Phytochromes: An Atomic Perspective on Photoactivation and Signaling

Burgie, E.S.; Vierstra, R.D.

doi:10.1105/tpc.114.131623

Cited by 167 publications

(204 citation statements)

References 107 publications

(245 reference statements)

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“…The majority of known (bacterio)phytochromes, including the one from Aradinopsis, 267 shows the bilin in a ZZZssa configuration in the dark. 193,268 Herein, the A-C rings are relatively coplanar and the D-ring is rotated out of the mean plane. The classic mechanistic proposal then involves a photochemical Z  E isomerization of the C15=C16 double bond (to yield the bilin in ZZEssa configuration), 269 which results in a flipping of ring D with associated changes in bilin-protein interactions, movement of the chromophore and protein conformational changes.…”

Section: Linear Tetrapyrroles -Phycobilinsmentioning

confidence: 99%

“…Taking the (bacterio)phytochromes and light-harvesting phycobiliproteins into account as well, a general picture is emerging. 193 On one hand we have the classic photochemical cis/trans isomerization with subsequent conformational changes in the protein acting as a signal output for the various signaling cascades. The majority of known (bacterio)phytochromes, including the one from Aradinopsis, 267 shows the bilin in a ZZZssa configuration in the dark.…”

Section: Linear Tetrapyrroles -Phycobilinsmentioning

confidence: 99%

“…274 Together with the ability to tune the specific absorption and emission wavelength, this leads to new fluorescent tag molecules with more scope for use than the commonly used green fluorescent proteins. 193 Recent reviews by Scheer et al 17 and Burgie and Vierstra 193 further illuminate this use of biliproteins as bioimaging agents and the path to designer photoresponsive proteins.…”

mentioning

confidence: 99%

“…The wide range of available mutant structures and those reconstituted with different chromophores offers significant potential to develop new cell biological reporter molecules and in optogenetics. 17,193 An example for the former is the use of small phytochrome fragments with mutations which result in highly fluorescent molecules. 274 Together with the ability to tune the specific absorption and emission wavelength, this leads to new fluorescent tag molecules with more scope for use than the commonly used green fluorescent proteins.…”

mentioning

confidence: 99%

“…191 The emerging picture on their structures, 192 mechanisms and photoresponses reveals in detail the structural changes that follow photoisomerization and include nm scale movements of the bilins, significant changes in protein structure and folding, and their ultimate impact on the signal output domains. 193 Secondly, linear tetrapyrroles function as accessory lightharvesting pigments in photosynthesis. They are parts of the phycobilisomes, highly organized pigment-protein complexes which act as antenna systems for photosystem II in cyanobacteria and red algae, amongst others.…”

mentioning

confidence: 99%

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Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

2015

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Tetrapyrrole-containing proteins are one of the most fundamental classes of enzymes in nature and it remains an open question to give a chemical rationale for the multitude of biological reactions that can be catalyzed by these pigmentprotein complexes. There are many fundamental processes where the same (i.e., chemically identical) porphyrin cofactor is involved in chemically quite distinct reactions. For example, heme is the active cofactor for oxygen transport and storage (hemoglobin, myoglobin) and for the incorporation of molecular oxygen in organic substrates (cytochrome P 450 ). It is involved in the terminal oxidation (cytochrome c oxidase) and the metabolism of H 2 O 2 (catalases and peroxidases) and catalyzes various electron transfer reactions in cytochromes. Likewise, in photosynthesis the same chlorophyll cofactor may function as a reaction center pigment (charge separation) or as an accessory pigment (exciton transfer) in light harvesting complexes (e.g., chlorophyll a). Whilst differences in the apoprotein sequences alone cannot explain the often drastic differences in physicochemical properties encountered for the same cofactor in diverse protein complexes, a critical factor for all biological functions must be the close structural interplay between bound cofactors and the respective apoprotein in addition to factors such as hydrogen bonding or electronic effects. Here, we explore how nature can use the same chemical molecule as a cofactor for chemically distinct reactions using the concept of conformational flexibility of tetrapyrroles. The multifaceted roles of tetrapyrroles are discussed in the context of the current knowledge on distorted porphyrins. Contemporary analytical methods now allow a more quantitative look at cofactors in protein complexes and the development of the field is illustrated by case studies on hemeproteins and photosynthetic complexes. Specific tetrapyrrole conformations are now used to prepare bioengineered designer proteins with specific catalytic or photochemical properties.

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Section: Linear Tetrapyrroles -Phycobilinsmentioning

confidence: 99%

Section: Linear Tetrapyrroles -Phycobilinsmentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

mentioning

confidence: 99%

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Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

2015

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Structural communication between the chromophore‐binding pocket and the N‐terminal extension in plant phytochrome phyB

et al. 2017

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The N-terminal extension (NTE) of plant phytochromes has been suggested to play a functional role in signaling photoinduced structural changes. Here, we use resonance Raman spectroscopy to study the effect of the NTE on the chromophore structure of B-type phytochromes from two evolutionarily distant plants. NTE deletion seems to have no effect on the chromophore in the inactive Pr state, but alters the torsion of the C-D ring methine bridge and the surrounding hydrogen bonding network in the physiologically active Pfr state. These changes are accompanied by a shift of the conformational equilibrium between two Pfr substates, which might affect the thermal isomerization rate of the C-D double bond and, thus, account for the effect of the NTE on the dark reversion kinetics.

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Nucleus‐to‐Plastid Phytochrome Signalling in Controlling Chloroplast Biogenesis

Yoo

Han

Chen

2020

Annual Plant Reviews Online

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The biogenesis of photosynthetically active chloroplasts in flowering plants (angiosperms) is initiated by light through the red and far‐red photoreceptors, phytochromes, which activate photosynthesis‐associated genes encoded by both the nuclear and plastid genomes. Because photoactivated phytochromes localize to the nucleus but not the plastids, phytochromes ought to control plastid transcription through nucleus‐to‐plastid or anterograde signalling. However, the mechanism of anterograde signalling remains poorly understood. Recent advances in our understanding of phytochrome signalling and plastid transcription led to the discovery of the framework of an anterograde signalling pathway, which links light‐dependent regulation of nuclear repressors of chloroplast biogenesis to the control of the assembly and activity of the bacterial‐type plastidial RNA polymerase for transcribing plastid‐encoded photosynthesis genes. This article is aimed to gather and reanalyze the evidence in the literature relevant to the phytochrome control of chloroplast biogenesis to forge a model of anterograde signalling mechanisms for the regulation of plastid transcription by light.

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Phytochromes: An Atomic Perspective on Photoactivation and Signaling

Cited by 167 publications

References 107 publications

Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Conformational control of cofactors in nature – the influence of protein-induced macrocycle distortion on the biological function of tetrapyrroles

Structural communication between the chromophore‐binding pocket and the N‐terminal extension in plant phytochrome phyB

Nucleus‐to‐Plastid Phytochrome Signalling in Controlling Chloroplast Biogenesis

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