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Sineshchekov VA. Two Distinct Molecular Types of Phytochrome A in Plants: Evidence of Existence and Implications for Functioning. Int J Mol Sci 2023; 24:8139. [DOI: https:/doi.org/10.3390/ijms24098139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023] Open
Abstract
Phytochrome (phy) system in plants comprising a small number of phytochromes with phyA and phyB as major ones is responsible for acquiring light information in the red—far-red region of the solar spectrum. It provides optimal strategy for plant development under changing light conditions throughout all its life cycle beginning from seed germination and seedling establishment to fruiting and plant senescence. The phyA was shown to participate in the regulation of this cycle which is especially evident at its early stages. It mediates three modes of reactions—the very low and low fluence responses (VLFR and LFR) and the high irradiance responses (HIR). The phyA is the sole light receptor in the far-red spectral region responsible for plant’s survival under a dense plant canopy where light is enriched with the far-red component. Its appearance is believed to be one of the main factors of plants′ successful evolution. So far, it is widely accepted that one molecular phyA species is responsible for its complex functional manifestations. In this review, the evidence of the existence of two distinct phyA types—major, light-labile and soluble phyA′ and minor, relatively light-stable and amphiphilic phyA″—is presented as what may account for the diverse modes of phyA action.
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Phytochrome A in plants comprises two structurally and functionally distinct populations — water-soluble phyA′ and amphiphilic phyA″. Biophys Rev 2022; 14:905-921. [DOI: 10.1007/s12551-022-00974-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2022] [Accepted: 06/14/2022] [Indexed: 10/17/2022] Open
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Nagano S, Sadeghi M, Balke J, Fleck M, Heckmann N, Psakis G, Alexiev U. Improved fluorescent phytochromes for in situ imaging. Sci Rep 2022; 12:5587. [PMID: 35379835 PMCID: PMC8980088 DOI: 10.1038/s41598-022-09169-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2021] [Accepted: 03/14/2022] [Indexed: 12/18/2022] Open
Abstract
AbstractModern biology investigations on phytochromes as near-infrared fluorescent pigments pave the way for the development of new biosensors, as well as for optogenetics and in vivo imaging tools. Recently, near-infrared fluorescent proteins (NIR-FPs) engineered from biliverdin-binding bacteriophytochromes and cyanobacteriochromes, and from phycocyanobilin-binding cyanobacterial phytochromes have become promising probes for fluorescence microscopy and in vivo imaging. However, current NIR-FPs typically suffer from low fluorescence quantum yields and short fluorescence lifetimes. Here, we applied the rational approach of combining mutations known to enhance fluorescence in the cyanobacterial phytochrome Cph1 to derive a series of highly fluorescent variants with fluorescence quantum yield exceeding 15%. These variants were characterised by biochemical and spectroscopic methods, including time-resolved fluorescence spectroscopy. We show that these new NIR-FPs exhibit high fluorescence quantum yields and long fluorescence lifetimes, contributing to their bright fluorescence, and provide fluorescence lifetime imaging measurements in E.coli cells.
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Tang K, Beyer HM, Zurbriggen MD, Gärtner W. The Red Edge: Bilin-Binding Photoreceptors as Optogenetic Tools and Fluorescence Reporters. Chem Rev 2021; 121:14906-14956. [PMID: 34669383 PMCID: PMC8707292 DOI: 10.1021/acs.chemrev.1c00194] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2021] [Indexed: 12/15/2022]
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.
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Affiliation(s)
- Kun Tang
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Hannes M. Beyer
- Institute
of Synthetic Biology, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse 1, D-40225 Düsseldorf, Germany
| | - Matias D. Zurbriggen
- Institute
of Synthetic Biology and CEPLAS, Heinrich-Heine-University
Düsseldorf, Universitätsstrasse
1, D-40225 Düsseldorf, Germany
| | - Wolfgang Gärtner
- Retired: Max Planck Institute
for Chemical Energy Conversion. At present: Institute for Analytical Chemistry, University
Leipzig, Linnéstrasse
3, 04103 Leipzig, Germany
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Fischer T, van Wilderen LJGW, Gnau P, Bredenbeck J, Essen LO, Wachtveitl J, Slavov C. Ultrafast Photoconversion Dynamics of the Knotless Phytochrome SynCph2. Int J Mol Sci 2021; 22:ijms221910690. [PMID: 34639031 PMCID: PMC8508867 DOI: 10.3390/ijms221910690] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 09/24/2021] [Accepted: 09/28/2021] [Indexed: 12/03/2022] Open
Abstract
The family of phytochrome photoreceptors contains proteins with different domain architectures and spectral properties. Knotless phytochromes are one of the three main subgroups classified by their distinct lack of the PAS domain in their photosensory core module, which is in contrast to the canonical PAS-GAF-PHY array. Despite intensive research on the ultrafast photodynamics of phytochromes, little is known about the primary kinetics in knotless phytochromes. Here, we present the ultrafast Pr ⇆ Pfr photodynamics of SynCph2, the best-known knotless phytochrome. Our results show that the excited state lifetime of Pr* (~200 ps) is similar to bacteriophytochromes, but much longer than in most canonical phytochromes. We assign the slow Pr* kinetics to relaxation processes of the chromophore-binding pocket that controls the bilin chromophore’s isomerization step. The Pfr photoconversion dynamics starts with a faster excited state relaxation than in canonical phytochromes, but, despite the differences in the respective domain architectures, proceeds via similar ground state intermediate steps up to Meta-F. Based on our observations, we propose that the kinetic features and overall dynamics of the ultrafast photoreaction are determined to a great extent by the geometrical context (i.e., available space and flexibility) within the binding pocket, while the general reaction steps following the photoexcitation are most likely conserved among the red/far-red phytochromes.
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Affiliation(s)
- Tobias Fischer
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
| | - Luuk J. G. W. van Wilderen
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Petra Gnau
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt am Main, Max-von-Laue Straße 1, 60438 Frankfurt, Germany; (L.J.G.W.v.W.); (J.B.)
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-Universität Marburg, Hans-Meerwein-Straße 4, 35032 Marburg, Germany; (P.G.); (L.-O.E.)
- Center for Synthetic Microbiology, Philipps-Universität Marburg, Hans-Meerwein-Straße 6, 35032 Marburg, Germany
| | - Josef Wachtveitl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
| | - Chavdar Slavov
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt am Main, Max-von-Laue Straße 7, 60438 Frankfurt, Germany;
- Correspondence: (J.W.); (C.S.)
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Sineshchekov VA, Bekasova OD. Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light‐Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes. Photochem Photobiol 2020; 96:750-767. [DOI: https:/doi.org/10.1111/php.13197] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/17/2019] [Indexed: 12/17/2023]
Abstract
AbstractThe evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain — bilins and cyclic — chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions—light‐harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D‐ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.
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Affiliation(s)
| | - Olga D. Bekasova
- Bach Institute of Biochemistry Fundamentals of Biotechnology Federal Research Centre Russian Academy of Sciences Moscow Russia
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Sineshchekov VA, Bekasova OD. Two Distinct Photoprocesses in Cyanobacterial Bilin Pigments: Energy Migration in Light-Harvesting Phycobiliproteins versus Photoisomerization in Phytochromes. Photochem Photobiol 2019; 96:750-767. [PMID: 31869438 DOI: 10.1111/php.13197] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2019] [Accepted: 11/17/2019] [Indexed: 01/29/2023]
Abstract
The evolution of oxygenic photosynthesis, respiration and photoperception are connected with the appearance of cyanobacteria. The key compounds, which are involved in these processes, are tetrapyrroles: open chain - bilins and cyclic - chlorophylls and heme. The latter are characterized by their covalent bond with the apoprotein resulting in the formation of biliproteins. This type of photoreceptors is unique in that it can perform important and opposite functions-light-harvesting in photosynthesis with the participation of phycobiliproteins and photoperception mediated by phycochromes and phytochromes. In this review, cyanobacterial phycobiliproteins and phytochrome Cph1 are considered from a comparative point of view. Structural features of these pigments, which provide their contrasting photophysical and photochemical characteristics, are analyzed. The determining factor in the case of energy migration with the participation of phycobiliproteins is blocking the torsional relaxations of the chromophore, its D-ring, in the excited state and their freedom, in the case of phytochrome photoisomerization. From the energetics point of view, this distinction is preconditioned by the height of the activation barrier for the photoreaction and relaxation in the excited state, which depends on the degree of the chromophore fixation by its protein surroundings.
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Affiliation(s)
| | - Olga D Bekasova
- Bach Institute of Biochemistry, Fundamentals of Biotechnology Federal Research Centre, Russian Academy of Sciences, Moscow, Russia
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Kirpich JS, Mix LT, Martin SS, Rockwell NC, Lagarias JC, Larsen DS. Protonation Heterogeneity Modulates the Ultrafast Photocycle Initiation Dynamics of Phytochrome Cph1. J Phys Chem Lett 2018; 9:3454-3462. [PMID: 29874080 PMCID: PMC6247788 DOI: 10.1021/acs.jpclett.8b01133] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/26/2023]
Abstract
Phytochrome proteins utilize ultrafast photoisomerization of a linear tetrapyrrole chromophore to detect the ratio of red to far-red light. Femtosecond photodynamics in the PAS-GAF-PHY photosensory core of the Cph1 phytochrome from Synechocystis sp. PCC6803 (Cph1Δ) were resolved with a dual-excitation-wavelength-interleaved pump-probe (DEWI) approach with two excitation wavelengths (600 and 660 nm) at three pH values (6.5, 8.0, and 9.0). Observed spectral and kinetic heterogeneity in the excited-state dynamics were described with a self-consistent model comprised of three spectrally distinct populations with different protonation states (Pr-I, Pr-II, and Pr-III), each composed of multiple kinetically distinct subpopulations. Apparent partitioning among these populations is dictated by pH, temperature, and excitation wavelength. Our studies provide insight into photocycle initiation dynamics at physiological temperatures, implicate the low-pH/low-temperature Pr-I state as the photoactive state in vitro, and implicate an internal hydrogen-bonding network in regulating the photochemical quantum yield.
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Affiliation(s)
- Julia S. Kirpich
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - L. Tyler Mix
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
| | - Shelley S. Martin
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Nathan C. Rockwell
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology, University of California, Davis, One Shields Ave, Davis, CA, 95616
| | - Delmar S. Larsen
- Department of Chemistry, University of California, Davis, One Shields Ave, Davis, 95616
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Ihalainen JA, Takala H, Lehtivuori H. Fast Photochemistry of Prototypical Phytochromes-A Species vs. Subunit Specific Comparison. Front Mol Biosci 2015; 2:75. [PMID: 26779488 PMCID: PMC4689126 DOI: 10.3389/fmolb.2015.00075] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/08/2015] [Accepted: 12/07/2015] [Indexed: 11/13/2022] Open
Abstract
Phytochromes are multi-domain red light photosensor proteins, which convert red light photons to biological activity utilizing the multitude of structural and chemical reactions. The steady increase in structural information obtained from various bacteriophytochromes has increased understanding about the functional mechanism of the photochemical processes of the phytochromes. Furthermore, a number of spectroscopic studies have revealed kinetic information about the light-induced reactions. The spectroscopic changes are, however, challenging to connect with the structural changes of the chromophore and the protein environment, as the excited state properties of the chromophores are very sensitive to the small structural and chemical changes of their environment. In this article, we concentrate on the results of ultra-fast spectroscopic experiments which reveal information about the important initial steps of the photoreactions of the phytochromes. We survey the excited state properties obtained during the last few decades. The differences in kinetics between different research laboratories are traditionally related to the differences of the studied species. However, we notice that the variation in the excited state properties depends on the subunit composition of the protein as well. This observation illustrates a feedback mechanism from the other domains to the chromophore. We propose that two feedback routes exist in phytochromes between the chromophore and the remotely located effector domain. The well-known connection between the subunits is the so-called tongue region, which changes its secondary structure while changing the light-activated state of the system. The other feedback route which we suggest is less obvious, it is made up of several water molecules ranging from the dimer interface to the vicinity of the chromophore, allowing even proton transfer reactions nearby the chromophore.
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Affiliation(s)
- Janne A Ihalainen
- Department of Biological and Environmental Sciences, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | - Heikki Takala
- Department of Biological and Environmental Sciences, Nanoscience Center, University of JyväskyläJyväskylä, Finland; Department of Anatomy, Institute of Biomedicine, University of HelsinkiHelsinki, Finland
| | - Heli Lehtivuori
- Department of Biological and Environmental Sciences, Nanoscience Center, University of JyväskyläJyväskylä, Finland; Department of Physics, Nanoscience Center, University of JyväskyläJyväskylä, Finland
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Lehtivuori H, Bhattacharya S, Angenent-Mari NM, Satyshur KA, Forest KT. Removal of Chromophore-Proximal Polar Atoms Decreases Water Content and Increases Fluorescence in a Near Infrared Phytofluor. Front Mol Biosci 2015; 2:65. [PMID: 26636092 PMCID: PMC4658570 DOI: 10.3389/fmolb.2015.00065] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2015] [Accepted: 11/02/2015] [Indexed: 11/13/2022] Open
Abstract
Genetically encoded fluorescent markers have revolutionized cell and molecular biology due to their biological compatibility, controllable spatiotemporal expression, and photostability. To achieve in vivo imaging in whole animals, longer excitation wavelength probes are needed due to the superior ability of near infrared light to penetrate tissues unimpeded by absorbance from biomolecules or autofluorescence of water. Derived from near infrared-absorbing bacteriophytochromes, phytofluors are engineered to fluoresce in this region of the electromagnetic spectrum, although high quantum yield remains an elusive goal. An invariant aspartate residue is of utmost importance for photoconversion in native phytochromes, presumably due to the proximity of its backbone carbonyl to the pyrrole ring nitrogens of the biliverdin (BV) chromophore as well as the size and charge of the side chain. We hypothesized that the polar interaction network formed by the charged side chain may contribute to the decay of the excited state via proton transfer. Thus, we chose to further probe the role of this amino acid by removing all possibility for polar interactions with its carboxylate side chain by incorporating leucine instead. The resultant fluorescent protein, WiPhy2, maintains BV binding, monomeric status, and long maximum excitation wavelength while minimizing undesirable protoporphyrin IXα binding in cells. A crystal structure and time-resolved fluorescence spectroscopy reveal that water near the BV chromophore is excluded and thus validate our hypothesis that removal of polar interactions leads to enhanced fluorescence by increasing the lifetime of the excited state. This new phytofluor maintains its fluorescent properties over a broad pH range and does not suffer from photobleaching. WiPhy2 achieves the best compromise to date between high fluorescence quantum yield and long illumination wavelength in this class of fluorescent proteins.
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Affiliation(s)
- Heli Lehtivuori
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA ; Department of Physics, Nanoscience Center, University of Jyväskylä Jyväskylä, Finland
| | | | | | - Kenneth A Satyshur
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
| | - Katrina T Forest
- Department of Bacteriology, University of Wisconsin-Madison Madison, WI, USA
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