1
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Hosokawa Y, Morita H, Nakamura M, Yamamoto J. A deazariboflavin chromophore kinetically stabilizes reduced FAD state in a bifunctional cryptochrome. Sci Rep 2023; 13:16682. [PMID: 37794070 PMCID: PMC10551024 DOI: 10.1038/s41598-023-43930-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2023] [Accepted: 09/30/2023] [Indexed: 10/06/2023] Open
Abstract
An animal-like cryptochrome derived from Chlamydomonas reinhardtii (CraCRY) is a bifunctional flavoenzyme harboring flavin adenine dinucleotide (FAD) as a photoreceptive/catalytic center and functions both in the regulation of gene transcription and the repair of UV-induced DNA lesions in a light-dependent manner, using different FAD redox states. To address how CraCRY stabilizes the physiologically relevant redox state of FAD, we investigated the thermodynamic and kinetic stability of the two-electron reduced anionic FAD state (FADH-) in CraCRY and related (6-4) photolyases. The thermodynamic stability of FADH- remained almost the same compared to that of all tested proteins. However, the kinetic stability of FADH- varied remarkably depending on the local structure of the secondary pocket, where an auxiliary chromophore, 8-hydroxy-7,8-didemethyl-5-deazariboflavin (8-HDF), can be accommodated. The observed effect of 8-HDF uptake on the enhancement of the kinetic stability of FADH- suggests an essential role of 8-HDF in the bifunctionality of CraCRY.
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Affiliation(s)
- Yuhei Hosokawa
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Hiroyoshi Morita
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Mai Nakamura
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan
| | - Junpei Yamamoto
- Graduate School of Engineering Science, Osaka University, 1-3 Machikaneyama, Toyonaka, Osaka, 560-8531, Japan.
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2
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Wen B, Xu L, Tang Y, Jiang Z, Ge M, Liu L, Zhu G. A single amino acid residue tunes the stability of the fully reduced flavin cofactor and photorepair activity in photolyases. J Biol Chem 2022; 298:102188. [PMID: 35753350 PMCID: PMC9356274 DOI: 10.1016/j.jbc.2022.102188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/14/2022] [Accepted: 06/15/2022] [Indexed: 11/25/2022] Open
Abstract
The ultraviolet-induced DNA lesions, cyclobutane pyrimidine dimers (CPDs) and pyrimidine (6-4) pyrimidone photoproducts (6-4 photoproducts), can be directly photorepaired by CPD photolyases and 6-4 photolyases, respectively. The fully reduced flavin (hydroquinone, HQ) cofactor is required for the catalysis of both types of these photolyases. On the other hand, flavin cofactor in the semi-reduced state, semiquinone (SQ), can be utilized by photolyase homologs, the cryptochromes. However, the evolutionary process of the transition of the functional states of` flavin cofactors in photolyases and cryptochromes remains mysterious. In this work, we investigated three representative photolyases (Escherichia coli CPD photolyase, Microcystis aeruginosa DASH, and Phaeodactylum tricornutum 6-4 photolyase). We show that the residue at a single site adjacent to the flavin cofactor (corresponding to Ala377 in E. coli CPD photolyase, hereafter referred to as site 377) can fine-tune the stability of the HQ cofactor. We found that, in the presence of a polar residue (such as Ser or Asn) at site 377, HQ was stabilized against oxidation. Furthermore, this polar residue enhanced the photorepair activity of these photolyases both in vitro and in vivo. In constrast, substitution of hydrophobic residues, such as Ile, at site 377 in these photolyases adversely affected the stability of HQ. We speculate that these differential residue preferences at site 377 in photolyase proteins might reflect an important evolutionary event that altered the stability of HQ on the timeline from expression of photolyases to that of cryptochromes.
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Affiliation(s)
- Bin Wen
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Lei Xu
- Anhui Province Key Laboratory of Active Biological Macro-molecules, Wannan Medical College, Wuhu 241002, Anhui, China
| | - Yawei Tang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Zhen Jiang
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Mengting Ge
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Li Liu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China
| | - Guoping Zhu
- Anhui Provincial Key Laboratory of Molecular Enzymology and Mechanism of Major Diseases, College of Life Sciences, Anhui Normal University, Wuhu 241000, Anhui, China.
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3
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Serial crystallography captures dynamic control of sequential electron and proton transfer events in a flavoenzyme. Nat Chem 2022; 14:677-685. [PMID: 35393554 DOI: 10.1038/s41557-022-00922-3] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/24/2020] [Accepted: 02/25/2022] [Indexed: 11/08/2022]
Abstract
Flavin coenzymes are universally found in biological redox reactions. DNA photolyases, with their flavin chromophore (FAD), utilize blue light for DNA repair and photoreduction. The latter process involves two single-electron transfers to FAD with an intermittent protonation step to prime the enzyme active for DNA repair. Here we use time-resolved serial femtosecond X-ray crystallography to describe how light-driven electron transfers trigger subsequent nanosecond-to-microsecond entanglement between FAD and its Asn/Arg-Asp redox sensor triad. We found that this key feature within the photolyase-cryptochrome family regulates FAD re-hybridization and protonation. After first electron transfer, the FAD•- isoalloxazine ring twists strongly when the arginine closes in to stabilize the negative charge. Subsequent breakage of the arginine-aspartate salt bridge allows proton transfer from arginine to FAD•-. Our molecular videos demonstrate how the protein environment of redox cofactors organizes multiple electron/proton transfer events in an ordered fashion, which could be applicable to other redox systems such as photosynthesis.
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4
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Cellini A, Shankar MK, Wahlgren WY, Nimmrich A, Furrer A, James D, Wranik M, Aumonier S, Beale EV, Dworkowski F, Standfuss J, Weinert T, Westenhoff S. Structural basis of the radical pair state in photolyases and cryptochromes. Chem Commun (Camb) 2022; 58:4889-4892. [PMID: 35352724 PMCID: PMC9008703 DOI: 10.1039/d2cc00376g] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
We present the structure of a photoactivated animal (6-4) photolyase in its radical pair state, captured by serial crystallography. We observe how a conserved asparigine moves towards the semiquinone FAD chromophore and stabilizes it by hydrogen bonding. Several amino acids around the final tryptophan radical rearrange, opening it up to the solvent. The structure explains how the protein environment stabilizes the radical pair state, which is crucial for function of (6-4) photolyases and cryptochromes. The structural response of the drosophila (6-4) photolyase to photoinduced electron transfer along a chain of tryptophans is revealed using a serial crystallographic snapshot of the protein in its radical pair state.![]()
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Affiliation(s)
- Andrea Cellini
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Madan Kumar Shankar
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Weixiao Yuan Wahlgren
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Amke Nimmrich
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Antonia Furrer
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Daniel James
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Maximilian Wranik
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sylvain Aumonier
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Emma V Beale
- Photon Science Division - Laboratory for Synchrotron Radiation and Femtochemistry (LSF), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Florian Dworkowski
- Photon Science Division - Laboratory for Macromolecules and Bioimaging (LSB), Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Jörg Standfuss
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Tobias Weinert
- Division of Biology and Chemistry-Laboratory for Biomolecular Research, Paul Scherrer Institut, 5232 Villigen, Switzerland
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
- Department of Chemistry-BMC, University of Uppsala, Husargatan 3, 75237 Uppsala, Sweden
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5
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Goett-Zink L, Kottke T. Plant Cryptochromes Illuminated: A Spectroscopic Perspective on the Mechanism. Front Chem 2021; 9:780199. [PMID: 34900940 PMCID: PMC8653763 DOI: 10.3389/fchem.2021.780199] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 11/05/2021] [Indexed: 11/13/2022] Open
Abstract
Plant cryptochromes are central blue light receptors for the control of land plant and algal development including the circadian clock and the cell cycle. Cryptochromes share a photolyase homology region with about 500 amino acids and bind the chromophore flavin adenine dinucleotide. Characteristic for plant cryptochromes is a conserved aspartic acid close to flavin and an exceptionally long C-terminal extension. The mechanism of activation by excitation and reduction of the chromophore flavin adenine dinucleotide has been controversially discussed for many years. Various spectroscopic techniques have contributed to our understanding of plant cryptochromes by providing high time resolution, ambient conditions and even in-cell approaches. As a result, unifying and differing aspects of photoreaction and signal propagation have been revealed in comparison to members from other cryptochrome subfamilies. Here, we review the insight from spectroscopy on the flavin photoreaction in plant cryptochromes and present the current models on the signal propagation from flavin reduction to dissociation of the C-terminal extension.
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Affiliation(s)
- Lukas Goett-Zink
- Department of Chemistry, Bielefeld University, Bielefeld, Germany
| | - Tilman Kottke
- Department of Chemistry, Bielefeld University, Bielefeld, Germany.,Biophysical Chemistry and Diagnostics, Medical School OWL, Bielefeld University, Bielefeld, Germany
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6
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Gindt YM, Connolly G, Vonder Haar AL, Kikhwa M, Schelvis JPM. Investigation of the pH-dependence of the oxidation of FAD in VcCRY-1, a member of the cryptochrome-DASH family. Photochem Photobiol Sci 2021; 20:831-841. [PMID: 34091863 DOI: 10.1007/s43630-021-00063-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Accepted: 05/31/2021] [Indexed: 11/29/2022]
Abstract
Vibrio cholerae cryptochrome-1 (VcCRY-1) is a member of the cryptochrome DASH family. The flavoprotein appears to use blue light both for repair of cyclobutane pyrimidine dimers (CPDs) on DNA and signal transduction. Earlier, we found that it was almost impossible to oxidize the FADH· state upon binding to a CPD, and, in the absence of substrate, the rate of FADH· oxidation was much larger at high pH (Gindt et al. in Biochemistry 54:2802-2805, 2015). Here, we present the pH-dependence of the oxidation of FADH· by ferricyanide, which revealed a switch between slow and fast oxidation with a pKa ≈ 7.0. Stopped-flow mixing was used to measure the oxidation of FADH- to FADH· at pH 6.7 and 7.5. Substrate binding was required to slow down this oxidation such that it could be measured with stopped flow, but there was only a small effect of pH. In addition, resonance Raman measurements of FADH· in VcCRY-1 at pH 6.5 and 7.5 were performed to probe for structural changes near the FAD cofactor related to the observed changes in rate of FADH· oxidation. Only substrate binding seemed to induce a change near the FAD cofactor that may relate to the change in oxidation kinetics. The pH-effect on the FADH· oxidation rate, which is rate-limited by the proton acceptor, does not seem to be due to a protein structural change near the FAD cofactor. Instead, a conserved glutamate in CRY-DASH may control the deprotonation of FADH· and give rise to the pH-effect.
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Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Gabrielle Connolly
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Amy L Vonder Haar
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Miryam Kikhwa
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA
| | - Johannes P M Schelvis
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ, 07043, USA.
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7
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Iwata T, Yamada D, Mikuni K, Agata K, Hitomi K, Getzoff ED, Kandori H. ATP binding promotes light-induced structural changes to the protein moiety of Arabidopsis cryptochrome 1. Photochem Photobiol Sci 2021; 19:1326-1331. [PMID: 32935701 DOI: 10.1039/d0pp00003e] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Cryptochromes (CRYs) are blue-light receptors involved in photomorphogenesis in plants. Flavin adenine dinucleotide (FAD) is one of the chromophores of cryptochromes; its resting state oxidized form is converted into a signalling state neutral semiquionod radical (FADH˙) form. Studies have shown that cryptochrome 1 from Arabidopsis thaliana (AtCRY1) can bind ATP at its photolyase homology region (PHR), resulting in accumulation of FADH˙ form. This study used light-induced difference Fourier transform infrared spectroscopy to investigate how ATP influences structural changes in AtCRY1-PHR during the photoreaction. In the presence of ATP, there were large changes in the signals from the protein backbone compared with in the absence of ATP. The deprotonation of a carboxylic acid was observed only in the presence of ATP; this was assigned as aspartic acid (Asp) 396 through measurement of Asp to glutamic acid mutants. This corresponds to the protonation state of Asp396 estimated from the reported pKa values of Asp396; that is, the side chain of Asp396 is deprotonated and protonated for the ATP-free and -bound forms, respectively, in our experimental condition at pH8. Therefore, Asp396 acts a proton donor to FAD when it is ptotonated. It was indicated that the protonation/deprotination process of Asp396 is correlated with the accunumulation of FADH˙ and protein conformational changes.
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Affiliation(s)
- Tatsuya Iwata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan. and Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274-8510, Japan
| | - Daichi Yamada
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | - Katsuhiro Mikuni
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | - Kazuya Agata
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
| | - Kenichi Hitomi
- Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA
| | - 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, USA
| | - Hideki Kandori
- Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555, Japan.
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8
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Karki N, Vergish S, Zoltowski BD. Cryptochromes: Photochemical and structural insight into magnetoreception. Protein Sci 2021; 30:1521-1534. [PMID: 33993574 DOI: 10.1002/pro.4124] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2021] [Revised: 05/10/2021] [Accepted: 05/11/2021] [Indexed: 12/21/2022]
Abstract
Cryptochromes (CRYs) function as blue light photoreceptors in diverse physiological processes in nearly all kingdoms of life. Over the past several decades, they have emerged as the most likely candidates for light-dependent magnetoreception in animals, however, a long history of conflicts between in vitro photochemistry and in vivo behavioral data complicate validation of CRYs as a magnetosensor. In this review, we highlight the origins of conflicts regarding CRY photochemistry and signal transduction, and identify recent data that provides clarity on potential mechanisms of signal transduction in magnetoreception. The review primarily focuses on examining differences in photochemistry and signal transduction in plant and animal CRYs, and identifies potential modes of convergent evolution within these independent lineages that may identify conserved signaling pathways.
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Affiliation(s)
- Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Satyam Vergish
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
| | - Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, Texas, USA
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9
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Yee EF, Oldemeyer S, Böhm E, Ganguly A, York DM, Kottke T, Crane BR. Peripheral Methionine Residues Impact Flavin Photoreduction and Protonation in an Engineered LOV Domain Light Sensor. Biochemistry 2021; 60:1148-1164. [PMID: 33787242 PMCID: PMC8107827 DOI: 10.1021/acs.biochem.1c00064] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/17/2023]
Abstract
Proton-coupled electron transfer reactions play critical roles in many aspects of sensory phototransduction. In the case of flavoprotein light sensors, reductive quenching of flavin excited states initiates chemical and conformational changes that ultimately transmit light signals to downstream targets. These reactions generally require neighboring aromatic residues and proton-donating side chains for rapid and coordinated electron and proton transfer to flavin. Although photoreduction of flavoproteins can produce either the anionic (ASQ) or neutral semiquinone (NSQ), the factors that favor one over the other are not well understood. Here we employ a biologically active variant of the light-oxygen-voltage (LOV) domain protein VVD devoid of the adduct-forming Cys residue (VVD-III) to probe the mechanism of flavin photoreduction and protonation. A series of isosteric and conservative residue replacements studied by rate measurements, fluorescence quantum yields, FTIR difference spectroscopy, and molecular dynamics simulations indicate that tyrosine residues facilitate charge recombination reactions that limit sustained flavin reduction, whereas methionine residues facilitate radical propagation and quenching and also gate solvent access for flavin protonation. Replacement of a single surface Met residue with Leu favors formation of the ASQ over the NSQ and desensitizes photoreduction to oxidants. In contrast, increasing site hydrophilicity by Gln substitution promotes rapid NSQ formation and weakens the influence of the redox environment. Overall, the photoreactivity of VVD-III can be understood in terms of redundant electron donors, internal hole quenching, and coupled proton transfer reactions that all depend upon protein conformation, dynamics, and solvent penetration.
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Affiliation(s)
- Estella F. Yee
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
| | - Sabine Oldemeyer
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Elena Böhm
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Abir Ganguly
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Darrin M. York
- Laboratory for Biomolecular Simulation Research, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ, USA
| | - Tilman Kottke
- Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, 33615 Bielefeld, Germany
| | - Brian R. Crane
- Department of Chemistry and Chemical Biology, Cornell University, Ithaca, New York 14853, United States
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10
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Einholz C, Nohr D, Rodriguez R, Topitsch A, Kern M, Goldmann J, Chileshe E, Okasha M, Weber S, Schleicher E. pH-dependence of signaling-state formation in Drosophila cryptochrome. Arch Biochem Biophys 2021; 700:108787. [PMID: 33545100 DOI: 10.1016/j.abb.2021.108787] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2020] [Revised: 01/22/2021] [Accepted: 01/25/2021] [Indexed: 11/30/2022]
Abstract
Cryptochromes, FAD-dependent blue light photoreceptors, undergo a series of electron transfer reactions after light excitation. Time-resolved optical spectroscopy was employed to investigate the pH dependence of all light-dependent reactions in the cryptochrome from fruit flies. Signal state formation experiments on a time scale of seconds were found to be strongly pH dependent, and formation of both anionic and neutral FAD radicals could be detected, with reaction rates increasing by a factor of ~2.5 from basic to neutral pH values. Additionally, the influence of the amino acid His378 was investigated in further detail: Two protein variants, DmCry H378A and H378Q, showed significantly reduced rate constants for signal state formation, which again differed at neutral and alkaline pH values. Hence, His378 was identified as an amino acid responsible for the pronounced pH dependence; however, this amino acid can be excluded as a proton donor for the protonation of the anionic FAD radical. Other conserved amino acids appear to alter the overall polarity of the binding pocket and thus to be responsible for the pronounced pH dependence. Furthermore, the influence of pH and other experimental parameters, such as temperature, glycerol or ferricyanide concentrations, on the intermediately formed FAD-tryptophan radical pair was explored, which deprotonates on a microsecond time scale with a clear pH dependence, and subsequently recombines within milliseconds. Surprisingly, the latter reaction showed no pH dependence; potential reasons are discussed. All results are reviewed in terms of the photoreceptor and potential magnetoreceptor functions of Drosophila cryptochrome.
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Affiliation(s)
- Christopher Einholz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Daniel Nohr
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Ryan Rodriguez
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Annika Topitsch
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Maria Kern
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Jacqueline Goldmann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Emma Chileshe
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Moustafa Okasha
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Albertstraße 21, 79104, Freiburg, Germany.
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11
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Zoltowski BD, Chelliah Y, Wickramaratne A, Jarocha L, Karki N, Xu W, Mouritsen H, Hore PJ, Hibbs RE, Green CB, Takahashi JS. Chemical and structural analysis of a photoactive vertebrate cryptochrome from pigeon. Proc Natl Acad Sci U S A 2019; 116:19449-19457. [PMID: 31484780 PMCID: PMC6765304 DOI: 10.1073/pnas.1907875116] [Citation(s) in RCA: 79] [Impact Index Per Article: 15.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Computational and biochemical studies implicate the blue-light sensor cryptochrome (CRY) as an endogenous light-dependent magnetosensor enabling migratory birds to navigate using the Earth's magnetic field. Validation of such a mechanism has been hampered by the absence of structures of vertebrate CRYs that have functional photochemistry. Here we present crystal structures of Columba livia (pigeon) CRY4 that reveal evolutionarily conserved modifications to a sequence of Trp residues (Trp-triad) required for CRY photoreduction. In ClCRY4, the Trp-triad chain is extended to include a fourth Trp (W369) and a Tyr (Y319) residue at the protein surface that imparts an unusually high quantum yield of photoreduction. These results are consistent with observations of night migratory behavior in animals at low light levels and could have implications for photochemical pathways allowing magnetosensing.
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Affiliation(s)
- Brian D Zoltowski
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Yogarany Chelliah
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Anushka Wickramaratne
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Lauren Jarocha
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Nischal Karki
- Department of Chemistry, Southern Methodist University, Dallas, TX 75275
- Center for Drug Discovery, Design, and Delivery, Southern Methodist University, Dallas, TX 75275
| | - Wei Xu
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, DE-26111 Oldenburg, Germany
- Research Center for Neurosensory Sciences, University of Oldenburg, DE-26111 Oldenburg, Germany
| | - Peter J Hore
- Department of Chemistry, University of Oxford, OX1 3QZ Oxford, United Kingdom
| | - Ryan E Hibbs
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Carla B Green
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
| | - Joseph S Takahashi
- Department of Neuroscience, Peter O'Donnell Jr. Brain Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390;
- Howard Hughes Medical Institute, University of Texas Southwestern Medical Center, Dallas, TX 75390
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12
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Holub D, Kubař T, Mast T, Elstner M, Gillet N. What accounts for the different functions in photolyases and cryptochromes: a computational study of proton transfers to FAD. Phys Chem Chem Phys 2019; 21:11956-11966. [PMID: 31134233 DOI: 10.1039/c9cp00694j] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Photolyases (PL) and cryptochromes (CRY) are light-sensitive flavoproteins, respectively, involved in DNA repair and signal transduction. Their activation is triggered by an electron transfer process, which partially or fully reduces the photo-activated FAD cofactor. The full reduction additionally requires a proton transfer to the isoalloxazine ring. In plant CRY, an efficient proton transfer takes place within several μs, enabled by a conserved aspartate working as a proton donor, whereas in E. coli PL a proton transfer occurs in the 4 s timescale without any obvious proton donor, indicating the presence of a long-range proton transfer pathway. Unexpectedly, the insertion of an aspartate as a proton donor in a suitable position for proton transfer in E. coli PL does not initiate a transfer process similar to plant CRY, but even prevents the formation of a protonated FAD. In the present work, thanks to a combination of classical molecular dynamics and state-of-the-art DFTB3/MM simulations, we identify a proton transfer pathway from bulk to FAD in E. coli PL associated with a free energy profile in agreement with the experimental kinetics data. The free energy profiles of the proton transfer between aspartate and FAD show an inversion of the driving force between plant CRY and E. coli PL mutants. In the latter, the proton transfer from the aspartate is faster than in plant CRY but also thermodynamically disfavoured, in agreement with the experimental data. Our results further illustrate the fine tuning of the electrostatic FAD environment and the adaptability of the FAD pocket to ensure the divergent functions of the members of the PL-CRY family.
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Affiliation(s)
- Daniel Holub
- Department for Theoretical Chemical Biology, Institute for Physical Chemistry, Karlsruhe Institute for Technology, Kaiserstr. 12, 76131, Karlsruhe, Germany.
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13
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Xu L, Wen B, Shao W, Yao P, Zheng W, Zhou Z, Zhang Y, Zhu G. Impacts of Cys392, Asp393, and ATP on the FAD Binding, Photoreduction, and the Stability of the Radical State of Chlamydomonas reinhardtii Cryptochrome. Chembiochem 2019; 20:940-948. [PMID: 30548754 DOI: 10.1002/cbic.201800660] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2018] [Indexed: 12/16/2022]
Abstract
Plant cryptochromes (CRYs) are blue-light receptors that regulate light-dependent growth, development, and circadian rhythms. A flavin adenine dinucleotide (FAD) cofactor is bound to the photolyase homology region (PHR) of plant CRYs and can be photoreduced to a neutral radical state under blue light. This photoreaction can trigger subsequent signal transduction. Plant CRYs can also bind an ATP molecule adjacent to FAD in a pocket of the PHR. Chlamydomonas reinhardtii contains a single plant CRY, named Chlamydomonas photolyase homologue 1 (CPH1). In CPH1, Cys392 and Asp393 are located near the FAD cofactor. Here we have shown that replacing Cys392 with Ser has little effect on the properties of CPH1. The C392N mutant, however, showed a faster photoreduction rate than wild-type CPH1, together with a significantly lower oxidation rate of the neutral radical state. Substituting an Asn residue for Asp393 in CPH1 improved the binding affinity for FAD as well as the stability of the neutral radical, but photoreduction in the case of this mutant was severely inhibited. In the presence of ATP, CPH1 and its mutants exhibited significantly higher binding affinity for FAD and slower oxidation of the neutral radical. These results reveal that the residues at site 392 and the presence of ATP can tune the stability of the neutral radical, that the Asp residue at site 393 is crucial for photoreduction, and that the photoreduction rate is not determined merely by the stability of the neutral radical in CPH1.
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Affiliation(s)
- Lei Xu
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
| | - Wengui Shao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Pengcheng Yao
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Wei Zheng
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Zhiqiang Zhou
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Yao Zhang
- Anhui Province Key Laboratory of Active Biological Macromolecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, P. R. China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, P. R. China
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14
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Xu L, Wen B, Wang Y, Tian C, Wu M, Zhu G. Residues at a Single Site Differentiate Animal Cryptochromes from Cyclobutane Pyrimidine Dimer Photolyases by Affecting the Proteins' Preferences for Reduced FAD. Chembiochem 2017; 18:1129-1137. [PMID: 28393477 DOI: 10.1002/cbic.201700145] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2017] [Indexed: 12/29/2022]
Abstract
Cryptochromes (CRYs) and photolyases belong to the cryptochrome/photolyase family (CPF). Reduced FAD is essential for photolyases to photorepair UV-induced cyclobutane pyrimidine dimers (CPDs) or 6-4 photoproducts in DNA. In Drosophila CRY (dCRY, a type I animal CRY), FAD is converted to the anionic radical but not to the reduced state upon illumination, which might induce a conformational change in the protein to relay the light signal downstream. To explore the foundation of these differences, multiple sequence alignment of 650 CPF protein sequences was performed. We identified a site facing FAD (Ala377 in Escherichia coli CPD photolyase and Val415 in dCRY), hereafter referred to as "site 377", that was distinctly conserved across these sequences: CPD photolyases often had Ala, Ser, or Asn at this site, whereas animal CRYs had Ile, Leu, or Val. The binding affinity for reduced FAD, but not the photorepair activity of E. coli photolyase, was dramatically impaired when replacing Ala377 with any of the three CRY residues. Conversely, in V415S and V415N mutants of dCRY, FAD was photoreduced to its fully reduced state after prolonged illumination, and light-dependent conformational changes of these mutants were severely inhibited. We speculate that the residues at site 377 play a key role in the different preferences of CPF proteins for reduced FAD, which differentiate animal CRYs from CPD photolyases.
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Affiliation(s)
- Lei Xu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Bin Wen
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Yuan Wang
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Changqing Tian
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
| | - Mingcai Wu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China.,Anhui Province Key Laboratory of Active Biological Macro-Molecules, Wannan Medical College, 22# Wenchang West Road, Wuhu, 241002, Anhui, China
| | - Guoping Zhu
- Institute of Molecular Biology and Biotechnology, Anhui Normal University, 1# Beijing East Road, Wuhu, 241000, Anhui, China
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15
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Schelvis JPM, Gindt YM. A Review of Spectroscopic and Biophysical-Chemical Studies of the Complex of Cyclobutane Pyrimidine Dimer Photolyase and Cryptochrome DASH with Substrate DNA. Photochem Photobiol 2017; 93:26-36. [PMID: 27891613 DOI: 10.1111/php.12678] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2016] [Accepted: 11/02/2016] [Indexed: 01/02/2023]
Abstract
Cyclobutane pyrimidine dimer (CPD) photolyase (PL) is a structure-specific DNA repair enzyme that uses blue light to repair CPD on DNA. Cryptochrome (CRY) DASH enzymes use blue light for the repair of CPD lesions on single-stranded (ss) DNA, although some may also repair these lesions on double-stranded (ds) DNA. In addition, CRY DASH may be involved in blue light signaling, similar to cryptochromes. The focus of this review is on spectroscopic and biophysical-chemical experiments of the enzyme-substrate complex that have contributed to a more detailed understanding of all the aspects of the CPD repair mechanism of CPD photolyase and CRY DASH. This will be performed in the backdrop of the available X-ray crystal structures of these enzymes bound to a CPD-like lesion. These structures helped to confirm conclusions that were drawn earlier from spectroscopic and biophysical-chemical experiments, and they have a critical function as a framework to design new experiments and to interpret new experimental data. This review will show the important synergy between X-ray crystallography and spectroscopic/biophysical-chemical investigations that is essential to obtain a sufficiently detailed picture of the overall mechanism of CPD photolyases and CRY DASH proteins.
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Affiliation(s)
| | - Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, NJ
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16
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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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17
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Gindt YM, Messyasz A, Jumbo PI. Binding of Substrate Locks the Electrochemistry of CRY-DASH into DNA Repair. Biochemistry 2015; 54:2802-5. [PMID: 25910181 DOI: 10.1021/acs.biochem.5b00307] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022]
Abstract
VcCry1, a member of the CRY-DASH family, may serve two diverse roles in vivo, including blue-light signaling and repair of UV-damaged DNA. We have discovered that the electrochemistry of the flavin adenine dinucleotide cofactor of VcCry1 is locked to cycle only between the hydroquinone and neutral semiquinone states when UV-damaged DNA is present. Other potential substrates, including undamaged DNA and ATP, have no discernible effect on the electrochemistry, and the kinetics of the reduction is unaffected by damaged DNA. Binding of the damaged DNA substrate determines the role of the protein and prevents the presumed photochemistry required for blue-light signaling.
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Affiliation(s)
- Yvonne M Gindt
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, United States
| | - Adriana Messyasz
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, United States
| | - Pamela I Jumbo
- Department of Chemistry and Biochemistry, Montclair State University, Montclair, New Jersey 07043, United States
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18
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Paulus B, Bajzath C, Melin F, Heidinger L, Kromm V, Herkersdorf C, Benz U, Mann L, Stehle P, Hellwig P, Weber S, Schleicher E. Spectroscopic characterization of radicals and radical pairs in fruit fly cryptochrome - protonated and nonprotonated flavin radical-states. FEBS J 2015; 282:3175-89. [PMID: 25879256 DOI: 10.1111/febs.13299] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2014] [Revised: 03/21/2015] [Accepted: 04/14/2015] [Indexed: 01/05/2023]
Abstract
Drosophila melanogaster cryptochrome is one of the model proteins for animal blue-light photoreceptors. Using time-resolved and steady-state optical spectroscopy, we studied the mechanism of light-induced radical-pair formation and decay, and the photoreduction of the FAD cofactor. Exact kinetics on a microsecond to minutes timescale could be extracted for the wild-type protein using global analysis. The wild-type exhibits a fast photoreduction reaction from the oxidized FAD to the FAD(•-) state with a very positive midpoint potential of ~ +125 mV, although no further reduction could be observed. We could also demonstrate that the terminal tryptophan of the conserved triad, W342, is directly involved in electron transfer; however, photoreduction could not be completely inhibited in a W342F mutant. The investigation of another mutation close to the FAD cofactor, C416N, rather unexpectedly reveals accumulation of a protonated flavin radical on a timescale of several seconds. The obtained data are critically discussed with the ones obtained from another protein, Escherichia coli photolyase, and we conclude that the amino acid opposite N(5) of the isoalloxazine moiety of FAD is able to (de)stabilize the protonated FAD radical but not to significantly modulate the kinetics of any light-inducted reactions.
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Affiliation(s)
- Bernd Paulus
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Csaba Bajzath
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Frédéric Melin
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Lorenz Heidinger
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Viktoria Kromm
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | | | - Ulrike Benz
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Lisa Mann
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Patricia Stehle
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Petra Hellwig
- Laboratoire de Bioélectrochimie et Spectroscopie Université de Strasbourg, France
| | - Stefan Weber
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
| | - Erik Schleicher
- Institut für Physikalische Chemie, Albert-Ludwigs-Universität Freiburg, Germany
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19
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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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20
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Hense A, Herman E, Oldemeyer S, Kottke T. Proton transfer to flavin stabilizes the signaling state of the blue light receptor plant cryptochrome. J Biol Chem 2014; 290:1743-51. [PMID: 25471375 DOI: 10.1074/jbc.m114.606327] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Plant cryptochromes regulate the circadian rhythm, flowering time, and photomorphogenesis in higher plants as responses to blue light. In the dark, these photoreceptors bind oxidized FAD in the photolyase homology region (PHR). Upon blue light absorption, FAD is converted to the neutral radical state, the likely signaling state, by electron transfer via a conserved tryptophan triad and proton transfer from a nearby aspartic acid. Here we demonstrate, by infrared and time-resolved UV-visible spectroscopy on the PHR domain, that replacement of the aspartic acid Asp-396 with cysteine prevents proton transfer. The lifetime of the radical is decreased by 6 orders of magnitude. This short lifetime does not permit to drive conformational changes in the C-terminal extension that have been associated with signal transduction. Only in the presence of ATP do both the wild type and mutant form a long-lived radical state. However, in the mutant, an anion radical is formed instead of the neutral radical, as found previously in animal type I cryptochromes. Infrared spectroscopic experiments demonstrate that the light-induced conformational changes of the PHR domain are conserved in the mutant despite the lack of proton transfer. These changes are not detected in the photoreduction of the non-photosensory d-amino acid oxidase to the anion radical. In conclusion, formation of the anion radical is sufficient to generate a protein response in plant cryptochromes. Moreover, the intrinsic proton transfer is required for stabilization of the signaling state in the absence of ATP.
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Affiliation(s)
- Anika Hense
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Elena Herman
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Sabine Oldemeyer
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
| | - Tilman Kottke
- From the Physical and Biophysical Chemistry, Department of Chemistry, Bielefeld University, Universitätsstrasse 25, 33615 Bielefeld, Germany
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21
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Müller P, Bouly JP, Hitomi K, Balland V, Getzoff ED, Ritz T, Brettel K. ATP binding turns plant cryptochrome into an efficient natural photoswitch. Sci Rep 2014; 4:5175. [PMID: 24898692 PMCID: PMC4046262 DOI: 10.1038/srep05175] [Citation(s) in RCA: 70] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2014] [Accepted: 04/14/2014] [Indexed: 12/30/2022] Open
Abstract
Cryptochromes are flavoproteins that drive diverse developmental light-responses in plants and participate in the circadian clock in animals. Plant cryptochromes have found application as photoswitches in optogenetics. We have studied effects of pH and ATP on the functionally relevant photoreduction of the oxidized FAD cofactor to the semi-reduced FADH· radical in isolated Arabidopsis cryptochrome 1 by transient absorption spectroscopy on nanosecond to millisecond timescales. In the absence of ATP, the yield of light-induced radicals strongly decreased with increasing pH from 6.5 to 8.5. With ATP present, these yields were significantly higher and virtually pH-independent up to pH 9. Analysis of our data in light of the crystallographic structure suggests that ATP-binding shifts the pKa of aspartic acid D396, the putative proton donor to FAD·−, from ~7.4 to >9, and favours a reaction pathway yielding long-lived aspartate D396−. Its negative charge could trigger conformational changes necessary for signal transduction.
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Affiliation(s)
- Pavel Müller
- 1] UMR-8221, CEA-Institut de Biologie et de Technologie de Saclay, CNRS, Université Paris Sud, 91191 Gif-sur-Yvette, France [2] UR 5, Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie, CNRS, 75005 Paris 6, France
| | - Jean-Pierre Bouly
- 1] UR 5, Physiologie Cellulaire et Moléculaire des Plantes, Université Pierre et Marie Curie, CNRS, 75005 Paris 6, France [2] Department of Physics and Astronomy, University of California, Irvine, California 92697, USA [3]
| | - Kenichi Hitomi
- 1] Department of Integrative Structural and Computational Biology and The Skaggs Institute for Chemical Biology, The Scripps Research Institute, La Jolla, California 92037, USA [2]
| | - Véronique Balland
- UMR CNRS 7591, Laboratoire d'Electrochimie Moléculaire, Université Paris Diderot, Sorbonne Paris Cité, 75205 Paris 13, France
| | - 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, USA
| | - Thorsten Ritz
- Department of Physics and Astronomy, University of California, Irvine, California 92697, USA
| | - Klaus Brettel
- UMR-8221, CEA-Institut de Biologie et de Technologie de Saclay, CNRS, Université Paris Sud, 91191 Gif-sur-Yvette, France
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22
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Dodson CA, Hore PJ, Wallace MI. A radical sense of direction: signalling and mechanism in cryptochrome magnetoreception. Trends Biochem Sci 2013; 38:435-46. [PMID: 23938034 DOI: 10.1016/j.tibs.2013.07.002] [Citation(s) in RCA: 83] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 10/26/2022]
Abstract
The remarkable phenomenon of magnetoreception in migratory birds and other organisms has fascinated biologists for decades. Much evidence has accumulated to suggest that birds sense the magnetic field of the Earth using photochemical transformations in cryptochrome flavoproteins. In the last 5 years this highly interdisciplinary field has seen advances in structural biology, biophysics, spin chemistry, and genetic studies in model organisms. We review these developments and consider how this chemical signal can be integrated into the cellular response.
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Affiliation(s)
- Charlotte A Dodson
- Department of Chemistry, University of Oxford, Chemistry Research Laboratory, 12 Mansfield Road, Oxford OX1 3TA, UK.
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23
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Cotruvo JA, Stich TA, Britt RD, Stubbe J. Mechanism of assembly of the dimanganese-tyrosyl radical cofactor of class Ib ribonucleotide reductase: enzymatic generation of superoxide is required for tyrosine oxidation via a Mn(III)Mn(IV) intermediate. J Am Chem Soc 2013; 135:4027-39. [PMID: 23402532 DOI: 10.1021/ja312457t] [Citation(s) in RCA: 81] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Ribonucleotide reductases (RNRs) utilize radical chemistry to reduce nucleotides to deoxynucleotides in all organisms. In the class Ia and Ib RNRs, this reaction requires a stable tyrosyl radical (Y(•)) generated by oxidation of a reduced dinuclear metal cluster. The Fe(III)2-Y(•) cofactor in the NrdB subunit of the class Ia RNRs can be generated by self-assembly from Fe(II)2-NrdB, O2, and a reducing equivalent. By contrast, the structurally homologous class Ib enzymes require a Mn(III)2-Y(•) cofactor in their NrdF subunit. Mn(II)2-NrdF does not react with O2, but it binds the reduced form of a conserved flavodoxin-like protein, NrdIhq, which, in the presence of O2, reacts to form the Mn(III)2-Y(•) cofactor. Here we investigate the mechanism of assembly of the Mn(III)2-Y(•) cofactor in Bacillus subtilis NrdF. Cluster assembly from Mn(II)2-NrdF, NrdI(hq), and O2 has been studied by stopped flow absorption and rapid freeze quench EPR spectroscopies. The results support a mechanism in which NrdI(hq) reduces O2 to O2(•-) (40-48 s(-1), 0.6 mM O2), the O2(•-) channels to and reacts with Mn(II)2-NrdF to form a Mn(III)Mn(IV) intermediate (2.2 ± 0.4 s(-1)), and the Mn(III)Mn(IV) species oxidizes tyrosine to Y(•) (0.08-0.15 s(-1)). Controlled production of O2(•-) by NrdIhq during class Ib RNR cofactor assembly both circumvents the unreactivity of the Mn(II)2 cluster with O2 and satisfies the requirement for an "extra" reducing equivalent in Y(•) generation.
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Affiliation(s)
- Joseph A Cotruvo
- Department of Chemistry, Massachusetts Institute of Technology, 77 Massachusetts Avenue, Cambridge, Massachusetts 02139, USA
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Iyanagi T, Xia C, Kim JJP. NADPH-cytochrome P450 oxidoreductase: prototypic member of the diflavin reductase family. Arch Biochem Biophys 2012; 528:72-89. [PMID: 22982532 PMCID: PMC3606592 DOI: 10.1016/j.abb.2012.09.002] [Citation(s) in RCA: 88] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2012] [Revised: 09/01/2012] [Accepted: 09/03/2012] [Indexed: 12/31/2022]
Abstract
NADPH-cytochrome P450 oxidoreductase (CYPOR) and nitric oxide synthase (NOS), two members of the diflavin oxidoreductase family, are multi-domain enzymes containing distinct FAD and FMN domains connected by a flexible hinge. FAD accepts a hydride ion from NADPH, and reduced FAD donates electrons to FMN, which in turn transfers electrons to the heme center of cytochrome P450 or NOS oxygenase domain. Structural analysis of CYPOR, the prototype of this enzyme family, has revealed the exact nature of the domain arrangement and the role of residues involved in cofactor binding. Recent structural and biophysical studies of CYPOR have shown that the two flavin domains undergo large domain movements during catalysis. NOS isoforms contain additional regulatory elements within the reductase domain that control electron transfer through Ca(2+)-dependent calmodulin (CaM) binding. The recent crystal structure of an iNOS Ca(2+)/CaM-FMN construct, containing the FMN domain in complex with Ca(2+)/CaM, provided structural information on the linkage between the reductase and oxgenase domains of NOS, making it possible to model the holo iNOS structure. This review summarizes recent advances in our understanding of the dynamics of domain movements during CYPOR catalysis and the role of the NOS diflavin reductase domain in the regulation of NOS isozyme activities.
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Affiliation(s)
- Takashi Iyanagi
- Department of Biochemistry, Medical College of Wisconsin, USA
- Department of Life Science, The Himeji Institute of Technology, University of Hyogo, Japan
| | - Chuanwu Xia
- Department of Biochemistry, Medical College of Wisconsin, USA
| | - Jung-Ja P. Kim
- Department of Biochemistry, Medical College of Wisconsin, USA
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Losi A, Gärtner W. The evolution of flavin-binding photoreceptors: an ancient chromophore serving trendy blue-light sensors. ANNUAL REVIEW OF PLANT BIOLOGY 2012; 63:49-72. [PMID: 22136567 DOI: 10.1146/annurev-arplant-042811-105538] [Citation(s) in RCA: 140] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Photoreceptor flavoproteins of the LOV, BLUF, and cryptochrome families are ubiquitous among the three domains of life and are configured as UVA/blue-light systems not only in plants-their original arena-but also in prokaryotes and microscopic algae. Here, we review these proteins' structure and function, their biological roles, and their evolution and impact in the living world, and underline their growing application in biotechnologies. We present novel developments such as the interplay of light and redox stimuli, emerging enzymatic and biological functions, lessons on evolution from picoalgae, metagenomics analysis, and optogenetics applications.
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Affiliation(s)
- Aba Losi
- Department of Physics, University of Parma, Parma, Italy.
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