1
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Zangl R, Soravia S, Saft M, Löffler JG, Schulte J, Rosner CJ, Bredenbeck J, Essen LO, Morgner N. Time-Resolved Ion Mobility Mass Spectrometry to Solve Conformational Changes in a Cryptochrome. J Am Chem Soc 2024; 146:14468-14478. [PMID: 38757172 DOI: 10.1021/jacs.3c13818] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/18/2024]
Abstract
Many biological mechanisms rely on the precise control of conformational changes in proteins. Understanding such dynamic processes requires methods for determining structures and their temporal evolution. In this study, we introduce a novel approach to time-resolved ion mobility mass spectrometry. We validated the method on a simple photoreceptor model and applied it to a more complex system, the animal-like cryptochrome from Chlamydomonas reinhardtii (CraCRY), to determine the role of specific amino acids affecting the conformational dynamics as reaction to blue light activation. In our setup, using a high-power LED mounted in the source region of an ion mobility mass spectrometer, we allow a time-resolved evaluation of mass and ion mobility spectra. Cryptochromes like CraCRY are a widespread type of blue light photoreceptors and mediate various light-triggered biological functions upon excitation of their inbuilt flavin chromophore. Another hallmark of cryptochromes is their flexible carboxy-terminal extension (CTE), whose structure and function as well as the details of its interaction with the photolyase homology region are not yet fully understood and differ among different cryptochromes types. Here, we addressed the highly conserved C-terminal domain of CraCRY, to study the effects of single mutations on the structural transition of the C-terminal helix α22 and the attached CTE upon lit-state formation. We show that D321, the putative proton acceptor of the terminal proton-coupled electron transfer event from Y373, is essential for triggering the large-scale conformational changes of helix α22 and the CTE in the lit state, while D323 influences the timing.
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Affiliation(s)
- Rene Zangl
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Sejla Soravia
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Martin Saft
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jan Gerrit Löffler
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Jonathan Schulte
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
| | - Christian Joshua Rosner
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Jens Bredenbeck
- Institute of Biophysics, Goethe University Frankfurt, Max-von-Laue-Str. 1, 60438 Frankfurt/Main, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg Hans-Meerwein-Str. 4, 35032 Marburg, Germany
| | - Nina Morgner
- Institute of Physical and Theoretical Chemistry, Goethe University Frankfurt Max-von-Laue-Str. 9, 60438 Frankfurt/Main, Germany
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2
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Direct experimental observation of blue-light-induced conformational change and intermolecular interactions of cryptochrome. Commun Biol 2022; 5:1103. [PMID: 36257983 PMCID: PMC9579160 DOI: 10.1038/s42003-022-04054-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Accepted: 09/30/2022] [Indexed: 11/30/2022] Open
Abstract
Cryptochromes are blue light receptors that mediate circadian rhythm and magnetic sensing in various organisms. A typical cryptochrome consists of a conserved photolyase homology region domain and a varying carboxyl-terminal extension across species. The structure of the flexible carboxyl-terminal extension and how carboxyl-terminal extension participates in cryptochrome’s signaling function remain mostly unknown. In this study, we uncover the potential missing link between carboxyl-terminal extension conformational changes and downstream signaling functions. Specifically, we discover that the blue-light induced opening of carboxyl-terminal extension in C. reinhardtii animal-like cryptochrome can structurally facilitate its interaction with Rhythm Of Chloroplast 15, a circadian-clock-related protein. Our finding is made possible by two technical advances. Using single-molecule Förster resonance energy transfer technique, we directly observe the displacement of carboxyl-terminal extension by about 15 Å upon blue light excitation. Combining structure prediction and solution X-ray scattering methods, we propose plausible structures of full-length cryptochrome under dark and lit conditions. The structures provide molecular basis for light active conformational changes of cryptochrome and downstream regulatory functions. Refined structures, protein-docking analysis and single molecule assays provides insights into light-induced conformational changes in the cryptochrome CraCRY.
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3
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Oldemeyer S, Haddad AZ, Fleming GR. Interconnection of the Antenna Pigment 8-HDF and Flavin Facilitates Red-Light Reception in a Bifunctional Animal-like Cryptochrome. Biochemistry 2019; 59:594-604. [PMID: 31846308 DOI: 10.1021/acs.biochem.9b00875] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Cryptochromes are ubiquitous flavin-binding light sensors closely related to DNA-repairing photolyases. The animal-like cryptochrome CraCRY from the green alga Chlamydomonas reinhardtii challenges the paradigm of cryptochromes as pure blue-light receptors by acting as a (6-4) photolyase, using 8-hydroxy-5-deazaflavin (8-HDF) as a light-harvesting antenna with a 17.4 Å distance to flavin and showing spectral sensitivity up to 680 nm. The expanded action spectrum is attributed to the presence of the flavin neutral radical (FADH•) in the dark, despite a rapid FADH• decay observed in vitro in samples exclusively carrying flavin. Herein, the red-light response of CraCRY carrying flavin and 8-HDF was studied, revealing a 3-fold prolongation of the FADH• lifetime in the presence of 8-HDF. Millisecond time-resolved ultraviolet-visible spectroscopy showed the red-light-induced formation and decay of an absorbance band at 458 nm concomitant with flavin reduction. Time-resolved Fourier transform infrared (FTIR) spectroscopy and density functional theory attributed these changes to the deprotonation of 8-HDF, challenging the paradigm of 8-HDF being permanently deprotonated in photolyases. FTIR spectra showed changes in the hydrogen bonding network of asparagine 395, a residue suggested to indirectly control flavin protonation, indicating the involvement of N395 in the stabilization of FADH•. Fluorescence spectroscopy revealed a decrease in the energy transfer efficiency of 8-HDF upon flavin reduction, possibly linked to 8-HDF deprotonation. The discovery of the interdependence of flavin and 8-HDF beyond energy transfer processes highlights the essential role of the antenna, introducing a new concept enabling CraCRY and possibly other bifunctional cryptochromes to fulfill their dual function.
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Affiliation(s)
- Sabine Oldemeyer
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Andrew Z Haddad
- Energy Technologies Area , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States
| | - Graham R Fleming
- Department of Chemistry , University of California , Berkeley , California 94720 , United States.,Molecular Biophysics and Integrated Bioimaging Division , Lawrence Berkeley National Laboratory , Berkeley , California 94720 , United States.,Kavli Energy Nanoscience Institute , Berkeley , California 94720 , United States
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4
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Lacombat F, Espagne A, Dozova N, Plaza P, Müller P, Brettel K, Franz-Badur S, Essen LO. Ultrafast Oxidation of a Tyrosine by Proton-Coupled Electron Transfer Promotes Light Activation of an Animal-like Cryptochrome. J Am Chem Soc 2019; 141:13394-13409. [PMID: 31368699 DOI: 10.1021/jacs.9b03680] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The animal-like cryptochrome of Chlamydomonas reinhardtii (CraCRY) is a recently discovered photoreceptor that controls the transcriptional profile and sexual life cycle of this alga by both blue and red light. CraCRY has the uncommon feature of efficient formation and longevity of the semireduced neutral form of its FAD cofactor upon blue light illumination. Tyrosine Y373 plays a crucial role by elongating , as fourth member, the electron transfer (ET) chain found in most other cryptochromes and DNA photolyases, which comprises a conserved tryptophan triad. Here, we report the full mechanism of light-induced FADH• formation in CraCRY using transient absorption spectroscopy from hundreds of femtoseconds to seconds. Electron transfer starts from ultrafast reduction of excited FAD to FAD•- by the proximal tryptophan (0.4 ps) and is followed by delocalized migration of the produced WH•+ radical along the tryptophan triad (∼4 and ∼50 ps). Oxidation of Y373 by coupled ET to WH•+ and deprotonation then proceeds in ∼800 ps, without any significant kinetic isotope effect, nor a pH effect between pH 6.5 and 9.0. The FAD•-/Y373• pair is formed with high quantum yield (∼60%); its intrinsic decay by recombination is slow (∼50 ms), favoring reduction of Y373• by extrinsic agents and protonation of FAD•- to form the long-lived, red-light absorbing FADH• species. Possible mechanisms of tyrosine oxidation by ultrafast proton-coupled ET in CraCRY, a process about 40 times faster than the archetypal tyrosine-Z oxidation in photosystem II, are discussed in detail.
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Affiliation(s)
- Fabien Lacombat
- PASTEUR, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Agathe Espagne
- PASTEUR, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Nadia Dozova
- PASTEUR, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Pascal Plaza
- PASTEUR, Département de chimie , École normale supérieure, PSL University, Sorbonne Université, CNRS , 75005 Paris , France
| | - Pavel Müller
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Univ. Paris-Sud, Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France
| | - Klaus Brettel
- Institute for Integrative Biology of the Cell (I2BC), CEA, CNRS , Univ. Paris-Sud, Université Paris-Saclay , 91198 , Gif-sur-Yvette cedex , France
| | - Sophie Franz-Badur
- Department of Chemistry, Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Center for Synthetic Microbiology , Philipps University , 35032 Marburg , Germany
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5
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Time-Resolved Infrared and Visible Spectroscopy on Cryptochrome aCRY: Basis for Red Light Reception. Biophys J 2019; 117:490-499. [PMID: 31326107 DOI: 10.1016/j.bpj.2019.06.027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Revised: 06/18/2019] [Accepted: 06/24/2019] [Indexed: 12/18/2022] Open
Abstract
Cryptochromes function as flavin-binding photoreceptors in bacteria, fungi, algae, land plants, and insects. The discovery of an animal-like cryptochrome in the green alga Chlamydomonas reinhardtii has expanded the spectral range of sensitivity of these receptors from ultraviolet A/blue light to almost the complete visible spectrum. The broadened light response has been explained by the presence of the flavin neutral radical as a chromophore in the dark. Concomitant with photoconversion of the flavin, an unusually long-lived tyrosyl radical with a red-shifted ultraviolet-visible spectrum is formed, which is essential for the function of the receptor. In this study, the microenvironment of this key residue, tyrosine 373, was scrutinized using time-resolved Fourier transform infrared spectroscopy on several variants of animal-like cryptochrome and density functional theory for band assignment. The reduced tyrosine takes on distinct hydrogen bond scenarios depending on the presence of the C-terminal extension and of a neighboring cysteine. Upon radical formation, all variants showed a signal at 1400 cm-1, which we assigned to the ν7'a marker band of the CO stretching mode. The exceptionally strong downshift of this band cannot be attributed to a loss of hydrogen bonding only. Time-resolved ultraviolet-visible spectroscopy on W322F, a mutant of the neighboring tryptophan residue, revealed a decrease of the tyrosyl radical lifetime by almost two orders of magnitude, along with a shift of the absorbance maximum from 416 to 398 nm. These findings strongly support the concept of a π-π stacking as an apolar interaction between Y373 and W322 to be responsible for the characteristics of the tyrosyl radical. This concept of radical stabilization has been unknown to cryptochromes so far but might be highly relevant for other homologs with a tetrad of tryptophans and tyrosines as electron donors.
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6
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Franz S, Ignatz E, Wenzel S, Zielosko H, Putu E, Maestre-Reyna M, Tsai MD, Yamamoto J, Mittag M, Essen LO. Structure of the bifunctional cryptochrome aCRY from Chlamydomonas reinhardtii. Nucleic Acids Res 2019; 46:8010-8022. [PMID: 30032195 PMCID: PMC6125616 DOI: 10.1093/nar/gky621] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2018] [Accepted: 07/17/2018] [Indexed: 02/06/2023] Open
Abstract
Photolyases and cryptochromes form an almost ubiquitous family of blue light photoreceptors involved in the repair and maintenance of DNA integrity or regulatory control. We found that one cryptochrome from the green alga Chlamydomonas reinhardtii (CraCRY) is capable of both, control of transcript levels and the sexual cycle of the alga in a positive (germination) and negative manner (mating ability), as well as catalyzing the repair of UV-DNA lesions. Its 1.6 Å crystal structure shows besides the FAD chromophore an aromatic tetrad that is indispensable in animal-like type I cryptochromes for light-driven change of their signaling-active redox state and formation of a stable radical pair. Given CraCRY’s catalytic activity as (6-4) photolyase in vivo and in vitro, we present the first co-crystal structure of a cryptochrome with duplex DNA comprising a (6-4) pyrimidine–pyrimidone lesion. This 2.9 Å structure reveals a distinct conformation for the catalytic histidine His1, H357, that challenges previous models of a single-photon driven (6-4) photolyase mechanism.
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Affiliation(s)
- Sophie Franz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Elisabeth Ignatz
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | - Sandra Wenzel
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Hannah Zielosko
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
| | | | - Manuel Maestre-Reyna
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Ming-Daw Tsai
- Institute of Biological Chemistry, Academia Sinica, 128 Academia Rd. Sec. 2, Taipei 115, Taiwan
| | - Junpei Yamamoto
- Division of Chemistry, Graduate School of Engineering Science, Osaka University, 1–3 Machikaneyama, Toyonaka, Osaka 560-8531, Japan
| | - Maria Mittag
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Lars-Oliver Essen
- Unit for Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- LOEWE Center of Synthetic Microbiology, Philipps University Marburg, Hans-Meerwein Straße 4, 35032 Marburg, Germany
- To whom correspondence should be addressed. Tel: +49 6421/28 22032; Fax: +49 6421/28 22012;
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7
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Abstract
Sensory photoreceptors underpin light-dependent adaptations of organismal physiology, development, and behavior in nature. Adapted for optogenetics, sensory photoreceptors become genetically encoded actuators and reporters to enable the noninvasive, spatiotemporally accurate and reversible control by light of cellular processes. Rooted in a mechanistic understanding of natural photoreceptors, artificial photoreceptors with customized light-gated function have been engineered that greatly expand the scope of optogenetics beyond the original application of light-controlled ion flow. As we survey presently, UV/blue-light-sensitive photoreceptors have particularly allowed optogenetics to transcend its initial neuroscience applications by unlocking numerous additional cellular processes and parameters for optogenetic intervention, including gene expression, DNA recombination, subcellular localization, cytoskeleton dynamics, intracellular protein stability, signal transduction cascades, apoptosis, and enzyme activity. The engineering of novel photoreceptors benefits from powerful and reusable design strategies, most importantly light-dependent protein association and (un)folding reactions. Additionally, modified versions of these same sensory photoreceptors serve as fluorescent proteins and generators of singlet oxygen, thereby further enriching the optogenetic toolkit. The available and upcoming UV/blue-light-sensitive actuators and reporters enable the detailed and quantitative interrogation of cellular signal networks and processes in increasingly more precise and illuminating manners.
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Affiliation(s)
- Aba Losi
- Department of Mathematical, Physical and Computer Sciences , University of Parma , Parco Area delle Scienze 7/A-43124 Parma , Italy
| | - Kevin H Gardner
- Structural Biology Initiative, CUNY Advanced Science Research Center , New York , New York 10031 , United States.,Department of Chemistry and Biochemistry, City College of New York , New York , New York 10031 , United States.,Ph.D. Programs in Biochemistry, Chemistry, and Biology , The Graduate Center of the City University of New York , New York , New York 10016 , United States
| | - Andreas Möglich
- Lehrstuhl für Biochemie , Universität Bayreuth , 95447 Bayreuth , Germany.,Research Center for Bio-Macromolecules , Universität Bayreuth , 95447 Bayreuth , Germany.,Bayreuth Center for Biochemistry & Molecular Biology , Universität Bayreuth , 95447 Bayreuth , Germany
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8
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Schroeder L, Oldemeyer S, Kottke T. Time-Resolved Infrared Spectroscopy on Plant Cryptochrome—Relevance of Proton Transfer and ATP Binding for Signaling. J Phys Chem A 2017; 122:140-147. [DOI: 10.1021/acs.jpca.7b10249] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Lea Schroeder
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- Physical and Biophysical
Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße
25, 33615 Bielefeld, Germany
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9
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Kottke T, Oldemeyer S, Wenzel S, Zou Y, Mittag M. Cryptochrome photoreceptors in green algae: Unexpected versatility of mechanisms and functions. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:4-14. [PMID: 28619534 DOI: 10.1016/j.jplph.2017.05.021] [Citation(s) in RCA: 37] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/21/2017] [Revised: 05/29/2017] [Accepted: 05/29/2017] [Indexed: 06/07/2023]
Abstract
Green algae have a highly complex and diverse set of cryptochrome photoreceptor candidates including members of the following subfamilies: plant, plant-like, animal-like, DASH and cryptochrome photolyase family 1 (CPF1). While some green algae encode most or all of them, others lack certain members. Here we present an overview about functional analyses of so far investigated cryptochrome photoreceptors from the green algae Chlamydomonas reinhardtii (plant and animal-like cryptochromes) and Ostreococcus tauri (CPF1) with regard to their biological significance and spectroscopic properties. Cryptochromes of both algae have been demonstrated recently to be involved to various extents in circadian clock regulation and in Chlamydomonas additionally in life cycle control. Moreover, CPF1 even performs light-driven DNA repair. The plant cryptochrome and CPF1 are UVA/blue light receptors, whereas the animal-like cryptochrome responds to almost the whole visible spectrum including red light. Accordingly, plant cryptochrome, animal-like cryptochrome and CPF1 differ fundamentally in their structural response to light as revealed by their visible and infrared spectroscopic signatures, and in the role of the flavin neutral radical acting as dark form or signaling state.
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Affiliation(s)
- Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany.
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstraße 25, 33615 Bielefeld, Germany
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Yong Zou
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University Jena, 07743 Jena, Germany.
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10
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Greiner A, Kelterborn S, Evers H, Kreimer G, Sizova I, Hegemann P. Targeting of Photoreceptor Genes in Chlamydomonas reinhardtii via Zinc-Finger Nucleases and CRISPR/Cas9. THE PLANT CELL 2017; 29:2498-2518. [PMID: 28978758 PMCID: PMC5774583 DOI: 10.1105/tpc.17.00659] [Citation(s) in RCA: 157] [Impact Index Per Article: 22.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/21/2017] [Revised: 09/19/2017] [Accepted: 10/04/2017] [Indexed: 05/18/2023]
Abstract
The fast-growing biflagellated single-celled chlorophyte Chlamydomonas reinhardtii is the most widely used alga in basic research. The physiological functions of the 18 sensory photoreceptors are of particular interest with respect to Chlamydomonas development and behavior. Despite the demonstration of gene editing in Chlamydomonas in 1995, the isolation of mutants lacking easily ascertained newly acquired phenotypes remains problematic due to low DNA recombination efficiency. We optimized gene-editing protocols for several Chlamydomonas strains (including wild-type CC-125) using zinc-finger nucleases (ZFNs), genetically encoded CRISPR/associated protein 9 (Cas9) from Staphylococcus aureus and Streptococcus pyogenes, and recombinant Cas9 and developed protocols for rapidly isolating nonselectable gene mutants. Using this technique, we disrupted the photoreceptor genes COP1/2, COP3 (encoding channelrhodopsin 1 [ChR1]), COP4 (encoding ChR2), COP5, PHOT, UVR8, VGCC, MAT3, and aCRY and created the chr1 chr2 and uvr8 phot double mutants. Characterization of the chr1, chr2, and mat3 mutants confirmed the value of photoreceptor mutants for physiological studies. Genes of interest were disrupted in 5 to 15% of preselected clones (∼1 out of 4000 initial cells). Using ZFNs, genes were edited in a reliable, predictable manner via homologous recombination, whereas Cas9 primarily caused gene disruption via the insertion of cotransformed DNA. These methods should be widely applicable to research involving green algae.
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Affiliation(s)
- Andre Greiner
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Simon Kelterborn
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Heide Evers
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Georg Kreimer
- Department of Biology, Friedrich-Alexander University, 91058 Erlangen, Germany
| | - Irina Sizova
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
| | - Peter Hegemann
- Institute of Biology, Experimental Biophysics, Humboldt University of Berlin, 10099 Berlin, Germany
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11
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König S, Juhas M, Jäger S, Kottke T, Büchel C. The cryptochrome-photolyase protein family in diatoms. JOURNAL OF PLANT PHYSIOLOGY 2017; 217:15-19. [PMID: 28720252 DOI: 10.1016/j.jplph.2017.06.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2017] [Revised: 06/28/2017] [Accepted: 06/29/2017] [Indexed: 06/07/2023]
Abstract
The cryptochrome - photolyase family (CPF) consists of homologous flavoproteins having completely different functions involving DNA repair, circadian rhythm and/or photoreception. From the original photolyases, working either as (6-4) or cyclobutane pyrimidine dimer photolyases, the animal- and plant-type cryptochromes, respectively, evolved and also the more intermediate DASH cryptochromes. Whereas animal cryptochromes work mostly in clock-related functions, plant cryptochromes are also directly involved in developmental processes such as hypocotyl elongation or flower induction. In diatoms, all types of cryptochromes and photolyases were predicted from genome sequences. However, up to now only two proteins have been characterised in more detail, CPF1 and CryP. CPF1 is related to animal-type cryptochromes, but works as a (6-4) photolyase in addition to having photoreceptor functions. It was shown to interact with the CLOCK:Bmal1 heterodimer in a heterologous system, and thus is probably involved in clock-related processes. Moreover, CPF1 directly influences transcription. The latter was also true for CryP, which is a cryptochrome distantly related to plant-type cryptochromes. In addition, CryP influences light-harvesting protein accumulation. For all diatom cryptochromes, down-stream signalling has to proceed via interaction partners different from the classical proteins involved in cryptochrome signalling in higher plants, because these candidates are missing in diatoms.
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Affiliation(s)
- Sarah König
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Matthias Juhas
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Stefanie Jäger
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Claudia Büchel
- Institute of Molecular Biosciences, Goethe University Frankfurt, 60438 Frankfurt, Germany.
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12
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Sommer C, Dietz MS, Patschkowski T, Mathes T, Kottke T. Light-Induced Conformational Changes in the Plant Cryptochrome Photolyase Homology Region Resolved by Selective Isotope Labeling and Infrared Spectroscopy. Photochem Photobiol 2017; 93:881-887. [DOI: 10.1111/php.12750] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Accepted: 02/10/2017] [Indexed: 11/28/2022]
Affiliation(s)
- Constanze Sommer
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
| | - Marina S. Dietz
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
| | - Thomas Patschkowski
- Proteome and Metabolome Research (Bio 27); Department of Biology; Bielefeld University; Bielefeld Germany
| | - Tilo Mathes
- Department of Biology; Experimental Biophysics; Humboldt-Universität zu Berlin; Berlin Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry; Department of Chemistry; Bielefeld University; Bielefeld Germany
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13
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Oldemeyer S, Franz S, Wenzel S, Essen LO, Mittag M, Kottke T. Essential Role of an Unusually Long-lived Tyrosyl Radical in the Response to Red Light of the Animal-like Cryptochrome aCRY. J Biol Chem 2016; 291:14062-14071. [PMID: 27189948 DOI: 10.1074/jbc.m116.726976] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2016] [Indexed: 11/06/2022] Open
Abstract
Cryptochromes constitute a group of flavin-binding blue light receptors in bacteria, fungi, plants, and insects. Recently, the response of cryptochromes to light was extended to nearly the entire visible spectral region on the basis of the activity of the animal-like cryptochrome aCRY in the green alga Chlamydomonas reinhardtii This finding was explained by the absorption of red light by the flavin neutral radical as the dark state of the receptor, which then forms the anionic fully reduced state. In this study, time-resolved UV-visible spectroscopy on the full-length aCRY revealed an unusually long-lived tyrosyl radical with a lifetime of 2.6 s, which is present already 1 μs after red light illumination of the flavin radical. Mutational studies disclosed the tyrosine 373 close to the surface to form the long-lived radical and to be essential for photoreduction. This residue is conserved exclusively in the sequences of other putative aCRY proteins distinguishing them from conventional (6-4) photolyases. Size exclusion chromatography showed the full-length aCRY to be a dimer in the dark at 0.5 mm injected concentration with the C-terminal extension as the dimerization site. Upon illumination, partial oligomerization was observed via disulfide bridge formation at cysteine 482 in close proximity to tyrosine 373. The lack of any light response in the C-terminal extension as evidenced by FTIR spectroscopy differentiates aCRY from plant and Drosophila cryptochromes. These findings imply that aCRY might have evolved a different signaling mechanism via a light-triggered redox cascade culminating in photooxidation of a yet unknown substrate or binding partner.
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Affiliation(s)
- Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld
| | - Sophie Franz
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straβe 4, 35039 Marburg
| | - Sandra Wenzel
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Lars-Oliver Essen
- Structural Biochemistry, Department of Chemistry, Philipps University Marburg, Hans-Meerwein Straβe 4, 35039 Marburg
| | - Maria Mittag
- Institute of General Botany and Plant Physiology, Friedrich Schiller University, Am Planetarium 1, 07743 Jena, Germany
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstr. 25, 33615 Bielefeld,.
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Wijaya IMM, Domratcheva T, Iwata T, Getzoff ED, Kandori H. Single Hydrogen Bond Donation from Flavin N5 to Proximal Asparagine Ensures FAD Reduction in DNA Photolyase. J Am Chem Soc 2016; 138:4368-76. [PMID: 27002596 DOI: 10.1021/jacs.5b10533] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The spread of the absorbance of the stable FADH(•) radical (300-700 nm) allows CPD photolyase to highly efficiently form FADH(-), making it functional for DNA repair. In this study, FTIR spectroscopy detected a strong hydrogen bond, from FAD N5-H to the carbonyl group of the Asn378 side chain, that is modulated by the redox state of FAD. The observed characteristic frequency shifts were reproduced in quantum-mechanical models of the flavin binding site, which were then employed to elucidate redox tuning governed by Asn378. We demonstrate that enhanced hydrogen bonding of the Asn378 side chain with the FADH(•) radical increases thermodynamic stabilization of the radical state, and further ensures kinetic stabilization and accumulation of the fully reduced FADH(-) state.
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Affiliation(s)
| | - Tatiana Domratcheva
- Department of Biomolecular Mechanisms, Max Planck Institute for Medical Research , Jahnstrasse 29, Heidelberg 69120, Germany
| | | | - Elizabeth D Getzoff
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute , La Jolla, California 92037, United States
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15
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Mitsui H, Maeda T, Yamaguchi C, Tsuji Y, Watari R, Kubo Y, Okano K, Okano T. Overexpression in yeast, photocycle, and in vitro structural change of an avian putative magnetoreceptor cryptochrome4. Biochemistry 2015; 54:1908-17. [PMID: 25689419 DOI: 10.1021/bi501441u] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022]
Abstract
Cryptochromes (CRYs) have been found in a wide variety of living organisms and can function as blue light photoreceptors, circadian clock molecules, or magnetoreceptors. Non-mammalian vertebrates have CRY4 in addition to the CRY1 and CRY2 circadian clock components. Though the function of CRY4 is not well understood, chicken CRY4 (cCRY4) may be a magnetoreceptor because of its high level of expression in the retina and light-dependent structural changes in retinal homogenates. To further characterize the photosensitive nature of cCRY4, we developed an expression system using budding yeast and purified cCRY4 at yields of submilligrams of protein per liter with binding of the flavin adenine dinucleotide (FAD) chromophore. Recombinant cCRY4 dissociated from anti-cCRY4 C1 mAb, which recognizes the C-terminal region of cCRY4, in a light-dependent manner and showed a light-dependent change in its trypsin digestion pattern, suggesting that cCRY4 changes its conformation with light irradiation in the absence of other retinal factors. Combinatorial analyses with UV-visible spectroscopy and immunoprecipitation revealed that there is chromophore reduction in the cCRY4 photocycle and formation of a flavosemiquinone radical intermediate that is likely accompanied by a conformational change in the carboxyl-terminal region. Thus, cCRY4 seems to be an intrinsically photosensitive and photoswitchable molecule and may exemplify a vertebrate model of cryptochrome with possible function as a photosensor and/or magnetoreceptor.
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Affiliation(s)
- Hiromasa Mitsui
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Toshinori Maeda
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Chiaki Yamaguchi
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yusuke Tsuji
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Ryuji Watari
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Yoko Kubo
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Keiko Okano
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
| | - Toshiyuki Okano
- Department of Electrical Engineering and Bioscience, Graduate School of Advanced Science and Engineering, Waseda University, Wakamatsu-cho 2-2, Shinjuku-ku, Tokyo 162-8480, Japan
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Herman E, Kottke T. Allosterically regulated unfolding of the A'α helix exposes the dimerization site of the blue-light-sensing aureochrome-LOV domain. Biochemistry 2015; 54:1484-92. [PMID: 25621532 DOI: 10.1021/bi501509z] [Citation(s) in RCA: 42] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Aureochromes have been shown to act as blue-light-regulated transcription factors in algae in the absence of phototropins. Aureochromes comprise a light-, oxygen-, or voltage-sensitive (LOV) domain as a sensory module binding the flavin chromophore and a basic region leucine zipper (bZIP) domain as an effector. The domain arrangement in aureochromes with an N-terminal effector is inversed to other LOV proteins. To clarify the role of the linking A'α helix in signaling, we have investigated the LOV domain of aureochrome1a from the diatom alga Phaeodactylum tricornutum without the N-terminal A'α helix but with the C-terminal Jα helix. Results were analyzed in comparison to those previously obtained on the LOV domain with both flanking helices and on the LOV domain with the A'α helix but without the Jα helix. Fourier transform infrared difference spectroscopy provides evidence by a band at 1656 cm(-1) that the A'α helix unfolds in response to light. This unfolding takes place only in the presence and as a consequence of the unfolding of the Jα helix, which points to an allosteric regulation. Size exclusion chromatography shows the LOV domain to be dimeric in the absence and monomeric in the presence of the A'α helix, implying that the folded helix covers the dimerization site. Therefore, the A'α helix directly modulates the oligomerization state of the LOV domain, whereas the Jα helix acts as an allosteric regulator. Both the allosteric control and the light-induced dimerization have not been observed in phototropin-LOV2 and point to a different signaling mechanism within the full-length proteins.
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Affiliation(s)
- Elena Herman
- Department of Chemistry, Physical and Biophysical Chemistry, Bielefeld University , Universitätsstraße 25, 33615 Bielefeld, Germany
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17
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Fortunato AE, Annunziata R, Jaubert M, Bouly JP, Falciatore A. Dealing with light: the widespread and multitasking cryptochrome/photolyase family in photosynthetic organisms. JOURNAL OF PLANT PHYSIOLOGY 2015; 172:42-54. [PMID: 25087009 DOI: 10.1016/j.jplph.2014.06.011] [Citation(s) in RCA: 62] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 06/17/2014] [Accepted: 06/19/2014] [Indexed: 05/19/2023]
Abstract
Light is essential for the life of photosynthetic organisms as it is a source of energy and information from the environment. Light excess or limitation can be a cause of stress however. Photosynthetic organisms exhibit sophisticated mechanisms to adjust their physiology and growth to the local environmental light conditions. The cryptochrome/photolyase family (CPF) is composed of flavoproteins with similar structures that display a variety of light-dependent functions. This family encompasses photolyases, blue-light activated enzymes that repair ultraviolet-light induced DNA damage, and cryptochromes, known for their photoreceptor functions in terrestrial plants. For this review, we searched extensively for CPFs in the available genome databases to trace the distribution and evolution of this protein family in photosynthetic organisms. By merging molecular data with current knowledge from the functional characterization of CPFs from terrestrial and aquatic organisms, we discuss their roles in (i) photoperception, (ii) biological rhythm regulation and (iii) light-induced stress responses. We also explore their possible implication in light-related physiological acclimation and their distribution in phototrophs living in different environments. The outcome of this structure-function analysis reconstructs the complex scenarios in which CPFs have evolved, as highlighted by the novel functions and biochemical properties of the most recently described family members in algae.
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Affiliation(s)
- Antonio Emidio Fortunato
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Rossella Annunziata
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Marianne Jaubert
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France
| | - Jean-Pierre Bouly
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France.
| | - Angela Falciatore
- Sorbonne Universités, UPMC Univ Paris 06, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France; CNRS, UMR 7238, Computational and Quantitative Biology, F-75006 Paris, France.
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18
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Conrad KS, Manahan CC, Crane BR. Photochemistry of flavoprotein light sensors. Nat Chem Biol 2014; 10:801-9. [PMID: 25229449 DOI: 10.1038/nchembio.1633] [Citation(s) in RCA: 167] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2014] [Accepted: 08/18/2014] [Indexed: 12/22/2022]
Abstract
Three major classes of flavin photosensors, light oxygen voltage (LOV) domains, blue light sensor using FAD (BLUF) proteins and cryptochromes (CRYs), regulate diverse biological activities in response to blue light. Recent studies of structure, spectroscopy and chemical mechanism have provided unprecedented insight into how each family operates at the molecular level. In general, the photoexcitation of the flavin cofactor leads to changes in redox and protonation states that ultimately remodel protein conformation and molecular interactions. For LOV domains, issues remain regarding early photochemical events, but common themes in conformational propagation have emerged across a diverse family of proteins. For BLUF proteins, photoinduced electron transfer reactions critical to light conversion are defined, but the subsequent rearrangement of hydrogen bonding networks key for signaling remains highly controversial. For CRYs, the relevant photocycles are actively debated, but mechanistic and functional studies are converging. Despite these challenges, our current understanding has enabled the engineering of flavoprotein photosensors for control of signaling processes within cells.
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Affiliation(s)
- Karen S Conrad
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Craig C Manahan
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
| | - Brian R Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York, USA
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19
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Müller P, Bouly JP. Searching for the mechanism of signalling by plant photoreceptor cryptochrome. FEBS Lett 2014; 589:189-92. [DOI: 10.1016/j.febslet.2014.12.008] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2014] [Revised: 12/02/2014] [Accepted: 12/02/2014] [Indexed: 12/01/2022]
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