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Lamparter T, Xue P, Elkurdi A, Kaeser G, Sauthof L, Scheerer P, Krauß N. Phytochromes in Agrobacterium fabrum. FRONTIERS IN PLANT SCIENCE 2021; 12:642801. [PMID: 33995441 PMCID: PMC8117939 DOI: 10.3389/fpls.2021.642801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/18/2021] [Indexed: 05/31/2023]
Abstract
The focus of this review is on the phytochromes Agp1 and Agp2 of Agrobacterium fabrum. These are involved in regulation of conjugation, gene transfer into plants, and other effects. Since crystal structures of both phytochromes are known, the phytochrome system of A. fabrum provides a tool for following the entire signal transduction cascade starting from light induced conformational changes to protein interaction and the triggering of DNA transfer processes.
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Affiliation(s)
- Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Afaf Elkurdi
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Luisa Sauthof
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Patrick Scheerer
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
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Gourinchas G, Etzl S, Winkler A. Bacteriophytochromes - from informative model systems of phytochrome function to powerful tools in cell biology. Curr Opin Struct Biol 2019; 57:72-83. [PMID: 30878713 PMCID: PMC6625962 DOI: 10.1016/j.sbi.2019.02.005] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Revised: 01/31/2019] [Accepted: 02/06/2019] [Indexed: 11/17/2022]
Abstract
Bacteriophytochromes are a subfamily of the diverse light responsive phytochrome photoreceptors. Considering their preferential interaction with biliverdin IXα as endogenous cofactor, they have recently been used for creating optogenetic tools and engineering fluorescent probes. Ideal absorption characteristics for the activation of bacteriophytochrome-based systems in the therapeutic near-infrared window as well the availability of biliverdin in mammalian tissues have resulted in tremendous progress in re-engineering bacteriophytochromes for diverse applications. At the same time, both the structural analysis and the functional characterization of diverse naturally occurring bacteriophytochrome systems have unraveled remarkable differences in signaling mechanisms and have so far only touched the surface of the evolutionary diversity within the family of bacteriophytochromes. This review highlights recent findings and future challenges.
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Affiliation(s)
- Geoffrey Gourinchas
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Stefan Etzl
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria; BioTechMed-Graz, 8010 Graz, Austria.
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Lamparter T, Krauß N, Scheerer P. Phytochromes from Agrobacterium fabrum. Photochem Photobiol 2017; 93:642-655. [DOI: 10.1111/php.12761] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/22/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Tilman Lamparter
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
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Bai Y, Rottwinkel G, Feng J, Liu Y, Lamparter T. Bacteriophytochromes control conjugation in Agrobacterium fabrum. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2016; 161:192-9. [PMID: 27261700 DOI: 10.1016/j.jphotobiol.2016.05.014] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2016] [Accepted: 05/11/2016] [Indexed: 10/21/2022]
Abstract
Bacterial conjugation, the transfer of single stranded plasmid DNA from donor to recipient cell, is mediated through the type IV secretion system. We performed conjugation assays using a transmissible artificial plasmid as reporter. With this assay, conjugation in Agrobacterium fabrum was modulated by the phytochromes Agp1 and Agp2, photoreceptors that are most sensitive in the red region of visible light. In conjugation studies with wild-type donor cells carrying a pBIN-GUSINT plasmid as reporter that lacked the Ti (tumor inducing) plasmid, no conjugation was observed. When either agp1(-) or agp2(-) knockout donor strains were used, plasmid DNA was delivered to the recipient, indicating that both phytochromes suppress conjugation in the wild type donor. In the recipient strains, the loss of Agp1 or Agp2 led to diminished conjugation. When wild type cells with Ti plasmid and pBIN-GUS reporter plasmid were used as donor, a high rate of conjugation was observed. The DNA transfer was down regulated by red or far-red light by a factor of 3.5. With agp1(-) or agp2(-) knockout donor cells, conjugation in the dark was about 10 times lower than with the wild type donor, and with the double knockout donor no conjugation was observed. These results imply that the phytochrome system has evolved to inhibit conjugation in the light. The decrease of conjugation under different temperature correlated with the decrease of phytochrome autophosphorylation.
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Affiliation(s)
- Yingnan Bai
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany; University of Electronic Science and Technology of China (UESTC), School of Science and Technology, No. 4, Sections 2, North Jianshe Road, Chengdu 610054, China
| | - Gregor Rottwinkel
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany
| | - Juan Feng
- University of Electronic Science and Technology of China (UESTC), School of Science and Technology, No. 4, Sections 2, North Jianshe Road, Chengdu 610054, China
| | - Yiyao Liu
- University of Electronic Science and Technology of China (UESTC), School of Science and Technology, No. 4, Sections 2, North Jianshe Road, Chengdu 610054, China
| | - Tilman Lamparter
- Karlsruhe Institute of Technology (KIT), Botanical Institute, Kaiserstr. 2, D-76131 Karlsruhe, Germany.
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Singer P, Wörner S, Lamparter T, Diller R. Spectroscopic Investigation on the Primary Photoreaction of Bathy Phytochrome Agp2-Pr ofAgrobacterium fabrum: Isomerization in a pH-dependent H-bond Network. Chemphyschem 2016; 17:1288-97. [DOI: 10.1002/cphc.201600199] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2016] [Indexed: 11/08/2022]
Affiliation(s)
- Patrick Singer
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
| | - Sybille Wörner
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Tilman Lamparter
- Botanical Institute; Karlsruhe Institute of Technology; Kaiserstraße 2 76131 Karlsruhe Germany
| | - Rolf Diller
- Department of Physics; University of Kaiserslautern; Erwin-Schrödinger-Strasse, Geb. 46 67663 Kaiserslautern Germany), Fax: +49-631-205-3902
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Ukaji Y, Sakata R, Soeta T. One-Carbon Homologation of Pyrrole Carboxaldehyde via Wittig Reaction and Mild Hydrolysis of Vinyl Ether – toward the Synthesis of a Sterically Locked Phytochrome Chromophore. HETEROCYCLES 2015. [DOI: 10.3987/com-14-13157] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ukaji Y, Tanaka Y, Iwamoto R, Sakata R, Soeta T, Endo K, Fujinami S, Inomata K. Regioselective Introduction of Substituents to the meso-Position of Pyrromethenone Derivative – Application to the Synthesis of Sterically Fixed Phytochrome Chromophore Anchored to the C15 meso-Position. HETEROCYCLES 2015. [DOI: 10.3987/com-14-s(k)97] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Singer P, Fey S, Göller AH, Hermann G, Diller R. Femtosecond Dynamics in the Lactim Tautomer of Phycocyanobilin: A Long-Wavelength Absorbing Model Compound for the Phytochrome Chromophore. Chemphyschem 2014; 15:3824-31. [DOI: 10.1002/cphc.201402383] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/02/2014] [Indexed: 11/11/2022]
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Linke M, Yang Y, Zienicke B, Hammam MAS, von Haimberger T, Zacarias A, Inomata K, Lamparter T, Heyne K. Electronic transitions and heterogeneity of the bacteriophytochrome Pr absorption band: An angle balanced polarization resolved femtosecond VIS pump-IR probe study. Biophys J 2014; 105:1756-66. [PMID: 24138851 DOI: 10.1016/j.bpj.2013.08.041] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 08/13/2013] [Accepted: 08/22/2013] [Indexed: 12/15/2022] Open
Abstract
Photoisomerization of biliverdin (BV) chromophore triggers the photoresponse in native Agp1 bacteriophytochrome. We discuss heterogeneity in phytochrome Pr form to account for the shape of the absorption profile. We investigated different regions of the absorption profile by angle balanced polarization resolved femtosecond VIS pump-IR probe spectroscopy. We studied the Pr form of Agp1 with its natural chromophore and with a sterically locked 18Et-BV (locked Agp1). We followed the dynamics and orientations of the carbonyl stretching vibrations of ring D and ring A in their ground and electronically excited states. Photoisomerization of ring D is reflected by strong signals of the ring D carbonyl vibration. In contrast, orientational data on ring A show no rotation of ring A upon photoexcitation. Orientational data allow excluding a ZZZasa geometry and corroborates a nontwisted ZZZssa geometry of the chromophore. We found no proof for heterogeneity but identified a new, to our knowledge, electronic transition in the absorption profile at 644 nm (S0→S2). Excitation of the S0→S2 transition will introduce a more complex photodynamics compared with S0→S1 transition. Our approach provides fundamental information on disentanglement of absorption profiles, identification of chromophore structures, and determination of molecular groups involved in the photoisomerization process of photoreceptors.
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Affiliation(s)
- Martin Linke
- Freie Universität Berlin, Department of Physics, Arnimallee 14, 14195 Berlin, Germany
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Piatkevich KD, Subach FV, Verkhusha VV. Far-red light photoactivatable near-infrared fluorescent proteins engineered from a bacterial phytochrome. Nat Commun 2014; 4:2153. [PMID: 23842578 PMCID: PMC3749836 DOI: 10.1038/ncomms3153] [Citation(s) in RCA: 86] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2013] [Accepted: 06/15/2013] [Indexed: 01/11/2023] Open
Abstract
Ability to modulate fluorescence of optical probes can be used to enhance signal-to-noise ratio for imaging within highly autofluorescent environments, such as intact tissues and living organisms. Here we report two phytochrome-based photoactivatable near-infrared fluorescent proteins, named PAiRFP1 and PAiRFP2. PAiRFPs utilize heme-derived biliverdin, ubiquitous in mammalian tissues, as the chromophore. Initially weakly fluorescent PAiRFPs undergo photoconversion into a highly fluorescent state with excitation/emission at 690 nm/717 nm following a brief irradiation with far-red light. After photoactivation, PAiRFPs slowly revert back to initial state, enabling multiple photoactivation-relaxation cycles. Low-temperature optical spectroscopy reveals several intermediates involved in PAiRFP photocycles, which all differ from that of the bacteriophytochrome precursor. PAiRFPs can be photoactivated in a spatially selective manner in mouse tissues, and optical modulation of their fluorescence allows for substantial contrast enhancement, making PAiRFPs advantageous over permanently fluorescent probes for in vivo imaging conditions of high autofluorescence and low signal levels.
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Affiliation(s)
- Kiryl D Piatkevich
- Department of Anatomy and Structural Biology, Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, USA
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Song C, Psakis G, Kopycki J, Lang C, Matysik J, Hughes J. The D-ring, not the A-ring, rotates in Synechococcus OS-B' phytochrome. J Biol Chem 2013; 289:2552-62. [PMID: 24327657 DOI: 10.1074/jbc.m113.520031] [Citation(s) in RCA: 39] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/16/2023] Open
Abstract
Phytochrome photoreceptors in plants and microorganisms switch photochromically between two states, controlling numerous important biological processes. Although this phototransformation is generally considered to involve rotation of ring D of the tetrapyrrole chromophore, Ulijasz et al. (Ulijasz, A. T., Cornilescu, G., Cornilescu, C. C., Zhang, J., Rivera, M., Markley, J. L., and Vierstra, R. D. (2010) Nature 463, 250-254) proposed that the A-ring rotates instead. Here, we apply magic angle spinning NMR to the two parent states following studies of the 23-kDa GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) domain fragment of phytochrome from Synechococcus OS-B'. Major changes occur at the A-ring covalent linkage to the protein as well as at the protein residue contact of ring D. Conserved contacts associated with the A-ring nitrogen rule out an A-ring photoflip, whereas loss of contact of the D-ring nitrogen to the protein implies movement of ring D. Although none of the methine bridges showed a chemical shift change comparable with those characteristic of the D-ring photoflip in canonical phytochromes, denaturation experiments showed conclusively that the same occurs in Synechococcus OS-B' phytochrome upon photoconversion. The results are consistent with the D-ring being strongly tilted in both states and the C15=C16 double bond undergoing a Z/E isomerization upon light absorption. More subtle changes are associated with the A-ring linkage to the protein. Our findings thus disprove A-ring rotation and are discussed in relation to the position of the D-ring, photoisomerization, and photochromicity in the phytochrome family.
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Affiliation(s)
- Chen Song
- From the Leids Instituut voor Chemisch Onderzoek, Universiteit Leiden, NL-2300 RA Leiden, The Netherlands
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12
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Zienicke B, Molina I, Glenz R, Singer P, Ehmer D, Escobar FV, Hildebrandt P, Diller R, Lamparter T. Unusual spectral properties of bacteriophytochrome Agp2 result from a deprotonation of the chromophore in the red-absorbing form Pr. J Biol Chem 2013; 288:31738-51. [PMID: 24036118 DOI: 10.1074/jbc.m113.479535] [Citation(s) in RCA: 43] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are widely distributed photoreceptors with a bilin chromophore that undergo a typical reversible photoconversion between the two spectrally different forms, Pr and Pfr. The phytochrome Agp2 from Agrobacterium tumefaciens belongs to the group of bathy phytochromes that have a Pfr ground state as a result of the Pr to Pfr dark conversion. Agp2 has untypical spectral properties in the Pr form reminiscent of a deprotonated chromophore as confirmed by resonance Raman spectroscopy. UV/visible absorption spectroscopy showed that the pKa is >11 in the Pfr form and ∼7.6 in the Pr form. Unlike other phytochromes, photoconversion thus results in a pKa shift of more than 3 units. The Pr/Pfr ratio after saturating irradiation with monochromatic light is strongly pH-dependent. This is partially due to a back-reaction of the deprotonated Pr chromophore at pH 9 after photoexcitation as found by flash photolysis. The chromophore protonation and dark conversion were affected by domain swapping and site-directed mutagenesis. A replacement of the PAS or GAF domain by the respective domain of the prototypical phytochrome Agp1 resulted in a protonated Pr chromophore; the GAF domain replacement afforded an inversion of the dark conversion. A reversion was also obtained with the triple mutant N12S/Q190L/H248Q, whereas each single point mutant is characterized by decelerated Pr to Pfr dark conversion.
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Affiliation(s)
- Benjamin Zienicke
- From the Botanical Institute, Karlsruhe Institute of Technology, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
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Ukaji Y, Takahashi K, Iwamoto R, Sakata R, Inomata K, Soeta T. DIRECT OXIDATION OF 4-METHYLPYRROLE-2-CARBOXYLATES WITH DDQ IN THE PRESENCE OF A GLYCOL. HETEROCYCLES 2012. [DOI: 10.3987/com-12-s(n)126] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Inomata K. Syntheses of Bilin Chromophores Toward the Investigation of Structure and Function of Phytochromes. HETEROCYCLES 2012. [DOI: 10.3987/rev-12-750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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Ulijasz AT, Vierstra RD. Phytochrome structure and photochemistry: recent advances toward a complete molecular picture. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:498-506. [PMID: 21733743 DOI: 10.1016/j.pbi.2011.06.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/14/2011] [Accepted: 06/14/2011] [Indexed: 05/31/2023]
Abstract
Phytochromes are nature's primary photoreceptors dedicated to detecting the red and far-red regions of the visible light spectrum, a region also essential for photosynthesis and thus crucial to the survival of plants and other photosynthetic organisms. Given their roles in measuring competition and diurnal/seasonal light fluctuations, understanding how phytochromes work at the molecular level would greatly aid in engineering crop plants better suited to specific agricultural settings. Recently, scientists have determined the three-dimensional structures of prokaryotic phytochromes, which now provide clues as to how these modular photoreceptors might work at the atomic level. The models point toward a largely unifying mechanism whereby novel knot, hairpin, and dimeric interfaces transduce photoreversible bilin isomerization into protein conformational changes that alter signal output.
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Affiliation(s)
- Andrew T Ulijasz
- Department of Biological Sciences, 3209 North Maryland Avenue, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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Vierstra RD, Zhang J. Phytochrome signaling: solving the Gordian knot with microbial relatives. TRENDS IN PLANT SCIENCE 2011; 16:417-426. [PMID: 21719341 DOI: 10.1016/j.tplants.2011.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 05/28/2023]
Abstract
Phytochromes encompass a diverse collection of biliproteins that regulate numerous photoresponses in plants and microorganisms. Whereas the plant versions have proven experimentally intractable for structural studies, the microbial forms have recently provided important insights into how these photoreceptors work at the atomic level. Here, we review the current understanding of these microbial phytochromes, which shows that they have a modular dimeric architecture that propagates light-driven rotation of the bilin to distal contacts between adjacent signal output domains. Surprising features underpinning this signaling include: a deeply buried chromophore; a knot and hairpin loop that stabilizes the photosensing domain; and an extended helical spine that translates conformational changes in the photosensing domain to the output domain. Conservation within the superfamily both in modular construction and sequence strongly suggests that higher plant phytochromes work similarly as light-regulated toggle switches.
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Affiliation(s)
- Richard D Vierstra
- Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Chen L, Iwamoto R, Ukaji Y, Inomata K. Total Synthesis of Doubly Locked 5Za15Ea-Biliverdin Derivative: A Convergent Synthesis of theE-antiDipyrrole Component Locked with a 7-Membered Ring. CHEM LETT 2011. [DOI: 10.1246/cl.2011.632] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
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Abstract
Phytochromes are environmental sensors, historically thought of as red/far-red photoreceptors in plants. Their photoperception occurs through a covalently linked tetrapyrrole chromophore, which undergoes a light-dependent conformational change propagated through the protein to a variable output domain. The phytochrome composition is modular, typically consisting of a PAS-GAF-PHY architecture for the N-terminal photosensory core. A collection of three-dimensional structures has uncovered key features, including an unusual figure-of-eight knot, an extension reaching from the PHY domain to the chromophore-binding GAF domain, and a centrally located, long α-helix hypothesized to be crucial for intramolecular signaling. Continuing identification of phytochromes in microbial systems has expanded the assigned sensory abilities of this family out of the red and into the yellow, green, blue, and violet portions of the spectrum. Furthermore, phytochromes acting not as photoreceptors but as redox sensors have been recognized. In addition, architectures other than PAS-GAF-PHY are known, thus revealing phytochromes to be a varied group of sensory receptors evolved to utilize their modular design to perceive a signal and respond accordingly. This review focuses on the structures of bacterial phytochromes and implications for signal transmission. We also discuss the small but growing set of bacterial phytochromes for which a physiological function has been ascertained.
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Affiliation(s)
- Michele E Auldridge
- Department of Bacteriology, University of Wisconsin-Madison, Madison, WI 53706, USA
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Strambi A, Durbeej B. Initial excited-state relaxation of the bilin chromophores of phytochromes: a computational study. Photochem Photobiol Sci 2011; 10:569-79. [DOI: 10.1039/c0pp00307g] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023]
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20
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Rodriguez-Romero J, Hedtke M, Kastner C, Müller S, Fischer R. Fungi, hidden in soil or up in the air: light makes a difference. Annu Rev Microbiol 2010; 64:585-610. [PMID: 20533875 DOI: 10.1146/annurev.micro.112408.134000] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.
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Affiliation(s)
- Julio Rodriguez-Romero
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Microbiology, D-76187 Karlsruhe, Germany
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21
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Nishiyama K, Kamiya A, Hammam MAS, Kinoshita H, Fujinami S, Ukaji Y, Inomata K. Total Syntheses of Sterically Locked Phycocyanobilin Derivatives Bearing a 15Z-antior a 15E-antiCD-Ring Component. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2010. [DOI: 10.1246/bcsj.20100168] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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Zienicke B, Chen LY, Khawn H, Hammam MAS, Kinoshita H, Reichert J, Ulrich AS, Inomata K, Lamparter T. Fluorescence of phytochrome adducts with synthetic locked chromophores. J Biol Chem 2010; 286:1103-13. [PMID: 21071442 DOI: 10.1074/jbc.m110.155143] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
We performed steady state fluorescence measurements with phytochromes Agp1 and Agp2 of Agrobacterium tumefaciens and three mutants in which photoconversion is inhibited. These proteins were assembled with the natural chromophore biliverdin (BV), with phycoerythrobilin (PEB), which lacks a double bond in the ring C-D-connecting methine bridge, and with synthetic bilin derivatives in which the ring C-D-connecting methine bridge is locked. All PEB and locked chromophore adducts are photoinactive. According to fluorescence quantum yields, the adducts may be divided into four different groups: wild type BV adducts exhibiting a weak fluorescence, mutant BV adducts with about 10-fold enhanced fluorescence, adducts with locked chromophores in which the fluorescence quantum yields are around 0.02, and PEB adducts with a high quantum yield of around 0.5. Thus, the strong fluorescence of the PEB adducts is not reached by the locked chromophore adducts, although the photoconversion energy dissipation pathway is blocked. We therefore suggest that ring D of the bilin chromophore, which contributes to the extended π-electron system of the locked chromophores, provides an energy dissipation pathway that is independent on photoconversion.
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Affiliation(s)
- Benjamin Zienicke
- Botanical Institute, Karlsruhe Institute of Technology, Campus South, Kaiserstrasse 2, D-76131 Karlsruhe, Germany
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Piwowarski P, Ritter E, Hofmann KP, Hildebrandt P, von Stetten D, Scheerer P, Michael N, Lamparter T, Bartl F. Light-induced activation of bacterial phytochrome Agp1 monitored by static and time-resolved FTIR spectroscopy. Chemphyschem 2010; 11:1207-14. [PMID: 20333618 DOI: 10.1002/cphc.200901008] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Phytochromes, which regulate many biological processes in plants, bacteria, and fungi, can exist in two stable states, Pr and Pfr, that can be interconverted by light, via a number of intermediates such as meta-Rc. Herein we employ FTIR spectroscopy to study the Pr-to-Pfr conversion of the bacteriophytochrome Agp1 from Agrobacterium tumefaciens. Static FTIR Pfr/Pr and meta-Rc/Pr difference spectra are disentangled in terms of cofactor and protein structural changes. Guided by DFT calculations on cofactor models, the chromophore conformational changes can be grouped into structural adjustments of the cofactor-protein interactions localized in the C-D dipyrrole moiety, that is, the photoisomerisation site, and in the A-B dipyrrole moiety including the protein attachment site. Whereas changes at the C and D rings appear to be largely completed in the meta-Rc state, the structural changes in the A-B unit occur during the transition from meta-Rc to Pfr, concomitant with the main protein structural changes, as demonstrated by static and time-resolved FTIR difference spectroscopy. We employ this technique to monitor, for the first time, the dynamics of the photocycle of phytochrome on the millisecond timescale. By extending the studies to genetically engineered protein variants of Agp1, we further demonstrate that H250 and D197 as well as the PHY domain are essential for formation of the Pfr state. Based on the IR spectroscopic and available crystallographic data we discuss the role of critical amino acid residues for the protein-cofactor interactions during the photoinduced reaction cycle.
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Affiliation(s)
- Patrick Piwowarski
- Institut für Medizinische Physik und Biophysik, Charité, Universitätsmedizin Berlin, Charitéplatz 1, 10098 Berlin, Germany
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Scheerer P, Michael N, Park JH, Nagano S, Choe HW, Inomata K, Borucki B, Krauß N, Lamparter T. Light-Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems. Chemphyschem 2010; 11:1090-105. [DOI: 10.1002/cphc.200900913] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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Iwamoto R, Ukaji Y, Inomata K. Regioselective Oxidation of Pyrrole Derivatives with DDQ and Its Synthetic Application. CHEM LETT 2010. [DOI: 10.1246/cl.2010.176] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022]
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26
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Structural basis for the photoconversion of a phytochrome to the activated Pfr form. Nature 2010; 463:250-4. [PMID: 20075921 PMCID: PMC2807988 DOI: 10.1038/nature08671] [Citation(s) in RCA: 110] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2009] [Accepted: 11/11/2009] [Indexed: 01/28/2023]
Abstract
Phytochromes are a collection of bilin-containing photoreceptors that regulate numerous photoresponses in plants and microorganisms through their ability to photointerconvert between a red light-absorbing, ground state Pr and a far-red light-absorbing, photoactivated state Pfr1,2. While the structures of several phytochromes as Pr have been determined3-7, little is known about the structure of Pfr and how it initiates signaling. Here, we describe the three-dimensional solution structure of the bilin-binding domain as Pfr using the cyanobacterial phytochrome from Synechococcus OSB’. Contrary to predictions, light-induced rotation of the A but not the D pyrrole ring is the primary motion of the chromophore during photoconversion. Subsequent rearrangements within the protein then affect intra- and interdomain contact sites within the phytochrome dimer. From our models, we propose that phytochromes act by propagating reversible light-driven conformational changes in the bilin to altered contacts between the adjacent output domains, which in most phytochromes direct differential phosphotransfer.
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Inomata K, Ukaji Y, Iwamoto R, Fujinami S, Sakata R. Oxidation of Pyrrole-2-carboxylates with o-Chloranil and Its Synthetic Application. HETEROCYCLES 2010. [DOI: 10.3987/com-10-s(e)110] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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28
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Borucki B, Seibeck S, Heyn MP, Lamparter T. Characterization of the covalent and noncovalent adducts of Agp1 phytochrome assembled with biliverdin and phycocyanobilin by circular dichroism and flash photolysis. Biochemistry 2009; 48:6305-17. [PMID: 19496558 DOI: 10.1021/bi900436v] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The functional role of the covalent attachment of the bilin chromophores biliverdin (BV) and phycocyanobilin (PCB) was investigated for phytochrome Agp1 from Agrobacterium tumefaciens using circular dichroism (CD) and transient absorption spectroscopy. Covalent and noncovalent adducts with these chromophores were prepared by using wild-type (WT) Agp1 (covalent BV and noncovalent PCB binding), mutant C20A in which the covalent BV binding site is eliminated, and mutant V249C in which the covalent PCB binding site is introduced. While the CD spectra of the P(r) forms of all these photochromic adducts are qualitatively the same, the CD spectrum of the P(fr) form of the covalent PCB adduct is unique in having a positive rotational strength in the Q-band which we assign to the Z-E isomerization of the C-D methine bridge. In the three other adducts, the Q-band CD in the P(fr) state is almost zero, suggesting that upon photoconversion a negative contribution from an out-of-plane rotation of the A ring of the chromophore compensates for the positive contribution from ring D. The contribution from ring A is absent or strongly reduced in the shorter pi-conjugation system of the covalent PCB adduct. The results from CD spectroscopy are consistent with a uniform geometry of the bilin chromophore in the covalent and noncovalent adducts. Transient absorption spectroscopy showed that the spectral changes and the kinetics of the P(r) to P(fr) photoconversion are not substantially affected by the covalent attachment of BV and PCB. The kinetics in the BV and PCB adducts mainly differ in the formation of P(fr) that is accelerated by 2 orders of magnitude in the PCB adducts, whereas the sequence of spectral transitions and the associated proton transfer processes are quite similar. We conclude that the P(r) to P(fr) photoconversion in the BV and PCB adducts of Agp1 involves the same relaxation processes and is thus governed by specific protein-cofactor interactions rather than by the chemical structure of the chromophore or the mode of attachment. The strongly reduced photostability of the noncovalent BV adduct suggests that covalent attachment in native Agp1 phytochrome prevents irreversible photobleaching and stabilizes the chromophore. The N-terminal peptide segment including amino acids 2-19 is essential for covalent attachment of the chromophore but dispensable for the spectral and kinetic properties of Agp1.
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Affiliation(s)
- Berthold Borucki
- Biophysics Group, Department of Physics, Freie Universitat Berlin, Arnimallee 14, 14195 Berlin, Germany.
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Borucki B, Lamparter T. A polarity probe for monitoring light-induced structural changes at the entrance of the chromophore pocket in a bacterial phytochrome. J Biol Chem 2009; 284:26005-16. [PMID: 19640848 DOI: 10.1074/jbc.m109.049056] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Light-induced structural changes at the entrance of the chromophore pocket of Agp1 phytochrome were investigated by using a thiol-reactive fluorescein derivative that is covalently attached to the genuine chromophore binding site (Cys-20) and serves as a polarity probe. In the apoprotein, the absorption spectrum of bound fluorescein is red-shifted with respect to that of the free label suggesting that the probe enters the hydrophobic chromophore pocket. Assembly of this construct with the chromophores phycocyanobilin or biliverdin is associated with a blue-shift of the fluorescein absorption band indicating the displacement of the probe out of the pocket. The probe does not affect the photochromic and kinetic properties of the noncovalent bilin adducts. Upon photoconversion to Pfr, the probe spectrum undergoes again a bathochromic shift and a strong rise in CD indicating a more hydrophobic and asymmetric environment. We propose that the environmental changes of the probe reflect conformational changes at the entrance of the chromophore pocket and are indicative for rearrangements of the chromophore ring A. Flash photolysis measurements showed that the absorption changes of the probe are kinetically coupled to the formation of Meta-R(C) and Pfr. In the biliverdin adduct, an additional component occurs that probably reflects a transition between two Meta-RC substates. Analogous results to that of the noncovalent phycocyanobilin adduct were obtained with the mutant V249C in which probe and chromophore are covalently attached. The conformational changes of the chromophore are correlated to proton transfer to the protein surface.
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Affiliation(s)
- Berthold Borucki
- Department of Physics, Biophysics Group, Freie Universität Berlin, Arnimallee 14, Berlin D-14195, Germany
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