The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters

Abstract

This review adds the bilin-binding phytochromes to the Chemical Reviews thematic issue “Optogenetics and Photopharmacology”. The work is structured into two parts. We first outline the photochemistry of the covalently bound tetrapyrrole chromophore and summarize relevant spectroscopic, kinetic, biochemical, and physiological properties of the different families of phytochromes. Based on this knowledge, we then describe the engineering of phytochromes to further improve these chromoproteins as photoswitches and review their employment in an ever-growing number of different optogenetic applications. Most applications rely on the light-controlled complex formation between the plant photoreceptor PhyB and phytochrome-interacting factors (PIFs) or C-terminal light-regulated domains with enzymatic functions present in many bacterial and algal phytochromes. Phytochrome-based optogenetic tools are currently implemented in bacteria, yeast, plants, and animals to achieve light control of a wide range of biological activities. These cover the regulation of gene expression, protein transport into cell organelles, and the recruitment of phytochrome- or PIF-tagged proteins to membranes and other cellular compartments. This compilation illustrates the intrinsic advantages of phytochromes compared to other photoreceptor classes, e.g., their bidirectional dual-wavelength control enabling instant ON and OFF regulation. In particular, the long wavelength range of absorption and fluorescence within the “transparent window” makes phytochromes attractive for complex applications requiring deep tissue penetration or dual-wavelength control in combination with blue and UV light-sensing photoreceptors. In addition to the wide variability of applications employing natural and engineered phytochromes, we also discuss recent progress in the development of bilin-based fluorescent proteins.

Photochemistry and transient intermediates in a bacteriophytochrome photocycle revealed by multiscale simulations

“…The PSM is then linked to an output module, which exerts a specific function depending on the species [19][20][21] . Due to such a modular domain architecture, and because they absorb and fluoresce within the so-called "transparent window", phytochromes are exploited in emerging fields as bioimaging and optogenetics 13,[22][23][24][25][26] .…”

Enhancing the Inhomogeneous Photodynamics of Canonical Bacteriophytochrome

“… 5 − 8 Phytochromes play an essential role in light-regulated processes, e.g., phototaxis, pigmentation, and photosynthesis, and are interesting also as targets for optogenetic applications, imaging in tissues, light-dependent gene expression, and possible medical applications. 9 − 14 BphP in the Deinococcus radiodurans cells, in addition to its responsibility for pigmentation and growth, is potentially involved in the resistance of these bacteria to ionizing radiation and mutagenic factors by participating in the DNA damage response. 15 …”

A red-green photochromic bacterial protein as a new contrast agent for improved photoacoustic imaging

“…More recently, bacterial phytochrome photoreceptors have been developed as optogenetic and imaging tools, characterized by absorption spectra covering the far red- near infrared portion of the electromagnetic spectrum, thanks to their ubiquitous biliverdin choromophore. [10] , [11] , [12] These receptors have several advantages for photoacoustic imaging since they have low fluorescence yields (typically 10 −2 -10 −3 ) [13] and high molar absorption coefficients (85,000–110,000 M −1 cm −1 ). [14] , [15] , [16] To further improve such applications such as contrast increase in photoacoustic imaging, reversibly switchable fluorescent proteins have been employed.…”