Formation of MgF ₃ ^--dependent complexes between an AAA ⁺ ATPase and σ ⁵⁴

The widely distributed bacterial σ ⁵⁴-dependent transcription regulates pathogenicity and numerous adaptive responses in diverse bacteria. Formation of the σ ⁵⁴-dependent open promoter complex is a multi-step process driven by AAA ⁺ ATPases. Non-hydrolysable nucleotide analogues are particularly suitable for studying such complexity by capturing various intermediate states along the energy coupling pathway. Here we report a novel ATP analogue, ADP-MgF ₃ ^-, which traps an AAA ⁺ ATPase with its target σ ⁵⁴. The MgF ₃ ^--dependent complex is highly homogeneous and functional assays suggest it may represent an early transcription intermediate state valuable for structural studies.