specificity.

Main Methods:

• Utilized AlphaFold to accurately predict the dimeric structures of various HKs, distinguishing between cis and trans configurations.
• Modeled multiple HKs to assess the evolutionary distribution of phosphorylation mechanisms.
• Analyzed structural features, specifically helix lengths around the dimerization and phosphorylation (DHp) domain, to identify determinants of the phosphorylation mechanism.

Main Results:

• AlphaFold accurately predicts whether an HK dimerizes in a cis or trans conformation.
• Both cis- and trans-acting HKs are prevalent in nature, with multiple evolutionary switches between mechanisms observed.
• Differences in the lengths of helices flanking the DHp loop are identified as the key molecular determinant of the phosphorylation mechanism.
• Minor structural alterations in these helices can induce a switch in the phosphorylation mechanism.

Conclusions:

• The phosphorylation mechanism in HKs is structurally determined by the lengths of surrounding helices.
• Evolutionary analysis shows frequent switching between cis and trans mechanisms, indicating their role in pathway divergence.
• Conserved phosphorylation mechanisms in specific HKs suggest their importance in maintaining system specificity, while switching allows for adaptation and diversification.