Light-induced protein structural dynamics in bacteriophytochrome revealed by time-resolved x-ray solution scattering

Abstract

Bacteriophytochromes (BphPs) are photoreceptors that regulate a wide range of biological mechanisms via red light–absorbing (Pr)–to–far-red light–absorbing (Pfr) reversible photoconversion. The structural dynamics underlying Pfr-to-Pr photoconversion in a liquid solution phase are not well understood. We used time-resolved x-ray solution scattering (TRXSS) to capture light-induced structural transitions in the bathy BphP photosensory module of Pseudomonas aeruginosa . Kinetic analysis of the TRXSS data identifies three distinct structural species, which are attributed to lumi-F, meta-F, and Pr, connected by time constants of 95 μs and 21 ms. Structural analysis based on molecular dynamics simulations shows that the light activation of PaBphP accompanies quaternary structural rearrangements from an “II”-framed close form of the Pfr state to an “O”-framed open form of the Pr state in terms of the helical backbones. This study provides mechanistic insights into how modular signaling proteins such as BphPs transmit structural signals over long distances and regulate their downstream biological responses.

Unassisted stimulation of autotrophic ethanol bioproduction by visible light

“…34,35 As a stimulus, light can be sensed by non-photosynthetic microbes via photoreceptor proteins that will activate regulatory networks governing surface attachment, motility, hydrocarbon degradation, biolm formation, and pathogenicity. 32,36 Here, we demonstrate that visible light on its own stimulates autotrophic and heterotrophic ethanol production by C. autoethanogenum via photoexcitation-induced stress. Simultaneously, acetate accumulation was inhibited during growth with either H 2 : CO : CO 2 or fructose.…”

“…34,35 As a stimulus, light can be sensed by non-photosynthetic microbes via photoreceptor proteins that will activate regulatory networks governing surface attachment, motility, hydrocarbon degradation, biofilm formation, and pathogenicity. 32,36…”

Genetically encoded non‐canonical amino acids reveal asynchronous dark reversion of chromophore, backbone, and side‐chains in EL222

“…If the intrinsic time scales of thio‐adduct breakage (picoseconds) (Kennis et al 2004), chain collapse (microseconds) (Hagen and Eaton 2000), protein monomerization (milliseconds) (Miyamori et al 2015), helix‐coil transitions (nanoseconds) (Jas and Kuczera 2018), and side‐chain rotation (picoseconds) (Cousin et al 2018), are all much faster than the experimentally determined dark recovery times of the whole population of EL222, what is then the reason for observed lifetimes (multi‐seconds) and what is the nature of the rate‐limiting step? Light‐induced protein structural dynamics and allostery typically follows a defined set of sequential conformational transitions (Gil et al 2017; Berntsson et al 2019; Lee et al 2022). The light‐induced dark‐to‐lit transition of EL222 is not an exception: FMN photochemistry drives, and therefore precedes, all subsequent conformational changes through a cascade of intermediates.…”

Genetically encoded non-canonical amino acids reveal asynchronous dark reversion of chromophore, backbone and side-chains in EL222

“…If the intrinsic time scales of thio-adduct breakage (picoseconds) ( 72 ), chain collapse (microseconds) ( 73 ), protein monomerization (milliseconds) ( 74 ), helix-coil transitions (nanoseconds) ( 75 ), and side-chain rotation (picoseconds) ( 76 ), are all much faster than the experimentally determined dark recovery times of the whole population of EL222, what is then the reason for observed lifetimes (multi-seconds) and what is the nature of the rate-limiting step? Light-induced protein structural dynamics and allostery typically follows a defined set of sequential conformational transitions ( 41, 77, 78 ). The light-induced dark-to-lit transition of EL222 is not an exception: FMN photochemistry drives, and therefore precedes, all subsequent conformational changes through a cascade of intermediates.…”