1
|
Ruf J, Bindschedler F, Buhrke D. The molecular mechanism of light-induced bond formation and breakage in the cyanobacteriochrome TePixJ. Phys Chem Chem Phys 2023; 25:6016-6024. [PMID: 36752541 PMCID: PMC9945933 DOI: 10.1039/d2cp05856a] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
Cyanobacteriochromes (CBCRs) are small and versatile photoreceptor proteins with high potential for biotechnological applications. Among them, the so-called DXCF-CBCRs exhibit an intricate secondary photochemistry: miliseconds after activation with light, a covalent linkage between a conserved cysteine residue and the light-absorbing tetrapyrrole chromophore is reversibly formed or broken. We employed time-resolved IR spectroscopy over ten orders of magnitude in time in conjunction with 2D-IR spectroscopy to investigate the molecular mechanism of this intriguing reaction in the DXCF-CBCR model system TePixJ from T. elongatus. The crosspeak pattern in the 2D-IR spectrum facilitated the assignment of the dominant signals to vibrational modes of the chromophore, which in turn enabled us to construct a mechanistic model for the photocycle reactions from the time-resolved IR spectra. Here, we assigned the time-resolved signals to several proton transfer steps and distinct geometric changes of the chromophore. We propose a model that describes how these events lead to the rearrangement of charges in the chromophore binding pocket, which serves as the trigger for the light-induced bond formation and breakage with the nearby cysteine.
Collapse
Affiliation(s)
- Jeannette Ruf
- Department of Chemistry, University of Zurich, Zurich, Switzerland.
| | | | - David Buhrke
- Department of Chemistry, University of Zurich, Zurich, Switzerland. .,Institute of Biology, Humboldt University Berlin, Germany
| |
Collapse
|
2
|
Rockwell NC, Moreno MV, Martin SS, Lagarias JC. Protein-chromophore interactions controlling photoisomerization in red/green cyanobacteriochromes. Photochem Photobiol Sci 2022; 21:471-491. [PMID: 35411484 PMCID: PMC9609751 DOI: 10.1007/s43630-022-00213-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2022] [Accepted: 03/21/2022] [Indexed: 10/18/2022]
Abstract
Photoreceptors in the phytochrome superfamily use 15,16-photoisomerization of a linear tetrapyrrole (bilin) chromophore to photoconvert between two states with distinct spectral and biochemical properties. Canonical phytochromes include master regulators of plant growth and development in which light signals trigger interconversion between a red-absorbing 15Z dark-adapted state and a metastable, far-red-absorbing 15E photoproduct state. Distantly related cyanobacteriochromes (CBCRs) carry out a diverse range of photoregulatory functions in cyanobacteria and exhibit considerable spectral diversity. One widespread CBCR subfamily typically exhibits a red-absorbing 15Z dark-adapted state similar to that of phytochrome that gives rise to a distinct green-absorbing 15E photoproduct. This red/green CBCR subfamily also includes red-inactive examples that fail to undergo photoconversion, providing an opportunity to study protein-chromophore interactions that either promote photoisomerization or block it. In this work, we identified a conserved lineage of red-inactive CBCRs. This enabled us to identify three substitutions sufficient to block photoisomerization in photoactive red/green CBCRs. The resulting red-inactive variants faithfully replicated the fluorescence and circular dichroism properties of naturally occurring examples. Converse substitutions restored photoconversion in naturally red-inactive CBCRs. This work thus identifies protein-chromophore interactions that control the fate of the excited-state population in red/green cyanobacteriochromes.
Collapse
Affiliation(s)
- Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| | - Marcus V Moreno
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California at Davis, Davis, CA, 95616, USA.
| |
Collapse
|
3
|
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.
Collapse
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
| |
Collapse
|
4
|
Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci 2021; 20:715-732. [PMID: 34002345 DOI: 10.1007/s43630-021-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Deactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm-1 (CA1) and between 1550 and 1450 cm-1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X-H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.
Collapse
|
5
|
Structural basis of the protochromic green/red photocycle of the chromatic acclimation sensor RcaE. Proc Natl Acad Sci U S A 2021; 118:2024583118. [PMID: 33972439 DOI: 10.1073/pnas.2024583118] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
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 pK a, 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.
Collapse
|
6
|
Unusual ring D fixation by three crucial residues promotes phycoviolobilin formation in the DXCF-type cyanobacteriochrome without the second Cys. Biochem J 2021; 478:1043-1059. [PMID: 33559683 DOI: 10.1042/bcj20210013] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2021] [Revised: 02/08/2021] [Accepted: 02/09/2021] [Indexed: 11/17/2022]
Abstract
Cyanobacteriochromes are linear tetrapyrrole-binding photoreceptors produced by cyanobacteria. Their chromophore-binding GAF domains are categorized into many lineages. Among them, dual Cys-type cyanobacteriochrome GAF domains possessing not only a highly conserved 'first Cys' but also a 'second Cys' are found from multiple lineages. The first Cys stably attaches to C31 of the A-ring, while the second Cys mostly shows reversible ligation to the C10 of the chromophore. Notably, the position of the second Cys in the primary sequence is diversified, and the most abundant dual Cys-type GAF domains have a 'second Cys' within the DXCF motif, which are called DXCF GAF domains. It has been long known that the second Cys in the DXCF GAF domains not only shows the reversible ligation but also is involved in isomerization activity (reduction in C4=C5 double bond) from the initially incorporated phycocyanobilin to phycoviolobilin. However, comprehensive site-directed mutagenesis on the DXCF GAF domains, AM1_6305g1 and AM1_1499g1, revealed that the second Cys is dispensable for isomerization activity, in which three residues participate by fixing the C- and D-rings. Fixation of the chromophore on both sides of the C5 bridge is necessary, even though one side of the fixation site is far from this bridge, with the other side at C31 fixed by the first Cys.
Collapse
|
7
|
Clinger JA, Chen E, Kliger DS, Phillips GN. Pump-Probe Circular Dichroism Spectroscopy of Cyanobacteriochrome TePixJ Yields: Insights into Its Photoconversion. J Phys Chem B 2021; 125:202-210. [PMID: 33355472 DOI: 10.1021/acs.jpcb.0c04822] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
The bilin-containing photoreceptor TePixJ, a member of the cyanobacteriochrome (CBCR) family of phytochromes, switches between blue-light-absorbing and green-light-absorbing states in order to drive phototaxis in Thermosynechococcus elongatus. Its photoswitching process involves the formation of a thioether linkage between the C10 carbon of phycoviolobilin and the sidechain of Cys494 during the change in state from green-absorbing to blue-absorbing forms. Complex changes in the binding pocket propagate the signal to other domains for downstream signaling. Here, we report time-resolved circular dichroism experiments in addition to pump-probe absorption measurements for interpretation of the biophysical mechanism of the green-to-blue photoconversion process of this receptor.
Collapse
Affiliation(s)
- Jonathan A Clinger
- Department of Biosciences, Rice University, Houston, Texas 77005, United States
| | - Eefei Chen
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - David S Kliger
- Department of Chemistry and Biochemistry, University of California, Santa Cruz, California 95064, United States
| | - George N Phillips
- Department of Biosciences, Rice University, Houston, Texas 77005, United States.,Department of Chemistry, Rice University, Houston, Texas 77005, United States
| |
Collapse
|
8
|
Phytochromes and Cyanobacteriochromes: Photoreceptor Molecules Incorporating a Linear Tetrapyrrole Chromophore. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2021; 1293:167-187. [PMID: 33398813 DOI: 10.1007/978-981-15-8763-4_10] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
In this chapter, we summarize the molecular mechanisms of the linear tetrapyrrole-binding photoreceptors, phytochromes, and cyanobacteriochromes. We especially focus on the color-tuning mechanisms and conformational changes during the photoconversion process. Furthermore, we introduce current status of development of the optogenetic tools based on these molecules. Huge repertoire of these photoreceptors with diverse spectral properties would contribute to development of multiplex optogenetic regulation. Among them, the photoreceptors incorporating the biliverdin IXα chromophore is advantageous for in vivo optogenetics because this is intrinsic in the mammalian cells, and absorbs far-red light penetrating into deep mammalian tissues.
Collapse
|
9
|
Abstract
Cyanobacteriochromes (CBCRs) are photoswitchable linear tetrapyrrole (bilin)-based light sensors in the phytochrome superfamily with a broad spectral range from the near UV through the far red (330 to 760 nm). The recent discovery of far-red absorbing CBCRs (frCBCRs) has garnered considerable interest from the optogenetic and imaging communities because of the deep penetrance of far-red light into mammalian tissue and the small size of the CBCR protein scaffold. The present studies were undertaken to determine the structural basis for far-red absorption by JSC1_58120g3, a frCBCR from the thermophilic cyanobacterium Leptolyngbya sp. JSC-1 that is a representative member of a phylogenetically distinct class. Unlike most CBCRs that bind phycocyanobilin (PCB), a phycobilin naturally occurring in cyanobacteria and only a few eukaryotic phototrophs, JSC1_58120g3's far-red absorption arises from incorporation of the PCB biosynthetic intermediate 181,182-dihydrobiliverdin (181,182-DHBV) rather than the more reduced and more abundant PCB. JSC1_58120g3 can also yield a far-red-absorbing adduct with the more widespread linear tetrapyrrole biliverdin IXα (BV), thus circumventing the need to coproduce or supplement optogenetic cell lines with PCB. Using high-resolution X-ray crystal structures of 181,182-DHBV and BV adducts of JSC1_58120g3 along with structure-guided mutagenesis, we have defined residues critical for its verdin-binding preference and far-red absorption. Far-red sensing and verdin incorporation make this frCBCR lineage an attractive template for developing robust optogenetic and imaging reagents for deep tissue applications.
Collapse
|
10
|
Isaksson L, Gustavsson E, Persson C, Brath U, Vrhovac L, Karlsson G, Orekhov V, Westenhoff S. Signaling Mechanism of Phytochromes in Solution. Structure 2020; 29:151-160.e3. [PMID: 32916102 DOI: 10.1016/j.str.2020.08.009] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2020] [Revised: 05/19/2020] [Accepted: 08/21/2020] [Indexed: 12/31/2022]
Abstract
Phytochrome proteins guide the red/far-red photoresponse of plants, fungi, and bacteria. Crystal structures suggest that the mechanism of signal transduction from the chromophore to the output domains involves refolding of the so-called PHY tongue. It is currently not clear how the two other notable structural features of the phytochrome superfamily, the so-called helical spine and a knot in the peptide chain, are involved in photoconversion. Here, we present solution NMR data of the complete photosensory core module from Deinococcus radiodurans. Photoswitching between the resting and the active states induces changes in amide chemical shifts, residual dipolar couplings, and relaxation dynamics. All observables indicate a photoinduced structural change in the knot region and lower part of the helical spine. This implies that a conformational signal is transduced from the chromophore to the helical spine through the PAS and GAF domains. The discovered pathway underpins functional studies of plant phytochromes and may explain photosensing by phytochromes under biological conditions.
Collapse
Affiliation(s)
- Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Göran Karlsson
- Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden; Swedish NMR Center, Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, 41390 Gothenburg, Sweden.
| |
Collapse
|
11
|
Abstract
![]()
Due
to the recent advances in X-ray free electron laser techniques,
bilin-containing cyanobacteriochrome photoreceptors have become prime
targets for the ever-expanding field of time-resolved structural biology.
However, to facilitate these challenging studies, it is essential
that the time scales of any structural changes during the photocycles
of cyanobacteriochromes be established. Here, we have used visible
and infrared transient absorption spectroscopy to probe the photocycle
of a model cyanobacteriochrome system, TePixJ. The kinetics span multiple
orders of magnitude from picoseconds to seconds. Localized changes
in the bilin binding pocket occur in picoseconds to nanoseconds, followed
by more large-scale changes in protein structure, including formation
and breakage of a second thioether linkage, in microseconds to milliseconds.
The characterization of the entire photocycle will provide a vital
frame of reference for future time-resolved structural studies of
this model photoreceptor.
Collapse
Affiliation(s)
- Samantha J O Hardman
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Derren J Heyes
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| | - Igor V Sazanovich
- Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Nigel S Scrutton
- Manchester Institute of Biotechnology and Department of Chemistry, School of Natural Sciences, Faculty of Science and Engineering, The University of Manchester, 131 Princess Street, Manchester M1 7DN, U.K
| |
Collapse
|
12
|
Evolution-inspired design of multicolored photoswitches from a single cyanobacteriochrome scaffold. Proc Natl Acad Sci U S A 2020; 117:15573-15580. [PMID: 32571944 DOI: 10.1073/pnas.2004273117] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/22/2023] Open
Abstract
Cyanobacteriochromes (CBCRs) are small, bistable linear tetrapyrrole (bilin)-binding light sensors which are typically found as modular components in multidomain cyanobacterial signaling proteins. The CBCR family has been categorized into many lineages that roughly correlate with their spectral diversity, but CBCRs possessing a conserved DXCF motif are found in multiple lineages. DXCF CBCRs typically possess two conserved Cys residues: a first Cys that remains ligated to the bilin chromophore and a second Cys found in the DXCF motif. The second Cys often forms a second thioether linkage, providing a mechanism to sense blue and violet light. DXCF CBCRs have been described with blue/green, blue/orange, blue/teal, and green/teal photocycles, and the molecular basis for some of this spectral diversity has been well established. We here characterize AM1_1499g1, an atypical DXCF CBCR that lacks the second cysteine residue and exhibits an orange/green photocycle. Based on prior studies of CBCR spectral tuning, we have successfully engineered seven AM1_1499g1 variants that exhibit robust yellow/teal, green/teal, blue/teal, orange/yellow, yellow/green, green/green, and blue/green photocycles. The remarkable spectral diversity generated by modification of a single CBCR provides a good template for multiplexing synthetic photobiology systems within the same cellular context, thereby bypassing the time-consuming empirical optimization process needed for multiple probes with different protein scaffolds.
Collapse
|
13
|
Song JY, Lee HY, Yang HW, Song JJ, Lagarias JC, Park YI. Spectral and photochemical diversity of tandem cysteine cyanobacterial phytochromes. J Biol Chem 2020; 295:6754-6766. [PMID: 32184354 DOI: 10.1074/jbc.ra120.012950] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2020] [Revised: 03/13/2020] [Indexed: 11/06/2022] Open
Abstract
The atypical trichromatic cyanobacterial phytochrome NpTP1 from Nostoc punctiforme ATCC 29133 is a linear tetrapyrrole (bilin)-binding photoreceptor protein that possesses tandem-cysteine residues responsible for shifting its light-sensing maximum to the violet spectral region. Using bioinformatics and phylogenetic analyses, here we established that tandem-cysteine cyanobacterial phytochromes (TCCPs) compose a well-supported monophyletic phytochrome lineage distinct from prototypical red/far-red cyanobacterial phytochromes. To investigate the light-sensing diversity of this family, we compared the spectroscopic properties of NpTP1 (here renamed NpTCCP) with those of three phylogenetically diverged TCCPs identified in the draft genomes of Tolypothrix sp. PCC7910, Scytonema sp. PCC10023, and Gloeocapsa sp. PCC7513. Recombinant photosensory core modules of ToTCCP, ScTCCP, and GlTCCP exhibited violet-blue-absorbing dark-states consistent with dual thioether-linked phycocyanobilin (PCB) chromophores. Photoexcitation generated singly-linked photoproduct mixtures with variable ratios of yellow-orange and red-absorbing species. The photoproduct ratio was strongly influenced by pH and by mutagenesis of TCCP- and phytochrome-specific signature residues. Our experiments support the conclusion that both photoproduct species possess protonated 15E bilin chromophores, but differ in the ionization state of the noncanonical "second" cysteine sulfhydryl group. We found that the ionization state of this and other residues influences subsequent conformational change and downstream signal transmission. We also show that tandem-cysteine phytochromes present in eukaryotes possess similar amino acid substitutions within their chromophore-binding pocket, which tune their spectral properties in an analogous fashion. Taken together, our findings provide a roadmap for tailoring the wavelength specificity of plant phytochromes to optimize plant performance in diverse natural and artificial light environments.
Collapse
Affiliation(s)
- Ji-Young Song
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ha Yong Lee
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Hee Wook Yang
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| | - Ji-Joon Song
- Department of Biological Science and KI for the BioCentury, Korea Advanced Institute of Science and Technology, Daejeon 34141, Korea
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California Davis, Davis, California 95616
| | - Youn-Il Park
- Department of Biological Sciences, Chungnam National University, Daejeon 34134, Korea
| |
Collapse
|
14
|
Photoreversible interconversion of a phytochrome photosensory module in the crystalline state. Proc Natl Acad Sci U S A 2019; 117:300-307. [PMID: 31852825 PMCID: PMC6955287 DOI: 10.1073/pnas.1912041116] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
A major hurdle in structurally defining the sequence of events that underpin the photointerconversion of phytochromes between their dark-adapted and photoactivated states has been the lack of crystals that undergo these transitions. Here, we describe a crystalline form of the GAF domain from Thermosynechococcus elongatus PixJ within the cyanobacteriochrome subfamily that undergoes reversible photointerconversion and thermal reversion back to the dark-adapted state. Preliminary cryocrystallography of irradiated crystals detected movements of the phycoviolobilin chromophore indicative of a D pyrrole ring rotation. However, X-ray hypersensitivity of both absorbing states might complicate interpretation. Fortunately, we found that PixJ is amenable to serial femtosecond X-ray diffraction methods, which we used to generate a 1.55-Å-resolution model of the dark-adapted state at room temperature. A major barrier to defining the structural intermediates that arise during the reversible photointerconversion of phytochromes between their biologically inactive and active states has been the lack of crystals that faithfully undergo this transition within the crystal lattice. Here, we describe a crystalline form of the cyclic GMP phosphodiesterases/adenylyl cyclase/FhlA (GAF) domain from the cyanobacteriochrome PixJ in Thermosynechococcus elongatus assembled with phycocyanobilin that permits reversible photoconversion between the blue light-absorbing Pb and green light-absorbing Pg states, as well as thermal reversion of Pg back to Pb. The X-ray crystallographic structure of Pb matches previous models, including autocatalytic conversion of phycocyanobilin to phycoviolobilin upon binding and its tandem thioether linkage to the GAF domain. Cryocrystallography at 150 K, which compared diffraction data from a single crystal as Pb or after irradiation with blue light, detected photoconversion product(s) based on Fobs − Fobs difference maps that were consistent with rotation of the bonds connecting pyrrole rings C and D. Further spectroscopic analyses showed that phycoviolobilin is susceptible to X-ray radiation damage, especially as Pg, during single-crystal X-ray diffraction analyses, which could complicate fine mapping of the various intermediate states. Fortunately, we found that PixJ crystals are amenable to serial femtosecond crystallography (SFX) analyses using X-ray free-electron lasers (XFELs). As proof of principle, we solved by room temperature SFX the GAF domain structure of Pb to 1.55-Å resolution, which was strongly congruent with synchrotron-based models. Analysis of these crystals by SFX should now enable structural characterization of the early events that drive phytochrome photoconversion.
Collapse
|
15
|
Gustavsson E, Isaksson L, Persson C, Mayzel M, Brath U, Vrhovac L, Ihalainen JA, Karlsson BG, Orekhov V, Westenhoff S. Modulation of Structural Heterogeneity Controls Phytochrome Photoswitching. Biophys J 2019; 118:415-421. [PMID: 31839260 DOI: 10.1016/j.bpj.2019.11.025] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Revised: 11/15/2019] [Accepted: 11/20/2019] [Indexed: 11/16/2022] Open
Abstract
Phytochromes sense red/far-red light and control many biological processes in plants, fungi, and bacteria. Although the crystal structures of dark- and light-adapted states have been determined, the molecular mechanisms underlying photoactivation remain elusive. Here, we demonstrate that the conserved tongue region of the PHY domain of a 57-kDa photosensory module of Deinococcus radiodurans phytochrome changes from a structurally heterogeneous dark state to an ordered, light-activated state. The results were obtained in solution by utilizing a laser-triggered activation approach detected on the atomic level with high-resolution protein NMR spectroscopy. The data suggest that photosignaling of phytochromes relies on careful modulation of structural heterogeneity of the PHY tongue.
Collapse
Affiliation(s)
- Emil Gustavsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Linnéa Isaksson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Cecilia Persson
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Maxim Mayzel
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Ulrika Brath
- Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Lidija Vrhovac
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyväskylä, Jyväskylä, Finland
| | - B Göran Karlsson
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Vladislav Orekhov
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden; Swedish NMR center, University of Gothenburg, Gothenburg, Sweden
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden.
| |
Collapse
|
16
|
Sato T, Kikukawa T, Miyoshi R, Kajimoto K, Yonekawa C, Fujisawa T, Unno M, Eki T, Hirose Y. Protochromic absorption changes in the two-cysteine photocycle of a blue/orange cyanobacteriochrome. J Biol Chem 2019; 294:18909-18922. [PMID: 31649035 DOI: 10.1074/jbc.ra119.010384] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2019] [Revised: 10/23/2019] [Indexed: 11/06/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are phytochrome-related photosensors with diverse spectral sensitivities spanning the entire visible spectrum. They covalently bind bilin chromophores via conserved cysteine residues and undergo 15Z/15E bilin photoisomerization upon light illumination. CBCR subfamilies absorbing violet-blue light use an additional cysteine residue to form a second bilin-thiol adduct in a two-Cys photocycle. However, the process of second thiol adduct formation is incompletely understood, especially the involvement of the bilin protonation state. Here, we focused on the Oscil6304_2705 protein from the cyanobacterium Oscillatoria acuminata PCC 6304, which photoconverts between a blue-absorbing 15Z state ( 15Z Pb) and orange-absorbing 15E state ( 15E Po). pH titration analysis revealed that 15Z Pb was stable over a wide pH range, suggesting that bilin protonation is stabilized by a second thiol adduct. As revealed by resonance Raman spectroscopy, 15E Po harbored protonated bilin at both acidic and neutral pH, but readily converted to a deprotonated green-absorbing 15Z state ( 15Z Pg) at alkaline pH. Site-directed mutagenesis revealed that the conserved Asp-71 and His-102 residues are required for second thiol adduct formation in 15Z Pb and bilin protonation in 15E Po, respectively. An Oscil6304_2705 variant lacking the second cysteine residue, Cys-73, photoconverted between deprotonated 15Z Pg and protonated 15E Pr, similarly to the protochromic photocycle of the green/red CBCR subfamily. Time-resolved spectroscopy revealed 15Z Pg formation as an intermediate in the 15E Pr-to- 15Z Pg conversion with a significant solvent-isotope effect, suggesting the sequential occurrence of 15EP-to-15Z photoisomerization, deprotonation, and second thiol adduct formation. Our findings uncover the details of protochromic absorption changes underlying the two-Cys photocycle of violet-blue-absorbing CBCR subfamilies.
Collapse
Affiliation(s)
- Teppei Sato
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Takashi Kikukawa
- Global Station for Soft Matter, Global Institution for Collaborative Research and Education, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan; Faculty of Advanced Life Science, Hokkaido University, Kita10 Nishi8, Kita-ku, Sapporo 060-0810, Japan
| | - Risako Miyoshi
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Kousuke Kajimoto
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Chinatsu Yonekawa
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Tomotsumi Fujisawa
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Masashi Unno
- Department of Chemistry and Applied Chemistry, Faculty of Science and Engineering, Saga University, Saga 840-8502, Japan
| | - Toshihiko Eki
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan
| | - Yuu Hirose
- Department of Applied Chemistry and Life Science, Toyohashi University of Technology, 1-1 Hibarigaoka, Tempaku, Toyohashi, Aichi 441-8580, Japan.
| |
Collapse
|
17
|
Fushimi K, Narikawa R. Cyanobacteriochromes: photoreceptors covering the entire UV-to-visible spectrum. Curr Opin Struct Biol 2019; 57:39-46. [DOI: 10.1016/j.sbi.2019.01.018] [Citation(s) in RCA: 47] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 01/08/2019] [Accepted: 01/28/2019] [Indexed: 10/27/2022]
|
18
|
Protein Engineering of Dual-Cys Cyanobacteriochrome AM1_1186g2 for Biliverdin Incorporation and Far-Red/Blue Reversible Photoconversion. Int J Mol Sci 2019; 20:ijms20122935. [PMID: 31208089 PMCID: PMC6628166 DOI: 10.3390/ijms20122935] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2019] [Revised: 06/09/2019] [Accepted: 06/12/2019] [Indexed: 01/14/2023] Open
Abstract
Cyanobacteria have cyanobacteriochromes (CBCRs), which are photoreceptors that bind to a linear tetrapyrrole chromophore and sense UV-to-visible light. A recent study revealed that the dual-Cys CBCR AM1_1186g2 covalently attaches to phycocyanobilin and exhibits unique photoconversion between a Pr form (red-absorbing dark state, λmax = 641 nm) and Pb form (blue-absorbing photoproduct, λmax = 416 nm). This wavelength separation is larger than those of the other CBCRs, which is advantageous for optical tools. Nowadays, bioimaging and optogenetics technologies are powerful tools for biological research. In particular, the utilization of far-red and near-infrared light sources is required for noninvasive applications to mammals because of their high potential to penetrate into deep tissues. Biliverdin (BV) is an intrinsic chromophore and absorbs the longest wavelength among natural linear tetrapyrrole chromophores. Although the BV-binding photoreceptors are promising platforms for developing optical tools, AM1_1186g2 cannot efficiently attach BV. Herein, by rationally introducing several replacements, we developed a BV-binding AM1_1186g2 variant, KCAP_QV, that exhibited reversible photoconversion between a Pfr form (far-red-absorbing dark state, λmax = 691 nm) and Pb form (λmax = 398 nm). This wavelength separation reached 293 nm, which is the largest among the known phytochrome and CBCR photoreceptors. In conclusion, the KCAP_QV molecule developed in this study can offer an alternative platform for the development of unique optical tools.
Collapse
|
19
|
Heyes DJ, Hardman SJO, Pedersen MN, Woodhouse J, De La Mora E, Wulff M, Weik M, Cammarata M, Scrutton NS, Schirò G. Light-induced structural changes in a full-length cyanobacterial phytochrome probed by time-resolved X-ray scattering. Commun Biol 2019; 2:1. [PMID: 30740537 PMCID: PMC6318211 DOI: 10.1038/s42003-018-0242-0] [Citation(s) in RCA: 100] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2018] [Accepted: 11/20/2018] [Indexed: 11/25/2022] Open
Abstract
Phytochromes are photoreceptor proteins that transmit a light signal from a photosensory region to an output domain. Photoconversion involves protein conformational changes whose nature is not fully understood. Here, we use time-resolved X-ray scattering and optical spectroscopy to study the kinetics of structural changes in a full-length cyanobacterial phytochrome and in a truncated form with no output domain. X-ray and spectroscopic signals on the µs/ms timescale are largely independent of the presence of the output domain. On longer time-scales, large differences between the full-length and truncated proteins indicate the timeframe during which the structural transition is transmitted from the photosensory region to the output domain and represent a large quaternary motion. The suggested independence of the photosensory-region dynamics on the µs/ms timescale defines a time window in which the photoreaction can be characterized (e.g. for optogenetic design) independently of the nature of the engineered output domain.
Collapse
Affiliation(s)
- Derren J. Heyes
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Samantha J. O. Hardman
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Martin N. Pedersen
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Joyce Woodhouse
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Eugenio De La Mora
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Michael Wulff
- European Synchrotron Radiation Facility, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Martin Weik
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| | - Marco Cammarata
- Univ. Rennes 1, CNRS, UBL, Institut de Physique de Rennes (IPR) - UMR 6251, 263 avenue du Général Leclerc, 35042 Rennes, France
| | - Nigel S. Scrutton
- Manchester Institute of Biotechnology, University of Manchester, 131 Princess St, Manchester, M1 7DN UK
| | - Giorgio Schirò
- Institut de Biologie Structurale, CNRS, Univ. Grenoble Alpes, CEA, 71 Avenue des Martyrs, 38044 Grenoble, France
| |
Collapse
|
20
|
Fushimi K, Enomoto G, Ikeuchi M, Narikawa R. Distinctive Properties of Dark Reversion Kinetics between Two Red/Green-Type Cyanobacteriochromes and their Application in the Photoregulation of cAMP Synthesis. Photochem Photobiol 2018; 93:681-691. [PMID: 28500699 DOI: 10.1111/php.12732] [Citation(s) in RCA: 32] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2016] [Accepted: 12/07/2016] [Indexed: 12/13/2022]
Abstract
Cyanobacteriochromes (CBCRs) are photoreceptors that bind to a linear tetrapyrrole within a conserved cGMP-phosphodiesterase/adenylate cyclase/FhlA (GAF) domain and exhibit reversible photoconversion. Red/green-type CBCR GAF domains that photoconvert between red- (Pr) and green-absorbing (Pg) forms occur widely in various cyanobacteria. A putative phototaxis regulator, AnPixJ, contains multiple red/green-type CBCR GAF domains. We previously reported that AnPixJ's second domain (AnPixJg2) but not its fourth domain (AnPixJg4) shows red/green reversible photoconversion. Herein, we found that AnPixJg4 showed Pr-to-Pg photoconversion and rapid Pg-to-Pr dark reversion, whereas AnPixJg2 showed a barely detectable dark reversion. Site-directed mutagenesis revealed the involvement of six residues in Pg stability. Replacement at the Leu294/Ile660 positions of AnPixJg2/AnPixJg4 showed the highest influence on dark reversion kinetics. AnPixJg2_DR6, wherein the six residues of AnPixJg2 were entirely replaced with those of AnPixJg4, showed a 300-fold faster dark reversion than that of the wild type. We constructed chimeric proteins by fusing the GAF domains with adenylate cyclase catalytic regions, such as AnPixJg2-AC, AnPixJg4-AC and AnPixJg2_DR6-AC. We detected successful enzymatic activation under red light for both AnPixJg2-AC and AnPixJg2_DR6-AC, and repression under green light for AnPixJg2-AC and under dark incubation for AnPixJg2_DR6-AC. These results provide platforms to develop cAMP synthetic optogenetic tools.
Collapse
Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Tokyo, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University, Shizuoka, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, Kawaguchi, Saitama, Japan
| |
Collapse
|
21
|
Wu XJ, Yang H, Sheng Y, Zhu YL, Li PP. Fluorescence Properties of a Novel Cyanobacteriochrome GAF Domain from Spirulina that Exhibits Moderate Dark Reversion. Int J Mol Sci 2018; 19:ijms19082253. [PMID: 30071622 PMCID: PMC6121604 DOI: 10.3390/ijms19082253] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Revised: 07/11/2018] [Accepted: 07/24/2018] [Indexed: 12/13/2022] Open
Abstract
Cyanobacteriochromes (CBCRs) are biliproteins for photoreception that are present in cyanobacteria. These proteins possess one or more unique cGMP-specific phosphodiesterase/adenylate cyclase/FhlA (GAF) domains that can covalently bind the linear tetrapyrrole (bilin). Light absorption triggers the photoisomerization of bilin between the 15Z and 15E photostates. The 15E photoproduct of some CBCR GAF domains can revert to the stable 15Z state in the absence of light. In some cases, this property makes these domains function as sensors of light intensity or as red/dark optogenetic switches. However, there have been few reports regarding the applicability of these fluorescent properties. Here, we report a red/green cyanobacteriochrome GAF domain from Spirulina subsalsa, designated SPI1085g3, which exhibited photoconversion from the red-absorbing dark state (Pr, λmax = 642 nm) to the orange-absorbing photoproduct state (Po, λmax = 590 nm), and exhibited moderate dark reversion (t1/2 = 3.3 min) from the Po state to the Pr state. The SPI1085g3 Pr state exhibited intense red fluorescence (λmax = 662 nm), with a quantum yield of 0.14. The fluorescence was switched off by red light irradiation and increased in the dark. Replacement of Cys448 of SPI1085g3 with Ser resulted in a slightly improved fluorescence quantum yield and nearly 13-fold faster dark reversion (t1/2 = 15.2 s) than that of the wild type. This novel red/dark-switchable fluorescent biliprotein expands the present repertoire and diversity of photoswitchable fluorescent protein candidates.
Collapse
Affiliation(s)
- Xian-Jun Wu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
| | - Hong Yang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Yi Sheng
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
| | - Yong-Li Zhu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
| | - Ping-Ping Li
- College of Biology and the Environment, Nanjing Forestry University, Nanjing 210037, China.
- Collaborative Innovation Center of Sustainable Forestry in Southern China of Jiangsu Province, Nanjing Forestry University, Nanjing 210037, China.
| |
Collapse
|
22
|
Lenngren N, Edlund P, Takala H, Stucki-Buchli B, Rumfeldt J, Peshev I, Häkkänen H, Westenhoff S, Ihalainen JA. Coordination of the biliverdin D-ring in bacteriophytochromes. Phys Chem Chem Phys 2018; 20:18216-18225. [DOI: 10.1039/c8cp01696h] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Vibrational spectroscopy and crystallography experiments provide a basis for understanding the isomerization reaction in phytochrome proteins.
Collapse
Affiliation(s)
- Nils Lenngren
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology
- Biochemistry and Biophysics
- University of Gothenburg
- SE-40530 Gothenburg
- Sweden
| | - Heikki Takala
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
- University of Helsinki
| | - Brigitte Stucki-Buchli
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Jessica Rumfeldt
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Ivan Peshev
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Heikki Häkkänen
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology
- Biochemistry and Biophysics
- University of Gothenburg
- SE-40530 Gothenburg
- Sweden
| | - Janne A. Ihalainen
- Department of Biological and Environmental Sciences
- Nanoscience Center
- University of Jyväskylä
- Finland
| |
Collapse
|
23
|
Blain-Hartung M, Rockwell NC, Lagarias JC. Light-Regulated Synthesis of Cyclic-di-GMP by a Bidomain Construct of the Cyanobacteriochrome Tlr0924 (SesA) without Stable Dimerization. Biochemistry 2017; 56:6145-6154. [PMID: 29072834 DOI: 10.1021/acs.biochem.7b00734] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022]
Abstract
Phytochromes and cyanobacteriochromes (CBCRs) use double-bond photoisomerization of their linear tetrapyrrole (bilin) chromophores within cGMP-specific phosphodiesterases/adenylyl cyclases/FhlA (GAF) domain-containing photosensory modules to regulate activity of C-terminal output domains. CBCRs exhibit photocycles that are much more diverse than those of phytochromes and are often found in large modular proteins such as Tlr0924 (SesA), one of three blue light regulators of cell aggregation in the cyanobacterium Thermosynechococcus elongatus. Tlr0924 contains a single bilin-binding GAF domain adjacent to a C-terminal diguanylate cyclase (GGDEF) domain whose catalytic activity requires formation of a dimeric transition state presumably supported by a multidomain extension at its N-terminus. To probe the structural basis of light-mediated signal propagation from the photosensory input domain to a signaling output domain for a representative CBCR, these studies explore the properties of a bidomain GAF-GGDEF construct of Tlr0924 (Tlr0924Δ) that retains light-regulated diguanylate cyclase activity. Surprisingly, circular dichroism spectroscopy and size exclusion chromatography data do not support formation of stable dimers in either the blue-absorbing 15ZPb dark state or the green-absorbing 15EPg photoproduct state of Tlr0924Δ. Analysis of variants containing site-specific mutations reveals that proper signal transmission requires both chromophorylation of the GAF domain and individual residues within the amphipathic linker region between GAF and GGDEF domains. On the basis of these data, we propose a model in which bilin binding and light signals are propagated from the GAF domain via the linker to alter the equilibrium and interconversion dynamics between active and inactive conformations of the GGDEF domain to favor or disfavor formation of catalytically competent dimers.
Collapse
Affiliation(s)
- Matthew Blain-Hartung
- Department of Molecular and Cellular Biology, University of California , Davis, California 95616, United States
| | - Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California , Davis, California 95616, United States
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California , Davis, California 95616, United States
| |
Collapse
|
24
|
Burgie ES, Bussell AN, Lye SH, Wang T, Hu W, McLoughlin KE, Weber EL, Li H, Vierstra RD. Photosensing and Thermosensing by Phytochrome B Require Both Proximal and Distal Allosteric Features within the Dimeric Photoreceptor. Sci Rep 2017; 7:13648. [PMID: 29057954 PMCID: PMC5651913 DOI: 10.1038/s41598-017-14037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Phytochromes (Phys) encompass a diverse collection of bilin-containing photoreceptors that help plants and microorganisms perceive light through photointerconversion between red light (Pr) and far-red light (Pfr)-absorbing states. In addition, Pfr reverts thermally back to Pr via a highly enthalpic process that enables temperature sensation in plants and possibly other organisms. Through domain analysis of the Arabidopsis PhyB isoform assembled recombinantly, coupled with measurements of solution size, photoconversion, and thermal reversion, we identified both proximal and distal features that influence all three metrics. Included are the downstream C-terminal histidine kinase-related domain known to promote dimerization and a conserved patch just upstream of an N-terminal Period/Arnt/Sim (PAS) domain, which upon removal dramatically accelerates thermal reversion. We also discovered that the nature of the bilin strongly influences Pfr stability. Whereas incorporation of the native bilin phytochromobilin into PhyB confers robust Pfr → Pr thermal reversion, that assembled with the cyanobacterial version phycocyanobilin, often used for optogenetics, has a dramatically stabilized Pfr state. Taken together, we conclude that Pfr acquisition and stability are impacted by a collection of opposing allosteric features that inhibit or promote photoconversion and reversion of Pfr back to Pr, thus allowing Phys to dynamically measure light, temperature, and possibly time.
Collapse
Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Adam N Bussell
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Shu-Hui Lye
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Tong Wang
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,CUNY Advanced Science Research Center, The City University of New York, New York, New York, 10031, USA
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Erin L Weber
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Huilin Li
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA. .,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
| |
Collapse
|
25
|
Oliinyk OS, Chernov KG, Verkhusha VV. Bacterial Phytochromes, Cyanobacteriochromes and Allophycocyanins as a Source of Near-Infrared Fluorescent Probes. Int J Mol Sci 2017; 18:E1691. [PMID: 28771184 PMCID: PMC5578081 DOI: 10.3390/ijms18081691] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2017] [Revised: 07/28/2017] [Accepted: 07/28/2017] [Indexed: 12/21/2022] Open
Abstract
Bacterial photoreceptors absorb light energy and transform it into intracellular signals that regulate metabolism. Bacterial phytochrome photoreceptors (BphPs), some cyanobacteriochromes (CBCRs) and allophycocyanins (APCs) possess the near-infrared (NIR) absorbance spectra that make them promising molecular templates to design NIR fluorescent proteins (FPs) and biosensors for studies in mammalian cells and whole animals. Here, we review structures, photochemical properties and molecular functions of several families of bacterial photoreceptors. We next analyze molecular evolution approaches to develop NIR FPs and biosensors. We then discuss phenotypes of current BphP-based NIR FPs and compare them with FPs derived from CBCRs and APCs. Lastly, we overview imaging applications of NIR FPs in live cells and in vivo. Our review provides guidelines for selection of existing NIR FPs, as well as engineering approaches to develop NIR FPs from the novel natural templates such as CBCRs.
Collapse
Affiliation(s)
- Olena S Oliinyk
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
| | - Konstantin G Chernov
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
| | - Vladislav V Verkhusha
- Department of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, 00290 Helsinki, Finland.
- Department of Anatomy and Structural Biology, and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| |
Collapse
|
26
|
Rockwell NC, Martin SS, Lagarias JC. There and Back Again: Loss and Reacquisition of Two‐Cys Photocycles in Cyanobacteriochromes. Photochem Photobiol 2017; 93:741-754. [DOI: 10.1111/php.12708] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/04/2016] [Accepted: 11/01/2016] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology University of California Davis CA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology University of California Davis CA
| | - John Clark Lagarias
- Department of Molecular and Cellular Biology University of California Davis CA
| |
Collapse
|
27
|
Chernov KG, Redchuk TA, Omelina ES, Verkhusha VV. Near-Infrared Fluorescent Proteins, Biosensors, and Optogenetic Tools Engineered from Phytochromes. Chem Rev 2017; 117:6423-6446. [DOI: 10.1021/acs.chemrev.6b00700] [Citation(s) in RCA: 178] [Impact Index Per Article: 25.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Affiliation(s)
- Konstantin G. Chernov
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Taras A. Redchuk
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Evgeniya S. Omelina
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
| | - Vladislav V. Verkhusha
- Department
of Biochemistry and Developmental Biology, Faculty of Medicine, University of Helsinki, Helsinki 00290, Finland
- Department
of Anatomy and Structural Biology and Gruss-Lipper Biophotonics Center, Albert Einstein College of Medicine, Bronx, New York 10461, United States
| |
Collapse
|
28
|
Gourinchas G, Etzl S, Göbl C, Vide U, Madl T, Winkler A. Long-range allosteric signaling in red light-regulated diguanylyl cyclases. SCIENCE ADVANCES 2017; 3:e1602498. [PMID: 28275738 PMCID: PMC5336353 DOI: 10.1126/sciadv.1602498] [Citation(s) in RCA: 77] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 01/10/2017] [Indexed: 05/06/2023]
Abstract
Nature has evolved an astonishingly modular architecture of covalently linked protein domains with diverse functionalities to enable complex cellular networks that are critical for cell survival. The coupling of sensory modules with enzymatic effectors allows direct allosteric regulation of cellular signaling molecules in response to diverse stimuli. We present molecular details of red light-sensing bacteriophytochromes linked to cyclic dimeric guanosine monophosphate-producing diguanylyl cyclases. Elucidation of the first crystal structure of a full-length phytochrome with its enzymatic effector, in combination with the characterization of light-induced changes in conformational dynamics, reveals how allosteric light regulation is fine-tuned by the architecture and composition of the coiled-coil sensor-effector linker and also the central helical spine. We anticipate that consideration of molecular principles of sensor-effector coupling, going beyond the length of the characteristic linker, and the appreciation of dynamically driven allostery will open up new directions for the design of novel red light-regulated optogenetic tools.
Collapse
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
| | - Christoph Göbl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
| | - Uršula Vide
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
| | - Tobias Madl
- Center for Integrated Protein Science Munich, Technische Universität München, Department of Chemistry, Lichtenbergstraße 4, 85748 Garching, Germany
- Institute of Structural Biology, Helmholtz Zentrum München, Ingolstädter Landstraße 1, 85764 Neuherberg, Germany
- Institute of Molecular Biology and Biochemistry, Medical University of Graz, Harrachgasse 21/III, 8010 Graz, Austria
| | - Andreas Winkler
- Institute of Biochemistry, Graz University of Technology, Petersgasse 12/II, 8010 Graz, Austria
- Corresponding author.
| |
Collapse
|
29
|
Fushimi K, Rockwell NC, Enomoto G, Ni-Ni-Win, Martin SS, Gan F, Bryant DA, Ikeuchi M, Lagarias JC, Narikawa R. Cyanobacteriochrome Photoreceptors Lacking the Canonical Cys Residue. Biochemistry 2016; 55:6981-6995. [PMID: 27935696 DOI: 10.1021/acs.biochem.6b00940] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors that sense near-ultraviolet to far-red light. Like the distantly related phytochromes, all CBCRs reported to date have a conserved Cys residue (the "canonical Cys" or "first Cys") that forms a thioether linkage to C31 of the linear tetrapyrrole (bilin) chromophore. Detection of ultraviolet, violet, and blue light is performed by at least three subfamilies of two-Cys CBCRs that require both the first Cys and a second Cys that forms a second covalent linkage to C10 of the bilin. In the well-characterized DXCF subfamily, the second Cys is part of a conserved Asp-Xaa-Cys-Phe motif. We here report novel CBCRs lacking the first Cys but retaining the DXCF Cys as part of a conserved Asp-Xaa-Cys-Ile-Pro (DXCIP) motif. Phylogenetic analysis demonstrates that DXCIP CBCRs are a sister to a lineage of DXCF CBCR domains from phototaxis sensors. Three such DXCIP CBCR domains (cce_4193g1, Cyan8802_2776g1, and JSC1_24240) were characterized after recombinant expression in Escherichia coli engineered to produce phycocyanobilin. All three covalently bound bilin and showed unidirectional photoconversion in response to green light. Spectra of acid-denatured proteins in the dark-adapted state do not correspond to those of known bilins. One DXCIP CBCR, cce_4193g1, exhibited very rapid dark reversion consistent with a function as a power sensor. However, Cyan8802_2776g1 exhibited slower dark reversion and would not have such a function. The full-length cce_4193 protein also possesses a DXCF CBCR GAF domain (cce_4193g2) with a covalently bound phycoviolobilin chromophore and a blue/green photocycle. Our studies indicate that CBCRs need not contain the canonical Cys residue to function as photochromic light sensors and that phototaxis proteins containing DXCIP CBCRs may potentially perceive both light quality and light intensity.
Collapse
Affiliation(s)
- Keiji Fushimi
- Department of Biological Science, Faculty of Science, Shizuoka University , Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| | - Nathan C Rockwell
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Gen Enomoto
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan
| | - Ni-Ni-Win
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan
| | - Shelley S Martin
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Fei Gan
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802 United States
| | - Donald A Bryant
- Department of Biochemistry and Molecular Biology, The Pennsylvania State University , University Park, Pennsylvania 16802 United States.,Department of Chemistry and Biochemistry, Montana State University , Bozeman, Montana 59717 United States
| | - Masahiko Ikeuchi
- Department of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo , Komaba, Meguro, Tokyo 153-8902, Japan.,Core Research for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012 Japan
| | - J Clark Lagarias
- Department of Molecular and Cellular Biology, University of California , Davis California 95616, United States
| | - Rei Narikawa
- Department of Biological Science, Faculty of Science, Shizuoka University , Ohya, Suruga-ku, Shizuoka 422-8529, Japan
| |
Collapse
|
30
|
Mapping light-driven conformational changes within the photosensory module of plant phytochrome B. Sci Rep 2016; 6:34366. [PMID: 27694986 PMCID: PMC5046071 DOI: 10.1038/srep34366] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2016] [Accepted: 09/09/2016] [Indexed: 12/04/2022] Open
Abstract
Organisms developed different photoreceptors to be able to adapt to changing environmental light conditions. Phytochromes are red/far-red (r/fr) photochromic photoreceptors that belong to the classical photoreceptors along with cryptochromes and phototropins. They convert absorbed light into a biological signal by switching between two states in a light-dependent manner therefore enabling the light control downstream signalling. Their Pfr conformation is the biological active form in plants, but until now only a structure of the ground state (Pr) was solved. Here, the authors provide information about structural changes occurring during photoconversion within phytochrome B and identify possible interaction sites for its N-terminal extension (NTE) utilising hydrogen/deuterium exchange rate analyses of its amide backbone. Especially, the newly identified light-dependency of two regions in the NTE are of particular interest for understanding the involvement of the phytochrome’s NTE in the regulation of its downstream signalling.
Collapse
|
31
|
Rockwell NC, Martin SS, Lagarias JC. Identification of Cyanobacteriochromes Detecting Far-Red Light. Biochemistry 2016; 55:3907-19. [DOI: 10.1021/acs.biochem.6b00299] [Citation(s) in RCA: 63] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| |
Collapse
|
32
|
Burgie E, Zhang J, Vierstra R. Crystal Structure of Deinococcus Phytochrome in the Photoactivated State Reveals a Cascade of Structural Rearrangements during Photoconversion. Structure 2016; 24:448-57. [DOI: 10.1016/j.str.2016.01.001] [Citation(s) in RCA: 107] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/04/2015] [Accepted: 01/02/2016] [Indexed: 11/30/2022]
|
33
|
Song C, Velazquez Escobar F, Xu XL, Narikawa R, Ikeuchi M, Siebert F, Gärtner W, Matysik J, Hildebrandt P. A Red/Green Cyanobacteriochrome Sustains Its Color Despite a Change in the Bilin Chromophore’s Protonation State. Biochemistry 2015; 54:5839-48. [DOI: 10.1021/acs.biochem.5b00735] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chen Song
- Leids
Instituut voor Chemisch Onderzoek, Universiteit Leiden, 2300 RA Leiden, The Netherlands
- Institut
für Analytische Chemie, Universität Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Francisco Velazquez Escobar
- Technische Universität Berlin, Institut für
Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Xiu-Ling Xu
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Rei Narikawa
- Department
of Life Sciences (Biology), Graduate School of Art and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department
of Biological Science, Faculty of Science, Shizuoka University, Shizuoka 422-8529, Japan
- Precursory Research for Embryonic Science and Technology (PRESTO), Meguro, Tokyo 153-8902, Japan
| | - Masahiko Ikeuchi
- Department
of Life Sciences (Biology), Graduate School of Art and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Japan
Science and Technology Agency (JST), Core Research for Evolutionary Science and Technology (CREST), Meguro, Tokyo 153-8902, Japan
| | - Friedrich Siebert
- Technische Universität Berlin, Institut für
Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Jörg Matysik
- Institut
für Analytische Chemie, Universität Leipzig, Linnéstraße
3, D-04103 Leipzig, Germany
| | - Peter Hildebrandt
- Technische Universität Berlin, Institut für
Chemie, Sekr. PC14, Straße
des 17. Juni 135, D-10623 Berlin, Germany
| |
Collapse
|
34
|
Anders K, Essen LO. The family of phytochrome-like photoreceptors: diverse, complex and multi-colored, but very useful. Curr Opin Struct Biol 2015; 35:7-16. [PMID: 26241319 DOI: 10.1016/j.sbi.2015.07.005] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2015] [Revised: 07/15/2015] [Accepted: 07/15/2015] [Indexed: 11/17/2022]
Abstract
Bilin-dependent GAF domain photoreceptors cover the whole spectrum of light with their absorbance properties. They can be divided into three groups according to the domain architecture of their photosensory module. Group I and Group II harbor phytochromes with PAS-GAF-PHY and GAF-PHY domain architecture, respectively. Group III consists of stand-alone GAF domain photoreceptors, the cyanobacteriochromes. Crystal structures of all three groups are now available to shed light on possible downstream signaling pathways. Structures of Group I and III photoreceptors in both states display changes in the secondary structures during photoconversion. The knowledge about the photoconversion in phytochromes and CBCRs make them promising targets for applications in life science and synthetic biology.
Collapse
Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps-University, Hans-Meerwein-Str. 4, D-35032 Marburg, Germany.
| |
Collapse
|
35
|
Song C, Narikawa R, Ikeuchi M, Gärtner W, Matysik J. Color Tuning in Red/Green Cyanobacteriochrome AnPixJ: Photoisomerization at C15 Causes an Excited-State Destabilization. J Phys Chem B 2015; 119:9688-95. [DOI: 10.1021/acs.jpcb.5b04655] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Chen Song
- Leids
Instituut voor Chemisch Onderzoek, Universiteit Leiden, P.O. Box 9502, 2300
RA Leiden, The Netherlands
- Institut
für Analytische Chemie, Universität Leipzig, Johannisallee
29, D-04103 Leipzig, Germany
| | - Rei Narikawa
- Department
of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku,
Shizuoka 422-8529, Japan
- Graduate
School of Art and Sciences, University of Tokyo, Komaba, Meguro, Tokyo 153-8902, Japan
- Precursory
Research for Embryonic Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Masahiko Ikeuchi
- Department
of Biological Science, Faculty of Science, Shizuoka University, Ohya, Suruga-ku,
Shizuoka 422-8529, Japan
- Core Research
for Evolutional Science and Technology, Japan Science and Technology Agency, 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Wolfgang Gärtner
- Max-Planck-Institut für Chemische Energiekonversion, Stiftstraße 34−36, D-45470 Mülheim an der Ruhr, Germany
| | - Jörg Matysik
- Leids
Instituut voor Chemisch Onderzoek, Universiteit Leiden, P.O. Box 9502, 2300
RA Leiden, The Netherlands
- Institut
für Analytische Chemie, Universität Leipzig, Johannisallee
29, D-04103 Leipzig, Germany
| |
Collapse
|
36
|
Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Hydrophobic Pocket for the C15-E,anti Chromophore in the Photoproduct. Biochemistry 2015; 54:3772-83. [DOI: 10.1021/acs.biochem.5b00438] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/01/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| |
Collapse
|
37
|
Rockwell NC, Martin SS, Lim S, Lagarias JC, Ames JB. Characterization of Red/Green Cyanobacteriochrome NpR6012g4 by Solution Nuclear Magnetic Resonance Spectroscopy: A Protonated Bilin Ring System in Both Photostates. Biochemistry 2015; 54:2581-600. [DOI: 10.1021/bi501548t] [Citation(s) in RCA: 32] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - Sunghyuk Lim
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| | - James B. Ames
- Department of Molecular
and Cellular Biology and ‡Department of Chemistry, University of California, Davis, California 95616, United States
| |
Collapse
|
38
|
Li F, Burgie ES, Yu T, Héroux A, Schatz GC, Vierstra RD, Orville AM. X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. J Am Chem Soc 2015; 137:2792-5. [PMID: 25650486 DOI: 10.1021/ja510923m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report that in the red light-absorbing (Pr) state, the bilin chromophore of the Deinococcus radiodurans proteobacterial phytochrome (DrBphP) is hypersensitive to X-ray photons used in typical synchrotron X-ray protein crystallography experiments. This causes the otherwise fully protonated chromophore to deprotonate without additional major structural changes. These results have major implications for our understanding of the structural and chemical characteristics of the resting and intermediate states of phytochromes and other photoreceptor proteins.
Collapse
Affiliation(s)
- Feifei Li
- Photon Sciences Directorate and ∥Biosciences Department, Brookhaven National Laboratory , Upton, New York 11973, United States
| | | | | | | | | | | | | |
Collapse
|
39
|
Rockwell NC, Martin SS, Gan F, Bryant DA, Lagarias JC. NpR3784 is the prototype for a distinctive group of red/green cyanobacteriochromes using alternative Phe residues for photoproduct tuning. Photochem Photobiol Sci 2015; 14:258-69. [DOI: 10.1039/c4pp00336e] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
We report chromophore–protein interactions used by cyanobacteriochrome NpR3784 and related proteins for spectral tuning of the green-absorbing photoproduct state. These interactions are distinct from those used by canonical red/green cyanobacteriochromes.
Collapse
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
| | - Shelley S. Martin
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
| | - Fei Gan
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- University Park
- USA
| | - Donald A. Bryant
- Department of Biochemistry and Molecular Biology
- The Pennsylvania State University
- University Park
- USA
- Department of Chemistry and Biochemistry
| | - J. Clark Lagarias
- Department of Molecular and Cell Biology
- University of California at Davis
- Davis
- USA
| |
Collapse
|
40
|
Rockwell NC, Martin SS, Lagarias JC. Identification of DXCF cyanobacteriochrome lineages with predictable photocycles. Photochem Photobiol Sci 2015; 14:929-41. [DOI: 10.1039/c4pp00486h] [Citation(s) in RCA: 47] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
Abstract
Two specialized subgroups of cyanobacteriochromes with predictable green/blue and blue/orange photocycles are defined by these studies.
Collapse
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - Shelley S. Martin
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| | - J. Clark Lagarias
- Department of Molecular and Cellular Biology
- University of California at Davis
- Davis
- USA
| |
Collapse
|
41
|
Pennacchietti F, Losi A, Xu XL, Zhao KH, Gärtner W, Viappiani C, Cella F, Diaspro A, Abbruzzetti S. Photochromic conversion in a red/green cyanobacteriochrome from Synechocystis PCC6803: quantum yields in solution and photoswitching dynamics in living E. coli cells. Photochem Photobiol Sci 2015; 14:229-37. [DOI: 10.1039/c4pp00337c] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photochromic conversion in GAF3 has been followed in solution and in E. coli cells.
Collapse
Affiliation(s)
| | - Aba Losi
- Dipartimento di Fisica e Scienze della Terra “Macedonio Melloni”
- Università di Parma
- Parma
- Italy
| | - Xiu-ling Xu
- Max-Planck-Institute for Chemical Energy Conversion
- D-45470 Mülheim
- Germany
| | - Kai-hong Zhao
- State Key Laboratory of Agricultural Microbiology
- Huazhong Agricultural University
- Wuhan 430070
- PR China
| | - Wolfgang Gärtner
- Max-Planck-Institute for Chemical Energy Conversion
- D-45470 Mülheim
- Germany
| | - Cristiano Viappiani
- Dipartimento di Fisica e Scienze della Terra “Macedonio Melloni”
- Università di Parma
- Parma
- Italy
- NEST
| | | | - Alberto Diaspro
- Fondazione Istituto Italiano di Tecnologia
- 16163 Genova
- Italy
- Nikon Imaging Center
- Fondazione Istituto Italiano di Tecnologia
| | | |
Collapse
|
42
|
Burgie ES, Vierstra RD. Phytochromes: an atomic perspective on photoactivation and signaling. THE PLANT CELL 2014; 26:4568-83. [PMID: 25480369 PMCID: PMC4311201 DOI: 10.1105/tpc.114.131623] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/10/2014] [Accepted: 11/14/2014] [Indexed: 05/19/2023]
Abstract
The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents.
Collapse
Affiliation(s)
- E Sethe Burgie
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| |
Collapse
|
43
|
Lim S, Rockwell NC, Martin SS, Dallas JL, Lagarias JC, Ames JB. Photoconversion changes bilin chromophore conjugation and protein secondary structure in the violet/orange cyanobacteriochrome NpF2164g3' [corrected]. Photochem Photobiol Sci 2014; 13:951-62. [PMID: 24745038 DOI: 10.1039/c3pp50442e] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Cyanobacteriochromes (CBCRs) are cyanobacterial photoreceptors distantly related to phytochromes. All CBCRs examined to date utilize a conserved Cys residue to form a covalent thioether linkage to the bilin chromophore. In the insert-Cys CBCR subfamily, a second conserved Cys can covalently link to the bilin C10 methine bridge, allowing detection of near-UV to blue light. The best understood insert-Cys CBCR is the violet/orange CBCR NpF2164g3 from Nostoc punctiforme, which has a stable second linkage in the violet-absorbing dark state. Photoconversion of NpF2164g3 leads to elimination of the second linkage and formation of an orange-absorbing photoproduct. We recently reported NMR chemical shift assignments for the orange-absorbing photoproduct state of NpF2164g3. We here present equivalent information for its violet-absorbing dark state. In both photostates, NpF2164g3 is monomeric in solution and regions containing the two conserved Cys residues essential for photoconversion are structurally disordered. In contrast to blue light receptors such as phototropin, NpF2164g3 is less structurally ordered in the dark state than in the photoproduct. The insert-Cys insertion loop and C-terminal helix exhibit light-dependent structural changes. Moreover, a motif containing an Asp residue also found in other CBCRs and in phytochromes adopts a random-coil structure in the dark state but a stable α-helix structure in the photoproduct. NMR analysis of the chromophore is consistent with a less ordered dark state, with A-ring resonances only resolved in the photoproduct. The C10 atom of the bilin chromophore exhibits a drastic change in chemical shift upon photoconversion, changing from 34.5 ppm (methylene) in the dark state to 115 ppm (methine) in the light-activated state. Our results provide structural insight into the two-Cys photocycle of NpF2164g3 and the structurally diverse mechanisms used for light perception by the larger phytochrome superfamily.
Collapse
Affiliation(s)
- Sunghyuk Lim
- Department of Chemistry, University of California, Davis, CA 95616, USA.
| | | | | | | | | | | |
Collapse
|
44
|
Oszkiel H, Wilczak J, Jank M. Biologically active substances-enriched diet regulates gonadotrope cell activation pathway in liver of adult and old rats. GENES AND NUTRITION 2014; 9:427. [PMID: 25156242 PMCID: PMC4172640 DOI: 10.1007/s12263-014-0427-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2014] [Accepted: 08/11/2014] [Indexed: 01/23/2023]
Abstract
According to the Hippocrates’ theorem “Let food be your medicine and medicine be your food”, dietary interventions may induce changes in the metabolic and inflammatory state by modulating the expression of important genes involved in the chronic disorders. The aim of the present study was to evaluate the influence of long-term (14 months) use of biologically active substances-enriched diet (BASE-diet) on transcriptomic profile of rats’ liver. The experiment was conducted on 36 Sprague–Dawley rats divided into two experimental groups (fed with control or BASE-diet, both n = 18). Control diet was a semi-synthetic diet formulated according to the nutritional requirements for laboratory animals. The BASE-diet was enriched with a mixture of polyphenolic compounds, β-carotene, probiotics, and n-3 and n-6 polyunsaturated fatty acids. In total, n = 3,017 differentially expressed (DE) genes were identified, including n = 218 DE genes between control and BASE groups after 3 months of feeding and n = 1,262 after 14 months. BASE-diet influenced the expression of genes involved particularly in the gonadotrope cell activation pathway and guanylate cyclase pathway, as well as in mast cell activation, gap junction regulation, melanogenesis and apoptosis. Especially genes involved in regulation of GnRH were strongly affected by BASE-diet. This effect was stronger with the age of animals and the length of diet use. It may suggest a link between the diet, reproductive system function and aging.
Collapse
Affiliation(s)
- Hanna Oszkiel
- Department of Physiological Sciences, Faculty of Veterinary Medicine, Warsaw University of Life Sciences, Nowoursynowska 159 Str., 02-776, Warsaw, Poland
| | | | | |
Collapse
|
45
|
Narikawa R, Enomoto G, Ni-Ni-Win, Fushimi K, Ikeuchi M. A New Type of Dual-Cys Cyanobacteriochrome GAF Domain Found in Cyanobacterium Acaryochloris marina, Which Has an Unusual Red/Blue Reversible Photoconversion Cycle. Biochemistry 2014; 53:5051-9. [DOI: 10.1021/bi500376b] [Citation(s) in RCA: 56] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Affiliation(s)
- Rei Narikawa
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- Department
of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku,
Shizuoka 422-8529, Japan
- PRESTO, Japan Science and Technology Agency (JST), 4-1-8 Honcho Kawaguchi, Saitama 332-0012, Japan
| | - Gen Enomoto
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Ni-Ni-Win
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
| | - Keiji Fushimi
- Department
of Biological Science, Faculty of Science, Shizuoka University, Suruga-ku,
Shizuoka 422-8529, Japan
| | - Masahiko Ikeuchi
- Department
of Life Sciences (Biology), Graduate School of Arts and Sciences, University of Tokyo, Komaba 3-8-1, Meguro, Tokyo 153-8902, Japan
- CREST, Japan Science and Technology Agency (JST), 4-1-8 Honcho
Kawaguchi, Saitama 332-0012, Japan
| |
Collapse
|
46
|
Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD. Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion. J Biol Chem 2014; 289:24573-87. [PMID: 25006244 DOI: 10.1074/jbc.m114.571661] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are multidomain photoswitches that drive light perception in plants and microorganisms by coupling photoreversible isomerization of their bilin chromophore to various signaling cascades. How changes in bilin conformation affect output by these photoreceptors remains poorly resolved and might include several species-specific routes. Here, we present detailed three-dimensional models of the photosensing module and a picture of an entire dimeric photoreceptor through structural analysis of the Deinococcus radiodurans phytochrome BphP assembled with biliverdin (BV). A 1.16-Å resolution crystal structure of the bilin-binding pocket in the dark-adapted red light-absorbing state illuminated the intricate network of bilin/protein/water interactions and confirmed the protonation and ZZZssa conformation of BV. Structural and spectroscopic comparisons with the photochemically compromised D207A mutant revealed that substitutions of Asp-207 allow inclusion of cyclic porphyrins in addition to BV. A crystal structure of the entire photosensing module showed a head-to-head, twisted dimeric arrangement with bowed helical spines and a hairpin protrusion connecting the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) and phytochrome-specific (PHY) domains. A key conserved hairpin feature is its anti-parallel, two β-strand stem, which we show by mutagenesis to be critical for BphP photochemistry. Comparisons of single particle electron microscopic images of the full-length BphP dimer in the red light-absorbing state and the photoactivated far-red light-absorbing state revealed a large scale reorientation of the PHY domain relative to the GAF domain, which alters the position of the downstream histidine kinase output module. Together, our data support a toggle model whereby bilin photoisomerization alters GAF/PHY domain interactions through conformational modification of the hairpin, which regulates signaling by impacting the relationship between sister output modules.
Collapse
Affiliation(s)
- E Sethe Burgie
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Tong Wang
- the Biology Department, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Adam N Bussell
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Joseph M Walker
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Huilin Li
- the Biology Department, Brookhaven National Laboratory, Upton, New York 11973, and the Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794
| | - Richard D Vierstra
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706,
| |
Collapse
|
47
|
Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome. Proc Natl Acad Sci U S A 2014; 111:10179-84. [PMID: 24982198 DOI: 10.1073/pnas.1403096111] [Citation(s) in RCA: 166] [Impact Index Per Article: 16.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
Many aspects of plant photomorphogenesis are controlled by the phytochrome (Phy) family of bilin-containing photoreceptors that detect red and far-red light by photointerconversion between a dark-adapted Pr state and a photoactivated Pfr state. Whereas 3D models of prokaryotic Phys are available, models of their plant counterparts have remained elusive. Here, we present the crystal structure of the photosensing module (PSM) from a seed plant Phy in the Pr state using the PhyB isoform from Arabidopsis thaliana. The PhyB PSM crystallized as a head-to-head dimer with strong structural homology to its bacterial relatives, including a 5(Z)syn, 10(Z)syn, 15(Z)anti configuration of the phytochromobilin chromophore buried within the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain, and a well-ordered hairpin protruding from the Phy-specific domain toward the bilin pocket. However, its Per/Arnt/Sim (PAS) domain, knot region, and helical spine show distinct structural differences potentially important to signaling. Included is an elongated helical spine, an extended β-sheet connecting the GAF domain and hairpin stem, and unique interactions between the region upstream of the PAS domain knot and the bilin A and B pyrrole rings. Comparisons of this structure with those from bacterial Phys combined with mutagenic studies support a toggle model for photoconversion that engages multiple features within the PSM to stabilize the Pr and Pfr end states after rotation of the D pyrrole ring. Taken together, this Arabidopsis PhyB structure should enable molecular insights into plant Phy signaling and provide an essential scaffold to redesign their activities for agricultural benefit and as optogenetic reagents.
Collapse
|
48
|
Hauck AFE, Hardman SJO, Kutta RJ, Greetham GM, Heyes DJ, Scrutton NS. The photoinitiated reaction pathway of full-length cyanobacteriochrome Tlr0924 monitored over 12 orders of magnitude. J Biol Chem 2014; 289:17747-57. [PMID: 24817121 PMCID: PMC4067208 DOI: 10.1074/jbc.m114.566133] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/05/2023] Open
Abstract
The coupling of photochemistry to protein chemical and structural change is crucial to biological light-activated signaling mechanisms. This is typified by cyanobacteriochromes (CBCRs), members of the phytochrome superfamily of photoreceptors that exhibit a high degree of spectral diversity, collectively spanning the entire visible spectrum. CBCRs utilize a basic E/Z isomerization of the bilin chromophore as the primary step in their photocycle, which consists of reversible photoconversion between two photostates. Despite intense interest in these photoreceptors as signal transduction modules a complete description of light-activated chemical and structural changes has not been reported. The CBCR Tlr0924 contains both phycocyanobilin and phycoviolobilin chromophores, and these two species photoisomerize in parallel via spectrally and kinetically equivalent intermediates before the second step of the photoreaction where the reaction pathways diverge, the loss of a thioether linkage to a conserved cysteine residue occurs, and the phycocyanobilin reaction terminates in a red-absorbing state, whereas the phycoviolobilin reaction proceeds more rapidly to a final green-absorbing state. Here time-resolved visible transient absorption spectroscopy (femtosecond to second) has been used, in conjunction with time-resolved IR spectroscopy (femtosecond to nanosecond) and cryotrapping techniques, to follow the entire photoconversion of the blue-absorbing states to the green- and red-absorbing states of the full-length form of Tlr0924 CBCR. Our analysis shows that Tlr0924 undergoes an unprecedented long photoreaction that spans from picoseconds to seconds. We show that the thermally driven, long timescale changes are less complex than those reported for the red/far-red photocycles of the related phytochrome photoreceptors.
Collapse
Affiliation(s)
- Anna F E Hauck
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Samantha J O Hardman
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Roger J Kutta
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Gregory M Greetham
- the Central Laser Facility, Research Complex at Harwell, Science and Technology Facilities Council, Harwell Oxford, Didcot OX11 0QX, United Kingdom
| | - Derren J Heyes
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| | - Nigel S Scrutton
- From the Manchester Institute of Biotechnology and Photon Science Institute, Faculty of Life Sciences, The University of Manchester, Manchester M13 9PL, United Kingdom and
| |
Collapse
|
49
|
Rockwell NC, Martin SS, Gulevich AG, Lagarias JC. Conserved Phenylalanine Residues Are Required for Blue-Shifting of Cyanobacteriochrome Photoproducts. Biochemistry 2014; 53:3118-30. [DOI: 10.1021/bi500037a] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Nathan C. Rockwell
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Shelley S. Martin
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - Alexander G. Gulevich
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| | - J. Clark Lagarias
- Department of Molecular and
Cellular Biology, University of California, Davis, California 95616, United States
| |
Collapse
|