Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes

Song, Ji-Young; Lee, Ha Yong; Yang, Hee Wook; Song, Ji‐Joon; Lagarias, J. Clark; Park, Youn‐Il

doi:10.1074/jbc.ra120.012950

Cited by 8 publications

(6 citation statements)

References 64 publications

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“…They undergo reversible photoconversion between two distinct light-absorbing states triggered by C15-Z/C15-E photoisomerization of the bilin chromophore (7,8). Phytochromes are distributed in higher plants, algae, bacteria, and fungi; they typically photoconvert between a red-absorbing C15-Z,anti dark state and a far-red lightabsorbing C15-E,anti photoproduct state, although recent studies have revealed substantial spectral diversity in some algal and cyanobacterial phytochromes (9,10). CBCRs are widely distributed among the cyanobacteria phylum and show marked variation in their absorbing wavelength, spanning the near-ultraviolet to the far-red part of the spectrum (reviewed recently in refs.…”

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confidence: 99%

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Nagae

Unno

Koizumi

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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Cyanobacteriochromes (CBCRs) are bilin-binding photosensors of the phytochrome superfamily that show remarkable spectral diversity. The green/red CBCR subfamily is important for regulating chromatic acclimation of photosynthetic antenna in cyanobacteria and is applied for optogenetic control of gene expression in synthetic biology. It is suggested that the absorption change of this subfamily is caused by the bilin C15-Z/C15-E photoisomerization and a subsequent change in the bilin protonation state. However, structural information and direct evidence of the bilin protonation state are lacking. Here, we report a high-resolution (1.63Å) crystal structure of the bilin-binding domain of the chromatic acclimation sensor RcaE in the red-absorbing photoproduct state. The bilin is buried within a “bucket” consisting of hydrophobic residues, in which the bilin configuration/conformation is C5-Z,syn/C10-Z,syn/C15-E,syn with the A- through C-rings coplanar and the D-ring tilted. Three pyrrole nitrogens of the A- through C-rings are covered in the α-face with a hydrophobic lid of Leu249 influencing the bilin pKa, whereas they are directly hydrogen bonded in the β-face with the carboxyl group of Glu217. Glu217 is further connected to a cluster of waters forming a hole in the bucket, which are in exchange with solvent waters in molecular dynamics simulation. We propose that the “leaky bucket” structure functions as a proton exit/influx pathway upon photoconversion. NMR analysis demonstrated that the four pyrrole nitrogen atoms are indeed fully protonated in the red-absorbing state, but one of them, most likely the B-ring nitrogen, is deprotonated in the green-absorbing state. These findings deepen our understanding of the diverse spectral tuning mechanisms present in CBCRs.

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confidence: 99%

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Nagae

Unno

Koizumi

et al. 2021

Proc. Natl. Acad. Sci. U.S.A.

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“…Cyanobacterial proteins contain the accompanying regions PAS-GAF-PHY [48]. Entire genome sequencing of cyanobacterial species, for example, Microcoleus IPAS B373 [49], Euhalothece Z-M001 [44], and Tolypothrix PCC7910 [50] are devoid of gene HY2, for phytochromobilin (PФB) synthase. Further, these cyanobacteria have pcyA gene that encodes phycocyanobilin (PCB): ferredoxin oxidoreductase that catalyzes the conversion of biliverdin (BV) to PCB, a significant cofactor of Cphs and CBCRs [32,51].…”

Section: Photosensitive Features Of Cbcr 41 Color Sensing By Cphs and Cbcrsmentioning

confidence: 99%

Cyanobacterial Phytochromes in Optogenetics

Selvam¹,

Vinoth²,

Balasubramaniyan³

et al. 2022

Epigenetics to Optogenetics - A New Paradigm in the Study of Biology

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Optogenetics initially used plant photoreceptors to monitor neural circuits, later it has expanded to include engineered plant photoreceptors. Recently photoreceptors from bacteria, algae and cyanobacteria have been used as an optogenetic tool. Bilin-based photoreceptors are common light-sensitive photoswitches in plants, algae, bacteria and cyanobacteria. Here we discuss the photoreceptors from cyanobacteria. Several new photoreceptors have been explored in cyanobacteria which are now proposed as cyanobacteriochrome. The domains in the cyanobacteriochrome, light-induced signaling transduction, photoconversion, are the most attractive features for the optogenetic system. The wider spectral feature of cyanobacteriochrome from UV to visible radiation makes it a light potential sensitive optogenetic tool. Besides, cyanobacterial phytochrome responses to yellow, orange and blue light have more application in optogenetics. This chapter summarizes the photoconversion, phototaxis, cell aggregation, cell signaling mediated by cyanobacteriochrome and cyanophytochrome. As there is a wide range of cyanobacteriochrome and its combination delivers a varied light-sensitive response. Besides coordination among cyanobacteriochromes in cell signaling reduces the engineering of photoreceptors for the optogenetic system.

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“…Recently, a new group of cyanobacterial PAS-GAF-PHY-composed proteins from, e.g., Nostoc punctiforme ATCC29133 (the first one in this group) were reported to carry a second cysteine capable of modifying the PCB chromophore by attachment to position 10 (see Figure 2). 15 This enzymatic bilin conversion resembles the reactivity found in CBCRs and generates remarkably blue-shifted absorption bands. We thus split the subgroup of canonical, cyanobacterial phytochromes into one represented by Cph1 (and orthologs) and a second one named TCCP (tandem cysteine cyanobacterial Phys).…”

Section: Introductionmentioning

confidence: 99%

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

et al. 2021

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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.

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Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes

Cited by 8 publications

References 64 publications

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE

Cyanobacterial Phytochromes in Optogenetics

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

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