A Eukaryotic-Like Interaction of Soluble Cyanobacterial Sensory Rhodopsin Transducer with DNA

Anabaena sensory rhodopsin is a recently discovered membrane photosensor with a unique signal transduction cascade. It interacts with a soluble tetrameric transducer [Anabaena sensory rhodopsin transducer (ASRT)] that can bind to promoter regions of several genes related to the utilization of light energy. Even though the X-ray crystal structure of ASRT is available, the mechanism of its interaction with DNA is still unknown. We used solution NMR to understand the mechanism of the DNA binding. Both X-ray crystal structures and solution NMR data reveal seven β-strands forming a rigid scaffold (β-face) and a flexible, partially disordered α-face, comprised by the C-termini and loops. We found that the conformation of the α-face in solution is very different from that in the crystals. While the C-termini of crystalline ASRT are solvent exposed and either α-helical or disordered, about half of ASRT monomers in solution feature buried C-terminal β-strand, with another half of C-tails being random coils. Titration of ASRT with a  20-bp fragment of the pec operon promoter showed that only monomers with β-structured C-tails bind the DNA. NMR signals suggest that specific Arg and Asn/Gln residues are involved in the interaction with DNA. The DNA binding occurs with micromolar affinity and a 1:1 stoichiometry (DNA:ASRT tetramer) and results in a significant ordering of the α-face involving the extension of the C-terminal β-strand and reorganization of the first loop. Such induced-fit type of interaction, which mainly utilizes loops between β-strands and results in the increase in their order, is typical for eukaryotic transcription factors of the immunoglobulin-like fold.

Graphical AbstractFigure optionsDownload high-quality image (200 K)Download as PowerPoint slideHighlights
► Solution structure of cytoplasmic photosensory transducer (ASRT) explored by NMR.
► The C-terminal part of ASRT exists in two conformations: β-strand or random coil.
► C-terminal β-strands are buried, while X-ray structure shows exposed α-helices.
► Only the conformation with C-terminal β-strand interacts with DNA.
► DNA binding induces ordering of interstrand loops, similar to eukaryotic factors.