Light‐induced complex formation of bacteriophytochrome RpBphP1 and gene repressor RpPpsR2 probed by SAXS

• Published in: The FEBS journal Vol. 286; no. 21; pp. 4261 - 4277
• Main Authors: Papiz, Miroslav Z., Bellini, Dom, Evans, Kate, Grossmann, J Günter, Fordham‐Skelton, Tony
• Format: Journal Article
• Language: English
• Published: England Blackwell Publishing Ltd 01-11-2019; John Wiley and Sons Inc
• Subjects: Bacterial Proteins - chemistry; Bacterial Proteins - genetics; bacteriophytochrome; Bundles; Complex formation; Crystal structure; Crystallography, X-Ray; Dimerization; Dimers; Domains; Gene expression; Gene Expression Regulation, Bacterial - genetics; Helices; Histidine; Histidine kinase; Homology; Illumination; Kinases; Light; Molecular structure; Original; photosynthesis; photo‐induced changes; Phytochrome - chemistry; Phytochrome - genetics; Phytochrome - radiation effects; Rendering; Rhodopseudomonas - genetics; Rhodopseudomonas - radiation effects; SAXS; Scattering, Small Angle; Small angle X ray scattering; Switches; X-Ray Diffraction; bacteriophytochrome; complex formation; photosynthesis; photo-induced changes; SAXS
• ISSN: 1742-464X; 1742-4658; 1742-4658
• DOI: 10.1111/febs.14973

Bacteriophytochrome proteins (BphPs) are molecular light switches that enable organisms to adapt to changing light conditions through the control of gene expression. Canonical type 1 BphPs have histidine kinase output domains, but type 3 RpBphP1, in the bacterium Rhodopseudomonas palustris (Rps. palustris), has a C terminal PAS9 domain and a two‐helix output sensor (HOS) domain. Type 1 BphPs form head‐to‐head parallel dimers; however, the crystal structure of RpBphP1ΔHOS, which does not contain the HOS domain, revealed pseudo anti‐parallel dimers. HOS domains are homologs of Dhp dimerization domains in type 1 BphPs. We show, by applying the small angle X‐ray scattering (SAXS) technique on full‐length RpBphP1, that HOS domains fulfill a similar role in the formation of parallel dimers. On illumination with far‐red light, RpBphP1 forms a complex with gene repressor RpPpsR2 through light‐induced structural changes in its HOS domains. An RpBphP1:RpPpsR2 complex is formed in the molecular ratio of 2 : 1 such that one RpBphP1 dimer binds one RpPpsR2 monomer. Molecular dimers have been modeled with Pfr and Pr SAXS data, suggesting that, in the Pfr state, stable dimeric four α‐helix bundles are formed between HOS domains, rendering RpBphP1functionally inert. On illumination with light of 760 nm wavelength, four α‐helix bundles formed by HOS dimers are disrupted, rendering helices available for binding with RpPpsR2.
The bacteriophytochrome RpBphP1 forms a complex with repressor RpPpsR2 when stimulated with far‐red light, causing a host of genes responsible for photosynthesis to be switched on. Photo‐isomerization of biliverdin IXα pigments causes long range structural changes from the far‐red (Pfr) to the red (Pr) absorbing state. These changes disrupt a four α‐helix bundle (magenta), making the HOS domain helix‐turn‐helix motif available for complex formation with RpPpsR2.