A high-throughput genetically directed protein crosslinking analysis reveals the physiological relevance of the ATP synthase 'inserted' state

ATP synthase, a highly conserved protein complex that has a subunit composition of alpha(3)beta(3)gamma delta epsilon ab(2)c(8-15) for the bacterial enzyme, is a key player in supplying energy to living organisms. This protein complex consists of a peripheral F-1 sector (alpha(3)beta(3)gamma delta epsilon) and a membrane-integrated F-o sector (ab(2)c(8-15)). Structural analyses of the isolated protein components revealed that, remarkably, the C-terminal domain of its epsilon-subunit seems to adopt two dramatically different structures, but the physiological relevance of this conformational change remains largely unknown. In an attempt to decipher this, we developed a high-throughput in vivo protein photo-cross-linking analysis pipeline based on the introduction of the unnatural amino acid into the target protein via the scarless genome-targeted site-directed mutagenesis technique, and probing the cross-linked products via the high-throughput polyacrylamide gel electrophoresis technique. Employing this pipeline, we examined the interactions involving the C-terminal helix of the epsilon-subunit in cells living under a variety of experimental conditions. These studies enabled us to uncover that the bacterial ATP synthase exists as an equilibrium between the 'inserted' and 'noninserted' state in cells, maintaining a moderate but significant level of net ATP synthesis when shifting to the former upon exposing to unfavorable energetically stressful conditions. Such a mechanism allows the bacterial ATP synthases to proportionally and instantly switch between two reversible functional states in responding to changing environmental conditions. Importantly, this high-throughput approach could allow us to decipher the physiological relevance of protein-protein interactions identified under in vitro conditions or to unveil novel physiological context-dependent protein-protein interactions that are unknown before.

Automated summary

ATP synthase is a highly conserved protein complex that supplies energy to living organisms. Studies have shown that structural changes in the epsilon-subunit of the protein complex significantly impact bacterial ATP synthase under energetically stressful conditions. A high-throughput in vivo protein photo-cross-linking analysis pipeline revealed the ability of bacterial ATP synthase to rapidly switch between two functional states in response to changing environmental conditions.