Light-Induced Conformational Changes of S. aurantiaca Bacteriophytochromes as Revealed by Atomic Force Microscopy

Abstract

Bacteriophytochromes (BphPs) are red-light photoreceptors found in photosynthetic and non-photosynthetic bacteria. BphPs are composed of a photosensory core module (PCM) that consists of three domains PAS, GAF, and PHY along with an effector domain, usually a histidine kinase (HK). BphPs utilize a covalently attached biliverdin (BV), an open-chain tetrapyrrole, to photoconvert between red (Pr) and far-red (Pfr) light-absorbing states. Due to the lack of crystal structures of intact BphPs in their respective Pr and Pfr states, we have utilized Atomic Force Microscopy (AFM) to characterize the structure of intact BphPs in biologically relevant media. Specifically, we have focused on the AFM analysis of BphPs from myxobacterium Stigmatella aurantiaca, SaBphP1 and SaBphP2, that share 41% sequence identity, both bind BV and have different Pr/Pfr photoconversion. Unlike classical BphPs, wild-type SaBphP1 lacks a highly conserved His that stabilizes BV and undergoes limited Pr/Pfr photoconversion that can be restored by a single Thr (Thr289) to His mutation in PCM. Individual dimers of intact SaBphP2 have been observed on a mica surface in solution and compared to truncated PAS GAF variants. Quaternary structural changes in length and width of intact BphPs with respect to Pr and Pfr states have been revealed by AFM and compared to published electron microscopy (EM) data. The proteins appear larger by AFM than EM due to the hydration of the protein and the tip convolution. The ratio of length to width of these BphPs determined by AFM agrees within 10% with the EM data for related BphP from Deinococcus radiodurans in its Pfr state. Furthermore, the volume, orientation, and structure of these BphPs are in agreement with respective protein models generated using PyMOL software and X-ray crystallographic structures of similar BphPs.