Phytochromes in Microorganisms

Vierstra, Richard D.; Karniol, Baruch

doi:10.1002/352760510x.ch8

Cited by 19 publications

(36 citation statements)

References 36 publications

(139 reference statements)

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“…By photoconverting between Pr and Pfr, Phys act as unique light-regulated switches in various signal transduction cascades. In bacteria and fungi, a canonical histidine kinase (HK) domain is typically present downstream of the PHY domain, thus allowing these Phys to participate in various two-component phosphorelays (1,4,5). Although higher plant Phys contain a C-terminal HK-related sequence that promotes dimerization (2, 3), it remains unclear if this domain has phosphotransferase activity (6) or is even involved in signal transmission (7,8).…”

Section: Phytochromes (Phys)mentioning

confidence: 99%

“…They play critical roles in various light-regulated processes, ranging from phototaxis and pigmentation in bacteria to seed germination, chloroplast development, shade avoidance, and flowering in higher plants (1,2). Phys are homodimeric complexes with each polypeptide containing an N-terminal chromophore-binding domain (CBD) that autocatalytically attaches via a thioether linkage a single linear tetrapyrrole (or bilin) chromophore, a PHY domain that is important for spectral integrity, and a C-terminal domain that promotes dimerization and often signal transmission (3).…”

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confidence: 99%

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High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

Wagner

Zhang

Brunzelle

et al. 2007

Journal of Biological Chemistry

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Phytochromes are red/far red light photochromic photoreceptors that direct many photosensory behaviors in the bacterial, fungal, and plant kingdoms. They consist of an N-terminal domain that covalently binds a bilin chromophore and a C-terminal region that transmits the light signal, often through a histidine kinase relay. Using x-ray crystallography, we recently solved the first three-dimensional structure of a phytochrome, using the chromophore-binding domain of Deinococcus radiodurans bacterial phytochrome assembled with its chromophore, biliverdin IX␣. Now, by engineering the crystallization interface, we have achieved a significantly higher resolution model. This 1.45 Å resolution structure helps identify an extensive buried surface between crystal symmetry mates that may promote dimerization in vivo. It also reveals that upon ligation of the C3 2 carbon of biliverdin to Cys 24 , the chromophore A-ring assumes a chiral center at C2, thus becoming 2(R),3(E)-phytochromobilin, a chemistry more similar to that proposed for the attached chromophores of cyanobacterial and plant phytochromes than previously appreciated. The evolution of bacterial phytochromes to those found in cyanobacteria and higher plants must have involved greater fitness using more reduced bilins, such as phycocyanobilin, combined with a switch of the attachment site from a cysteine near the N terminus to one conserved within the cGMP phosphodiesterase/ adenyl cyclase/FhlA domain. From analysis of site-directed mutants in the D. radiodurans phytochrome, we show that this bilin preference was partially driven by the change in binding site, which ultimately may have helped photosynthetic organisms optimize shade detection. Collectively, these three-dimensional structural results better clarify bilin/protein interactions and help explain how higher plant phytochromes evolved from prokaryotic progenitors. Phytochromes (Phys)3 comprise a ubiquitous superfamily of photoreceptors present in the plant, fungal, and bacterial kingdoms. They play critical roles in various light-regulated processes, ranging from phototaxis and pigmentation in bacteria to seed germination, chloroplast development, shade avoidance, and flowering in higher plants (1, 2). Phys are homodimeric complexes with each polypeptide containing an N-terminal chromophore-binding domain (CBD) that autocatalytically attaches via a thioether linkage a single linear tetrapyrrole (or bilin) chromophore, a PHY domain that is important for spectral integrity, and a C-terminal domain that promotes dimerization and often signal transmission (3). Through unique interactions among the bilin and the CBD and PHY domains, Phys can exist as two metastable conformers, a red light (R)-absorbing Pr form and a far red light (FR)-absorbing Pfr form. By photoconverting between Pr and Pfr, Phys act as unique light-regulated switches in various signal transduction cascades. In bacteria and fungi, a canonical histidine kinase (HK) domain is typically present downstream of the PHY domain, thus allowing these P...

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Section: Phytochromes (Phys)mentioning

confidence: 99%

mentioning

confidence: 99%

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

Wagner

Zhang

Brunzelle

et al. 2007

Journal of Biological Chemistry

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224

440

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“…Phytochromes (Phys) 3 include a large and diverse superfamily of sensory photoreceptors that use a bilin (or linear tetrapyrrole) chromophore for light detection (1)(2)(3). These chromoproteins were first discovered in higher plants based on their control of many agriculturally relevant processes and have since been found by sequence searches in lower plants, algae, and numerous proteobacteria, cyanobacteria, and fungi.…”

mentioning

confidence: 99%

“…The most common in microorganisms is a histidine kinase (HK) domain that allows Phys to participate in specific two-component signal transduction cascades (3). Higher plant Phys have C-terminal sequences related to HK domains (2,3), but it has not yet been confirmed that they function as protein kinases.…”

mentioning

confidence: 99%

“…One useful feature is their remarkable stability across a wide range of temperatures, which enhances their survival during NMR data collection. Another was revealed from sequence alignments, which showed that they are members of a previously uncharacterized subfamily of Phys that lacks the N-terminal PAS domain, previously considered important for holo-protein assembly and photochromicity (2,3). Truncations containing just the ϳ200-amino acid GAF domain are photoactive, thus placing them within the acceptable size range for NMR studies (35,36).…”

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Characterization of Two Thermostable Cyanobacterial Phytochromes Reveals Global Movements in the Chromophore-binding Domain during Photoconversion

Ulijasz

Cornilescu

Stetten

et al. 2008

Journal of Biological Chemistry

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1 H-15 N two-dimensional NMR spectra of isotopically labeled preparations of the SyB-Cph1 GAF domain revealed that a number of amino acids change their environment during photoconversion of Pr to Pfr, which can be reversed by subsequent photoconversion back to Pr. Through three-dimensional NMR spectroscopy before and after light photoexcitation, it should now be possible to define the movements of the chromophore and binding pocket during photoconversion. We also generated a series of strongly red fluorescent derivatives of SyB-Cph1, which based on their small size and thermostability may be useful as cell biological reporters. Phytochromes (Phys)3 include a large and diverse superfamily of sensory photoreceptors that use a bilin (or linear tetrapyrrole) chromophore for light detection (1-3). These chromoproteins were first discovered in higher plants based on their control of many agriculturally relevant processes and have since been found by sequence searches in lower plants, algae, and numerous proteobacteria, cyanobacteria, and fungi. For photoautotrophic organisms, Phys are particularly important for optimizing photosynthetic potential where they measure the fluence rate, duration, and the direction of light and help detect shading by competitors (1, 4).The signature feature of canonical Phys is their ability to photoconvert between two stable states, a red light-absorbing Pr form that is typically the parent state of the photoreceptor, and a far-red light-absorbing Pfr form that is often biologically active (1-3) (for examples of exceptions see Refs. 5-7). This activity is directed by a series of structural domains that play specific roles in photoperception. A large N-terminal region encompasses the chromophore-binding domain (CBD); it includes a proximal Per/Arndt/Sim (PAS) domain immediately followed by a cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domain. The CBD autocatalytically attaches the bilin via a thioether linkage and together with the chromophore generates the unique photochromic absorption properties of Phys.For proteobacterial (BphP) and fungal Phys, biliverdin (BV) is used as the chromophore (8). BV is synthesized by oxidative cleavage of heme by a heme oxygenase (HO) and then attached to the apoprotein through its A-pyrrole ring vinyl side chain to a positionally conserved cysteine upstream of the PAS domain (9, 10). For cyanobacterial (Cph) and plant Phys, phycocyanobilin (PCB) and phytochromobilin (P⌽B) are used as the chromophore, respectively (2,11,12). PCB/P⌽B are synthesized by enzymatic reduction of BV using a BV reductase (BVR) and then attached through their A-ring ethylidene side chains to a

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Femtosecond time‐resolved spectroscopy on biological photoreceptor chromophores

Schmitt¹,

Dietzek

Hermann

et al. 2007

Laser & Photonics Reviews

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This paper reviews our results on femtosecond timeresolved spectroscopy (transient absorption, transient-grating and fluorescence spectroscopy) to study the photophysics and photochemistry of the two very important biological photoreceptor chromophores phycocyanobilin (PCB) and protochlorophyllide a (PChla). The compound PCB serves as a model chromophore for the photoreceptor phytochrome. By means of transient-grating spectroscopy where the excitation wavelength was varied over the spectral region of the S0 → S1-absorption the ultrafast processes were studied upon excitation with varying excess energy delivered to the system. On the basis of the results obtained, both the rate of the photoreaction in PCB and the rate of the decay of different excited-state species via different decay channels depend on the excitation wavelength. Furthermore, transient absorption experiments illuminating the excited-state dynamics of PChla, a porphyrin-like compound and, as substrate of the NADPH/protochlorophyllide oxidoreductase (POR), a precursor of the chlorophyll biosynthesis are presented. In addition to pump-energy-dependent measurements performed with PChla dissolved in methanol, the excited-state dynamics of PChla was interrogated in different solvents that were chosen to mimic different environmental conditions. In addition to the femtosecond time-resolved absorption experiments the picosecond time-resolved fluorescence of the system was studied. The transient absorption and time-resolved fluorescence data allow suggesting a detailed model for the excited-state relaxation of PChla describing the excited-state processes in terms of The model suggested to account for the excited-state relaxation processes in protochlorophyllide a upon photoexcitation is presented a branching of the initially excited state population into a reactive and nonreactive path. Thus, the excited-state potential energy surface exhibits two distinct S1 and Sx minima separated from the Franck-Condon region along two most likely orthogonal reaction coordinates. Finally, the model derived is related to models suggested to account for the reduction of PChla to chlorophyllide a within the natural enzymatic environment of POR.

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Phytochromes in Microorganisms

Cited by 19 publications

References 36 publications

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

High Resolution Structure of Deinococcus Bacteriophytochrome Yields New Insights into Phytochrome Architecture and Evolution

Characterization of Two Thermostable Cyanobacterial Phytochromes Reveals Global Movements in the Chromophore-binding Domain during Photoconversion

Femtosecond time‐resolved spectroscopy on biological photoreceptor chromophores

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