1
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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Avian cryptochrome 4 binds superoxide. Comput Struct Biotechnol J 2024; 26:11-21. [PMID: 38204818 PMCID: PMC10776438 DOI: 10.1016/j.csbj.2023.12.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/06/2023] [Accepted: 12/12/2023] [Indexed: 01/12/2024] Open
Abstract
Flavin-binding cryptochromes are blue-light sensitive photoreceptors that have been implicated with magnetoreception in some species. The photocycle involves an intra-protein photo-reduction of the flavin cofactor, generating a magnetosensitive radical pair, and its subsequent re-oxidation. Superoxide (O2 • - ) is generated in the re-oxidation with molecular oxygen. The resulting O2 • - -containing radical pairs have also been hypothesised to underpin various magnetosensitive traits, but due to fast spin relaxation when tumbling in solution would require immobilisation. We here describe our insights in the binding of superoxide to cryptochrome 4 from C. livia based on extensive all-atom molecular dynamics studies and density-functional theory calculations. The positively charged "crypt" region that leads to the flavin binding pocket transiently binds O2 • - at 5 flexible binding sites centred on arginine residues. Typical binding times amounted to tens of nanoseconds, but exceptional binding events extended to several hundreds of nanoseconds and slowed the rotational diffusion, thereby realising rotational correlation times as large as 1 ns. The binding sites are particularly efficient in scavenging superoxide escaping from a putative generation site close to the flavin-cofactor, possibly implying a functional relevance. We discuss our findings in view of a potential magnetosensitivity of biological flavin semiquinone/superoxide radical pairs.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France
| | - Daniel R. Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, United Kingdom
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2
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Kretschmer K, Frederiksen A, Reinholdt P, Kongsted J, Solov’yov IA. Understanding the Red Shift in the Absorption Spectrum of the FAD Cofactor in ClCry4 Protein. J Phys Chem B 2024; 128:5320-5326. [PMID: 38805723 PMCID: PMC11163422 DOI: 10.1021/acs.jpcb.4c00710] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2024] [Revised: 05/03/2024] [Accepted: 05/16/2024] [Indexed: 05/30/2024]
Abstract
It is still a puzzle that has not been entirely solved how migratory birds utilize the Earth's magnetic field for biannual migration. The most consistent explanation thus far is rooted in the modulation of the biological function of the cryptochrome 4 (Cry4) protein by an external magnetic field. This phenomenon is closely linked with the flavin adenine dinucleotide (FAD) cofactor that is noncovalently bound in the protein. Cry4 is activated by blue light, which is absorbed by the FAD cofactor. Subsequent electron and proton transfers trigger radical pair formation in the protein, which is sensitive to the external magnetic field. An important long-lasting redox state of the FAD cofactor is the signaling (FADH•) state, which is present after the transient electron transfer steps have been completed. Recent experimental efforts succeeded in crystallizing the Cry4 protein from Columbia livia (ClCry4) with all of the important residues needed for protein photoreduction. This specific crystallization of Cry4 protein so far is the only avian cryptochrome crystal structure available, which, however, has great similarity to the Cry4 proteins of night migratory birds. The previous experimental studies of the ClCry4 protein included the absorption properties of the protein in its different redox states. The absorption spectrum of the FADH• state demonstrated a peculiar red shift compared to the photoabsorption properties of the FAD cofactor in its FADH• state in other Cry proteins from other species. The aim of this study is to understand this red shift by employing the tools of computational microscopy and, in particular, a QM/MM approach that relies on the polarizable embedding approximation.
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Affiliation(s)
- Katarina Kretschmer
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Str. 9-11, 26129 Oldenburg, Germany
| | - Anders Frederiksen
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Str. 9-11, 26129 Oldenburg, Germany
| | - Peter Reinholdt
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK 5230 Odense, Denmark
| | - Jacob Kongsted
- Department of Physics, Chemistry and Pharmacy, University of Southern Denmark, DK 5230 Odense, Denmark
| | - Ilia A. Solov’yov
- Institute of Physics, Carl von Ossietzky Universität Oldenburg, Carl-von-Ossietzky Str. 9-11, 26129 Oldenburg, Germany
- Research Centre for Neurosensory
Science, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky
Str. 9-11, 26129 Oldenburg, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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3
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Laurien M, Mende L, Luhrmann L, Frederiksen A, Aldag M, Spiecker L, Clemmesen C, Solov'yov IA, Gerlach G. Magnetic orientation in juvenile Atlantic herring ( Clupea harengus) could involve cryptochrome 4 as a potential magnetoreceptor. J R Soc Interface 2024; 21:20240035. [PMID: 38835248 DOI: 10.1098/rsif.2024.0035] [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: 01/18/2024] [Accepted: 04/08/2024] [Indexed: 06/06/2024] Open
Abstract
The Earth's magnetic field can provide reliable directional information, allowing migrating animals to orient themselves using a magnetic compass or estimate their position relative to a target using map-based orientation. Here we show for the first time that young, inexperienced herring (Clupea harengus, Ch) have a magnetic compass when they migrate hundreds of kilometres to their feeding grounds. In birds, such as the European robin (Erithacus rubecula), radical pair-based magnetoreception involving cryptochrome 4 (ErCRY4) was demonstrated; the molecular basis of magnetoreception in fish is still elusive. We show that cry4 expression in the eye of herring is upregulated during the migratory season, but not before, indicating a possible use for migration. The amino acid structure of herring ChCRY4 shows four tryptophans and a flavin adenine dinucleotide-binding site, a prerequisite for a magnetic receptor. Using homology modelling, we successfully reconstructed ChCRY4 of herring, DrCRY4 of zebrafish (Danio rerio) and StCRY4 of brown trout (Salmo trutta) and showed that ChCRY4, DrCRY4 and ErCRY4a, but not StCRY4, exhibit very comparable dynamic behaviour. The electron transfer could take place in ChCRY4 in a similar way to ErCRY4a. The combined behavioural, transcriptomic and simulation experiments provide evidence that CRY4 could act as a magnetoreceptor in Atlantic herring.
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Affiliation(s)
- Malien Laurien
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lara Mende
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lena Luhrmann
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Anders Frederiksen
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Mandus Aldag
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Lisa Spiecker
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Catriona Clemmesen
- Marine Evolutionary Ecology, GEOMAR Helmholtz Centre for Ocean Research Kiel , Kiel 24105, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
| | - Gabriele Gerlach
- Institute of Biology and Environmental Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg , Oldenburg 26111, Germany
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4
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Schuhmann F, Ramsay JL, Kattnig DR, Solov’yov IA. Structural Rearrangements of Pigeon Cryptochrome 4 Undergoing a Complete Redox Cycle. J Phys Chem B 2024; 128:3844-3855. [PMID: 38568745 PMCID: PMC11056986 DOI: 10.1021/acs.jpcb.4c00424] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2024] [Revised: 03/04/2024] [Accepted: 03/11/2024] [Indexed: 04/26/2024]
Abstract
Cryptochrome is currently the major contender of a protein to underpin magnetoreception, the ability to sense the Earth's magnetic field. Among various types of cryptochromes, cryptochrome 4 has been identified as the likely magnetoreceptor in migratory birds. All-atom molecular dynamics (MD) studies have offered first insights into the structural dynamics of cryptochrome but are limited to a short time scale due to large computational demands. Here, we employ coarse-grained MD simulations to investigate the emergence of long-lived states and conformational changes in pigeon cryptochrome 4. Our coarse-grained simulations complete the picture by permitting observation on a significantly longer time scale. We observe conformational transitions in the phosphate-binding loop of pigeon cryptochrome 4 upon activation and identify prominent motions in residues 440-460, suggesting a possible role as a signaling state of the protein or as a gated interaction site for forming protein complexes that might facilitate downstream processes. The findings highlight the importance of considering longer time scales in studying cryptochrome dynamics and magnetoreception. Coarse-grained MD simulations offer a valuable tool to unravel the complex behavior of cryptochrome proteins and shed new light on the mechanisms underlying their role in magnetoreception. Further exploration of these conformational changes and their functional implications may contribute to a deeper understanding of the molecular mechanisms of magnetoreception in birds.
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Affiliation(s)
- Fabian Schuhmann
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
- Niels
Bohr International Academy, Niels Bohr Institute, University of Copenhagen, Blegdamsvej 17, Copenhagen 2100, Denmark
| | - Jessica L. Ramsay
- Living
Systems Institute and Department of Physics, University of Exeter, Stocker Rd., Exeter EX4
4QD, U.K.
| | - Daniel R. Kattnig
- Living
Systems Institute and Department of Physics, University of Exeter, Stocker Rd., Exeter EX4
4QD, U.K.
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Str. 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Science, Carl von
Ossietzky Universität Oldenburg, Carl-von-Ossietzky-Str. 9-11, Oldenburg 26129, Germany
- Center
for Nanoscale Dynamics (CENAD), Carl von
Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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5
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Frederiksen A, Aldag M, Solov’yov IA, Gerhards L. Activation of Cryptochrome 4 from Atlantic Herring. BIOLOGY 2024; 13:262. [PMID: 38666874 PMCID: PMC11048568 DOI: 10.3390/biology13040262] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/15/2024] [Revised: 04/04/2024] [Accepted: 04/11/2024] [Indexed: 04/28/2024]
Abstract
Marine fish migrate long distances up to hundreds or even thousands of kilometers for various reasons that include seasonal dependencies, feeding, or reproduction. The ability to perceive the geomagnetic field, called magnetoreception, is one of the many mechanisms allowing some fish to navigate reliably in the aquatic realm. While it is believed that the photoreceptor protein cryptochrome 4 (Cry4) is the key component for the radical pair-based magnetoreception mechanism in night migratory songbirds, the Cry4 mechanism in fish is still largely unexplored. The present study aims to investigate properties of the fish Cry4 protein in order to understand the potential involvement in a radical pair-based magnetoreception. Specifically, a computationally reconstructed atomistic model of Cry4 from the Atlantic herring (Clupea harengus) was studied employing classical molecular dynamics (MD) and quantum mechanics/molecular mechanics (QM/MM) methods to investigate internal electron transfers and the radical pair formation. The QM/MM simulations reveal that electron transfers occur similarly to those found experimentally and computationally in Cry4 from European robin (Erithacus rubecula). It is therefore plausible that the investigated Atlantic herring Cry4 has the physical and chemical properties to form radical pairs that in turn could provide fish with a radical pair-based magnetic field compass sensor.
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Affiliation(s)
- Anders Frederiksen
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Mandus Aldag
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
| | - Ilia A. Solov’yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
- Research Centre for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129 Oldenburg, Germany; (A.F.); (M.A.); (I.A.S.)
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6
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Saft M, Schneider L, Ho CC, Maiterth E, Menke J, Sendker F, Steinchen W, Essen LO. One More for Light-triggered Conformational Changes in Cryptochromes: CryP from Phaeodactylum tricornutum. J Mol Biol 2024; 436:168408. [PMID: 38123123 DOI: 10.1016/j.jmb.2023.168408] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2023] [Revised: 12/01/2023] [Accepted: 12/14/2023] [Indexed: 12/23/2023]
Abstract
Cryptochromes are a ubiquitously occurring class of photoreceptors. Together with photolyases, they form the Photolyase Cryptochrome Superfamily (PCSf) by sharing a common protein architecture and binding mode of the FAD chromophore. Despite these similarities, PCSf members exert different functions. Photolyases repair UV-induced DNA damage by photocatalytically driven electron transfer between FADH¯ and the DNA lesion, whereas cryptochromes are light-dependent signaling molecules and trigger various biological processes by photoconversion of their FAD redox and charge states. Given that most cryptochromes possess a C-terminal extension (CTE) of varying length, the functions of their CTE have not yet been fully elucidated and are hence highly debated. In this study, the role of the CTE was investigated for a novel subclass of the PCSf, the CryP-like cryptochromes, by hydrogen/deuterium exchange and mass-spectrometric analysis. Striking differences in the relative deuterium uptake were observed in different redox states of CryP from the diatom Phaeodactylum tricornutum. Based on these measurements we propose a model for light-triggered conformational changes in CryP-like cryptochromes that differs from other known cryptochrome families like the insect or plant cryptochromes.
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Affiliation(s)
- Martin Saft
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Leonie Schneider
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Chun-Chih Ho
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Elias Maiterth
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Josephine Menke
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany
| | - Franziska Sendker
- Evolutionary Biochemistry Group, Max Planck Institute for Terrestrial Microbiology, 35043 Marburg, Germany
| | - Wieland Steinchen
- Center of Synthetic Microbiology (SYNMIKRO), Philipps University Marburg, 35032 Marburg, Germany
| | - Lars-Oliver Essen
- Department of Chemistry, Philipps University Marburg, 35032 Marburg, Germany.
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7
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Luo J. Sensitivity enhancement of radical-pair magnetoreceptors as a result of spin decoherence. J Chem Phys 2024; 160:074306. [PMID: 38380753 DOI: 10.1063/5.0182172] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2023] [Accepted: 01/15/2024] [Indexed: 02/22/2024] Open
Abstract
Electron spin relaxation is, on many occasions, considered an elephant in the room that challenges the idea of a radical-pair compass, a leading hypothesis for the navigation of migratory avian species. It has been widely recognized that an effective radical-pair magnetoreceptor requires a relaxation time that is long enough for an external magnetic field as weak as the geomagnetic field to significantly modify the coherent spin dynamics. However, previous studies proposed that certain spin relaxation, far quicker than the radical recombination reactions, could enhance, rather than degrade, the directional sensitivity of a radical-pair magnetoreceptor. Here, I investigate relaxation effects on the singlet-triplet interconversion of a model radical pair and find that the enhancement effect originates from population relaxation over a period of several microseconds as a result of efficient spin decoherence. Insights into the truncated spin systems shed light on the physics behind them. I further investigate the possibilities of such enhancement in cryptochrome-based magnetoreception, in which electron hopping takes place between tryptophan residues.
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Affiliation(s)
- Jiate Luo
- Physical and Theoretical Chemistry Laboratory, Department of Chemistry, University of Oxford, South Parks Road, Oxford OX1 3QZ, United Kingdom
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8
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Langebrake C, Manthey G, Frederiksen A, Lugo Ramos JS, Dutheil JY, Chetverikova R, Solov'yov IA, Mouritsen H, Liedvogel M. Adaptive evolution and loss of a putative magnetoreceptor in passerines. Proc Biol Sci 2024; 291:20232308. [PMID: 38320616 PMCID: PMC10846946 DOI: 10.1098/rspb.2023.2308] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 01/08/2024] [Indexed: 02/08/2024] Open
Abstract
Migratory birds possess remarkable accuracy in orientation and navigation, which involves various compass systems including the magnetic compass. Identifying the primary magnetosensor remains a fundamental open question. Cryptochromes (Cry) have been shown to be magnetically sensitive, and Cry4a from a migratory songbird seems to show enhanced magnetic sensitivity in vitro compared to Cry4a from resident species. We investigate Cry and their potential involvement in magnetoreception in a phylogenetic framework, integrating molecular evolutionary analyses with protein dynamics modelling. Our analysis is based on 363 bird genomes and identifies different selection regimes in passerines. We show that Cry4a is characterized by strong positive selection and high variability, typical characteristics of sensor proteins. We identify key sites that are likely to have facilitated the evolution of an optimized sensory protein for night-time orientation in songbirds. Additionally, we show that Cry4 was lost in hummingbirds, parrots and Tyranni (Suboscines), and thus identified a gene deletion, which might facilitate testing the function of Cry4a in birds. In contrast, the other avian Cry (Cry1 and Cry2) were highly conserved across all species, indicating basal, non-sensory functions. Our results support a specialization or functional differentiation of Cry4 in songbirds which could be magnetosensation.
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Affiliation(s)
- Corinna Langebrake
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Georg Manthey
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Juan S. Lugo Ramos
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- The Francis Crick Institute, London NW1 1AT, UK
| | - Julien Y. Dutheil
- Research Group Molecular Systems Evolution, MPI Evolutionary Biology, 24306 Plön, Germany
| | - Raisa Chetverikova
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Ilia A. Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Henrik Mouritsen
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
- Research Centre for Neurosensory Sciences, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
| | - Miriam Liedvogel
- Institute of Avian Research ‘Vogelwarte Helgoland’, 26386 Wilhelmshaven, Germany
- MPRG Behavioural Genomics, MPI Evolutionary Biology, 24306 Plön, Germany
- Biology and Environmental Sciences Department, Carl von Ossietzky Universität Oldenburg, 26129 Oldenburg
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9
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Mat A, Vu HH, Wolf E, Tessmar-Raible K. All Light, Everywhere? Photoreceptors at Nonconventional Sites. Physiology (Bethesda) 2024; 39:0. [PMID: 37905983 DOI: 10.1152/physiol.00017.2023] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2023] [Revised: 10/29/2023] [Accepted: 10/29/2023] [Indexed: 11/02/2023] Open
Abstract
One of the biggest environmental alterations we have made to our species is the change in the exposure to light. During the day, we typically sit behind glass windows illuminated by artificial light that is >400 times dimmer and has a very different spectrum than natural daylight. On the opposite end are the nights that are now lit up by several orders of magnitude. This review aims to provide food for thought as to why this matters for humans and other animals. Evidence from behavioral neuroscience, physiology, chronobiology, and molecular biology is increasingly converging on the conclusions that the biological nonvisual functions of light and photosensory molecules are highly complex. The initial work of von Frisch on extraocular photoreceptors in fish, the identification of rhodopsins as the molecular light receptors in animal eyes and eye-like structures and cryptochromes as light sensors in nonmammalian chronobiology, still allowed for the impression that light reception would be a relatively restricted, localized sense in most animals. However, light-sensitive processes and/or sensory proteins have now been localized to many different cell types and tissues. It might be necessary to consider nonlight-responding cells as the exception, rather than the rule.
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Affiliation(s)
- Audrey Mat
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- VIPS2, Vienna BioCenter, Vienna, Austria
| | - Hong Ha Vu
- Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
| | - Eva Wolf
- Institute of Molecular Physiology, Johannes Gutenberg-University, Mainz, Germany
- Institute of Molecular Biology, Mainz, Germany
| | - Kristin Tessmar-Raible
- Max Perutz Labs, University of Vienna, Vienna BioCenter, Vienna, Austria
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
- Carl-von-Ossietzky University, Oldenburg, Germany
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10
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Li N, Wang P, Xie Y, Wang B, Zhu C, Xue L, Han X, Gu N, Sun J. Expression of clMagR/clCry4 protein in mBMSCs provides T 2-contrast enhancement of MRI. Acta Biomater 2023; 172:309-320. [PMID: 37778484 DOI: 10.1016/j.actbio.2023.09.039] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2023] [Revised: 09/16/2023] [Accepted: 09/25/2023] [Indexed: 10/03/2023]
Abstract
Here, we propose for the first time the evaluation of magnetosensitive clMagR/clCry4 as a magnetic resonance imaging (MRI) reporter gene that imparts sensitivity to endogenous contrast in eukaryotic organisms. Using a lentiviral vector, we introduced clMagR/clCry4 into C57BL/6 mice-derived bone marrow mesenchymal stem cells (mBMSCs), which could specifically bind with iron, significantly affected MRI transverse relaxation, and generated readily detectable contrast without adverse effects in vivo. Specifically, clMagR/clCry4 makes mBMSCs beneficial for enhancing the sensitivity of MRI-R2 for iron-bearing granules, in which cells recruit exogenous iron and convert these stores into an MRI-detectable contrast; this is not achievable with control cells. Additionally, Prussian blue staining was performed together with ultrathin cell slices to provide direct evidence of natural iron-bearing granules being detectable on MRI. Hence, it was inferred that the sensitivity of MRI detection should be correlated with clMagR/clCry4 and exogenous iron. Taken together, the clMagR/clCry4 has great potential as an MRI reporter gene. STATEMENT OF SIGNIFICANCE: In this study, we propose the evaluation of magnetosensitive clMagR/clCry4 as an MRI reporter gene, imparting detection sensitivity to eukaryotic mBMSCs for endogenous contrast. At this point, the clMagR and clCry4 were located within the cytoplasm and possibly influence each other. The clMagR/clCry4 makes mBMSCs beneficial for enhancing the sensitivity of MRI-R2 for iron-bearing granules, in which protein could specifically bind with iron and convert these stores into MRI-detectable contrast; this is not achieved by control cells. The viewpoint was speculated that the clMagR/clCry4 and exogenous iron were complementary to each other. Additionally, Prussian blue staining was performed together with TEM observations to provide direct evidence that the iron-bearing granules were sensitive to MRI.
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Affiliation(s)
- Nuan Li
- Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Peng Wang
- Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China; Department of Sports Medicine and Adult Reconstructive Surgery, the Affiliated Drum Tower Hospital of Nanjing University, Nanjing 210008, China
| | - Yuanyuan Xie
- Clinical Stem Cell Center, the Affiliated Drum Tower Hospital of Nanjing University, Nanjing 210008, China
| | - Bin Wang
- Clinical Stem Cell Center, the Affiliated Drum Tower Hospital of Nanjing University, Nanjing 210008, China
| | - Chenzhuo Zhu
- Southeast University-Monash University Joint Graduate School, Southeast University, Suzhou 215123, China
| | - Le Xue
- Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Xiaofeng Han
- School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China
| | - Ning Gu
- Medical School, Nanjing University, Nanjing 210093, China
| | - Jianfei Sun
- Jiangsu Key Laboratory of Biomaterials and Devices, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing 210096, China.
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11
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Muheim R, Phillips JB. Effects of low-level RF fields reveal complex pattern of magnetic input to the avian magnetic compass. Sci Rep 2023; 13:19970. [PMID: 37968316 PMCID: PMC10651899 DOI: 10.1038/s41598-023-46547-5] [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: 08/28/2023] [Accepted: 11/02/2023] [Indexed: 11/17/2023] Open
Abstract
The avian magnetic compass can be disrupted by weak narrow-band and broadband radio-frequency (RF) fields in the lower MHz range. However, it is unclear whether disruption of the magnetic compass results from the elimination of the perception pattern produced by the magnetic field or from qualitative changes that make the pattern unrecognizable. We show that zebra finches trained in a 4-arm maze to orient relative to the magnetic field are disoriented when tested in the presence of low-level (~ 10 nT) Larmor-frequency RF fields. However, they are able to orient when tested in such RF fields if trained under this condition, indicating that the RF field alters, but does not eliminate, the magnetic input. Larmor-frequency RF fields of higher intensities, with or without harmonics, dramatically alter the magnetic compass response. In contrast, exposure to broadband RF fields in training, in testing, or in both training and testing eliminates magnetic compass information. These findings demonstrate that low-level RF fields at intensities found in many laboratory and field experiments may have very different effects on the perception of the magnetic field in birds, depending on the type and intensity of the RF field, and the birds' familiarity with the RF-generated pattern.
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Affiliation(s)
- Rachel Muheim
- Department of Biology, Lund University, Biology Building, 223 62, Lund, Sweden.
| | - John B Phillips
- Department of Biological Sciences, Virginia Tech, Blacksburg, VA, 24061-0406, USA
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12
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Vu HH, Behrmann H, Hanić M, Jeyasankar G, Krishnan S, Dannecker D, Hammer C, Gunkel M, Solov'yov IA, Wolf E, Behrmann E. A marine cryptochrome with an inverse photo-oligomerization mechanism. Nat Commun 2023; 14:6918. [PMID: 37903809 PMCID: PMC10616196 DOI: 10.1038/s41467-023-42708-2] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2023] [Accepted: 10/19/2023] [Indexed: 11/01/2023] Open
Abstract
Cryptochromes (CRYs) are a structurally conserved but functionally diverse family of proteins that can confer unique sensory properties to organisms. In the marine bristle worm Platynereis dumerilii, its light receptive cryptochrome L-CRY (PdLCry) allows the animal to discriminate between sunlight and moonlight, an important requirement for synchronizing its lunar cycle-dependent mass spawning. Using cryo-electron microscopy, we show that in the dark, PdLCry adopts a dimer arrangement observed neither in plant nor insect CRYs. Intense illumination disassembles the dimer into monomers. Structural and functional data suggest a mechanistic coupling between the light-sensing flavin adenine dinucleotide chromophore, the dimer interface, and the C-terminal tail helix, with a likely involvement of the phosphate binding loop. Taken together, our work establishes PdLCry as a CRY protein with inverse photo-oligomerization with respect to plant CRYs, and provides molecular insights into how this protein might help discriminating the different light intensities associated with sunlight and moonlight.
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Affiliation(s)
- Hong Ha Vu
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Heide Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
| | - Gayathri Jeyasankar
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Shruthi Krishnan
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Dennis Dannecker
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Constantin Hammer
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany
| | - Monika Gunkel
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26129, Oldenburg, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, 26111, Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, 26129, Oldenburg, Germany
| | - Eva Wolf
- Institute of Molecular Physiology (IMP), Johannes Gutenberg-University Mainz, Hanns-Dieter-Hüsch-Weg 17, 55128, Mainz, Germany.
- Institute of Molecular Biology (IMB), 55128, Mainz, Germany.
| | - Elmar Behrmann
- University of Cologne, Faculty of Mathematics and Natural Sciences, Institute of Biochemistry, Zülpicher Straße 47, 50674, Cologne, Germany.
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13
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Golesworthy MJ, Zollitsch T, Luo J, Selby D, Jarocha LE, Henbest KB, Paré-Labrosse O, Bartölke R, Schmidt J, Xu J, Mouritsen H, Hore PJ, Timmel CR, Mackenzie SR. Singlet-triplet dephasing in radical pairs in avian cryptochromes leads to time-dependent magnetic field effects. J Chem Phys 2023; 159:105102. [PMID: 37694754 DOI: 10.1063/5.0166675] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2023] [Accepted: 08/21/2023] [Indexed: 09/12/2023] Open
Abstract
Cryptochrome 4a (Cry4a) has been proposed as the sensor at the heart of the magnetic compass in migratory songbirds. Blue-light excitation of this protein produces magnetically sensitive flavin-tryptophan radical pairs whose properties suggest that Cry4a could indeed be suitable as a magnetoreceptor. Here, we use cavity ring-down spectroscopy to measure magnetic field effects on the kinetics of these radical pairs in modified Cry4a proteins from the migratory European robin and from nonmigratory pigeon and chicken. B1/2, a parameter that characterizes the magnetic field-dependence of the reactions, was found to be larger than expected on the basis of hyperfine interactions and to increase with the delay between pump and probe laser pulses. Semiclassical spin dynamics simulations show that this behavior is consistent with a singlet-triplet dephasing (STD) relaxation mechanism. Analysis of the experimental data gives dephasing rate constants, rSTD, in the range 3-6 × 107 s-1. A simple "toy" model due to Maeda, Miura, and Arai [Mol. Phys. 104, 1779-1788 (2006)] is used to shed light on the origin of the time-dependence and the nature of the STD mechanism. Under the conditions of the experiments, STD results in an exponential approach to spin equilibrium at a rate considerably slower than rSTD. We attribute the loss of singlet-triplet coherence to electron hopping between the second and third tryptophans of the electron transfer chain and comment on whether this process could explain differences in the magnetic sensitivity of robin, chicken, and pigeon Cry4a's.
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Affiliation(s)
| | - Tilo Zollitsch
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Jiate Luo
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Dan Selby
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | - Lauren E Jarocha
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
- Department of Chemistry, Furman University, Greenville, South Carolina 29613, USA
| | - Kevin B Henbest
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
| | | | - Rabea Bartölke
- AG Neurosensory Sciences/Animal Navigation, Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Jessica Schmidt
- AG Neurosensory Sciences/Animal Navigation, Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Jingjing Xu
- AG Neurosensory Sciences/Animal Navigation, Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Henrik Mouritsen
- AG Neurosensory Sciences/Animal Navigation, Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Centre for Neurosensory Sciences, University of Oldenburg, Oldenburg, Germany
| | - P J Hore
- Department of Chemistry, University of Oxford, Oxford, United Kingdom
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14
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Merlin C. Insect magnetoreception: a Cry for mechanistic insights. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2023; 209:785-792. [PMID: 37184693 DOI: 10.1007/s00359-023-01636-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Revised: 04/24/2023] [Accepted: 05/04/2023] [Indexed: 05/16/2023]
Abstract
Migratory animals can detect and use the Earth's magnetic field for orientation and navigation, sometimes over distances spanning thousands of kilometers. How they do so remains, however, one of the greatest mysteries in all sensory biology. Here, the author reviews the progress made to understand the molecular bases of the animal magnetic sense focusing on insect species, the only species in which genetic studies have so far been possible. The central hypothesis in the field posits that magnetically sensitive radical pairs formed by photoexcitation of cryptochrome proteins are key to animal magnetoreception. The author provides an overview of our current state of knowledge for the involvement of insect light-sensitive type I and light-insensitive type II cryptochromes in this enigmatic sense, and highlights some of the unanswered questions to gain a comprehensive understanding of magnetoreception at the organismal level.
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Affiliation(s)
- Christine Merlin
- Center for Biological Clock Research and Department of Biology, Texas A&M University, College Station, TX, 77845, USA.
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15
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Zhang L, Malkemper EP. Cryptochromes in mammals: a magnetoreception misconception? Front Physiol 2023; 14:1250798. [PMID: 37670767 PMCID: PMC10475740 DOI: 10.3389/fphys.2023.1250798] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Accepted: 08/01/2023] [Indexed: 09/07/2023] Open
Abstract
Cryptochromes are flavoproteins related to photolyases that are widespread throughout the plant and animal kingdom. They govern blue light-dependent growth in plants, control circadian rhythms in a light-dependent manner in invertebrates, and play a central part in the circadian clock in vertebrates. In addition, cryptochromes might function as receptors that allow animals to sense the Earth's magnetic field. As cryptochromes are also present in mammals including humans, the possibility of a magnetosensitive protein is exciting. Here we attempt to provide a concise overview of cryptochromes in mammals. We briefly review their canonical role in the circadian rhythm from the molecular level to physiology, behaviour and diseases. We then discuss their disputed light sensitivity and proposed role in the magnetic sense in mammals, providing three mechanistic hypotheses. Specifically, mammalian cryptochromes could form light-induced radical pairs in particular cellular milieus, act as magnetoreceptors in darkness, or as secondary players in a magnetoreception signalling cascade. Future research can test these hypotheses to investigate if the role of mammalian cryptochromes extends beyond the circadian clock.
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Affiliation(s)
| | - E. Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Max Planck Institute for Neurobiology of Behavior—caesar, Bonn, Germany
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16
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Williams D. Eagle eyed or bird brained? Eye (Lond) 2023; 37:2426-2430. [PMID: 37353509 PMCID: PMC10397276 DOI: 10.1038/s41433-023-02568-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 04/24/2023] [Accepted: 04/25/2023] [Indexed: 06/25/2023] Open
Abstract
The importance of the visual system to birds for behaviours from feeding, mate choice, flying, navigation and determination of seasons, together with the presence of photoreceptors in the retina, the pineal and the brain, render the avian visual system a particularly fruitful model for understanding of eye-brain interactions. In this review we will particularly focus on the pigeon, since here we have a brain stereotactically mapped and a genome fully sequenced, together with a particular bird, the homing pigeon, with remarkable ability to navigate over hundreds of miles and return to exactly the same roosting site with exceptional precision. We might denigrate the avian species by the term bird brained, but here are animals with phenomenal abilities to use their exceptional vision, their eagle eyedness, to best advantage.
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17
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Frederiksen A, Langebrake C, Hanić M, Manthey G, Mouritsen H, Liedvogel M, Solov’yov IA. Mutational Study of the Tryptophan Tetrad Important for Electron Transfer in European Robin Cryptochrome 4a. ACS OMEGA 2023; 8:26425-26436. [PMID: 37521624 PMCID: PMC10373462 DOI: 10.1021/acsomega.3c02963] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/29/2023] [Accepted: 06/23/2023] [Indexed: 08/01/2023]
Abstract
The ability of migratory birds to sense magnetic fields has been known for decades, although the understanding of the underlying mechanism is still elusive. Currently, the strongest magnetoreceptor candidate in birds is a protein called cryptochrome 4a. The cryptochrome 4a protein has changed through evolution, apparently endowing some birds with a more pronounced magnetic sensitivity than others. Using phylogenetic tools, we show that a specific tryptophan tetrad and a tyrosine residue predicted to be essential for cryptochrome activation are highly conserved in the avian clade. Through state-of-the-art molecular dynamics simulations and associated analyses, we also studied the role of these specific residues and the associated mutants on the overall dynamics of the protein. The analyses of the single residue mutations were used to judge how far a local change in the protein structure can impact specific dynamics of European robin cryptochrome 4a. We conclude that the replacements of each of the tryptophans one by one with a phenylalanine do not compromise the overall stability of the protein.
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Affiliation(s)
- Anders Frederiksen
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Corinna Langebrake
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Maja Hanić
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Georg Manthey
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Henrik Mouritsen
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
| | - Miriam Liedvogel
- Institute
of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
- Department
of Biology and Environmental Sciences, Carl
von Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- MPRG
Behavioural Genomics, Max Planck Institute
for Evolutionary Biology, August-Thienemann-Str. 2, Plön 24306, Germany
| | - Ilia A. Solov’yov
- Institute
of Physics, Carl von Ossietzky Universität
Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Research
Centre for Neurosensory Sciences, Carl von
Ossietzky University of Oldenburg, Carl-von-Ossietzky Strasse 9-11, Oldenburg 26129, Germany
- Department
of Physics, Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky University of Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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18
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Hanić M, Antill LM, Gehrckens AS, Schmidt J, Görtemaker K, Bartölke R, El-Baba TJ, Xu J, Koch KW, Mouritsen H, Benesch JLP, Hore PJ, Solov'yov IA. Dimerization of European Robin Cryptochrome 4a. J Phys Chem B 2023. [PMID: 37428840 PMCID: PMC10364083 DOI: 10.1021/acs.jpcb.3c01305] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 07/12/2023]
Abstract
Homo-dimer formation is important for the function of many proteins. Although dimeric forms of cryptochromes (Cry) have been found by crystallography and were recently observed in vitro for European robin Cry4a, little is known about the dimerization of avian Crys and the role it could play in the mechanism of magnetic sensing in migratory birds. Here, we present a combined experimental and computational investigation of the dimerization of robin Cry4a resulting from covalent and non-covalent interactions. Experimental studies using native mass spectrometry, mass spectrometric analysis of disulfide bonds, chemical cross-linking, and photometric measurements show that disulfide-linked dimers are routinely formed, that their formation is promoted by exposure to blue light, and that the most likely cysteines are C317 and C412. Computational modeling and molecular dynamics simulations were used to generate and assess a number of possible dimer structures. The relevance of these findings to the proposed role of Cry4a in avian magnetoreception is discussed.
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Affiliation(s)
- Maja Hanić
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Lewis M Antill
- Graduate School of Science and Engineering, Saitama University, 255 Shimo-okubo, Sakura Ward, Saitama 338-8570, Japan
- Japan Science and Technology Agency, Precursory Research for Embryonic Science and Technology, 4-1-8 Honcho, Kawaguchi, Saitama 332-0012, Japan
| | - Angela S Gehrckens
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Jessica Schmidt
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Katharina Görtemaker
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
| | - Rabea Bartölke
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Tarick J El-Baba
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Karl-Wilhelm Koch
- Department of Neuroscience, Division of Biochemistry, Carl von Ossietzky University of Oldenburg, Oldenburg D-26111, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
| | - Justin L P Benesch
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
- Kavli Institute for NanoScience Discovery, University of Oxford, Dorothy Crowfoot Hodgkin Building, Oxford OX1 3QU, U.K
| | - P J Hore
- Department of Chemistry, Physical & Theoretical Chemistry Laboratory, University of Oxford, South Parks Road, Oxford OX1 3QZ, U.K
| | - Ilia A Solov'yov
- Institute of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
- Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26111, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Ammerländer Heerstr. 114-118, Oldenburg 26129, Germany
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19
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Zhang Y, Zhang Y, Zhao J, He J, Xuanyuan Z, Pan W, Sword GA, Chen F, Wan G. Probing Transcriptional Crosstalk between Cryptochromes and Iron-sulfur Cluster Assembly 1 ( MagR) in the Magnetoresponse of a Migratory Insect. Int J Mol Sci 2023; 24:11101. [PMID: 37446278 DOI: 10.3390/ijms241311101] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2023] [Revised: 06/30/2023] [Accepted: 07/03/2023] [Indexed: 07/15/2023] Open
Abstract
Many organisms can sense and respond to magnetic fields (MFs), with migratory species in particular utilizing geomagnetic field information for long-distance migration. Cryptochrome proteins (Crys) along with a highly conserved Iron-sulfur cluster assembly protein (i.e., MagR) have garnered significant attention for their involvement in magnetoresponse (including magnetoreception). However, in vivo investigations of potential transcriptional crosstalk between Crys and MagR genes have been limited. The brown planthopper, Nilaparvata lugens, is a major migratory pest insect and an emerging model for studying MF intensity-related magnetoresponse. Here, we explored in vivo transcriptional crosstalk between Crys (Cry1 and Cry2) and MagR in N. lugens. The expression of Crys and MagR were found to be sensitive to MF intensity changes as small as several micro-teslas. Knocking down MagR expression led to a significant downregulation of Cry1, but not Cry2. The knockdown of either Cry1 or Cry2 individually did not significantly affect MagR expression. However, their double knockdown resulted in significant upregulation of MagR. Our findings clearly indicate transcriptional crosstalk between MagR and Crys known to be involved in magnetoresponse. This work advances the understanding of magnetoresponse signaling and represents a key initial step towards elucidating the functional consequences of these novel in vivo interactions.
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Affiliation(s)
- Yuning Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Ying Zhang
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jingyu Zhao
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Jinglan He
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Zongjin Xuanyuan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Weidong Pan
- Beijing Key Laboratory of Bioelectromagnetics, Institute of Electrical Engineering, Chinese Academy of Sciences, Beijing 100190, China
| | - Gregory A Sword
- Department of Entomology, Texas A&M University, College Station, TX 77843, USA
| | - Fajun Chen
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
| | - Guijun Wan
- Department of Entomology, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
- Key Laboratory of Integrated Pest Management on Crops in East China, College of Plant Protection, Nanjing Agricultural University, Nanjing 210095, China
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20
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Fraikin GY, Belenikina NS, Rubin AB. Molecular Bases of Signaling Processes Regulated by Cryptochrome Sensory Photoreceptors in Plants. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:770-782. [PMID: 37748873 DOI: 10.1134/s0006297923060056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 09/27/2023]
Abstract
The blue-light sensors, cryptochromes, compose the extensive class of flavoprotein photoreceptors, regulating signaling processes in plants underlying their development, growth, and metabolism. In several algae, cryptochromes may act not only as sensory photoreceptors but also as photolyases, catalyzing repair of the UV-induced DNA lesions. Cryptochromes bind FAD as the chromophore at the photolyase homologous region (PHR) domain and contain the cryptochrome C-terminal extension (CCE), which is absent in photolyases. Photosensory process in cryptochrome is initiated by photochemical chromophore conversions, including formation of the FAD redox forms. In the state with the chromophore reduced to neutral radical (FADH×), the photoreceptor protein undergoes phosphorylation, conformational changes, and disengagement from the PHR domain and CCE with subsequent formation of oligomers of cryptochrome molecules. Photooligomerization is a structural basis of the functional activities of cryptochromes, since it ensures formation of their complexes with a variety of signaling proteins, including transcriptional factors and regulators of transcription. Interactions in such complexes change the protein signaling activities, leading to regulation of gene expression and plant photomorphogenesis. In recent years, multiple papers, reporting novel, more detailed information about the molecular mechanisms of above-mentioned processes were published. The present review mainly focuses on analysis of the data contained in these publications, particularly regarding structural aspects of the cryptochrome transitions into photoactivated states and regulatory signaling processes mediated by the cryptochrome photoreceptors in plants.
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Affiliation(s)
| | | | - Andrey B Rubin
- Lomonosov Moscow State University, Moscow, 119991, Russia
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21
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Hong G, Pachter R. Effects of inter-radical interactions and scavenging radicals on magnetosensitivity: spin dynamics simulations of proposed radical pairs. EUROPEAN BIOPHYSICS JOURNAL : EBJ 2023; 52:27-37. [PMID: 36792823 DOI: 10.1007/s00249-023-01630-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/07/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 02/17/2023]
Abstract
Although the magnetosensitivity to weak magnetic fields, such as the geomagnetic field, which was exhibited by radical pairs that are potentially responsible for avian navigation, has been previously investigated by spin dynamics simulations, understanding this behavior for proposed radical pairs in other species is limited. These include, for example, radical pairs formed in the single-cell green alga Chlamydomonas reinhardtii (CraCRY) and in Columba livia (ClCRY4). In addition, the radical pair of FADH• with the one-electron reduced cyclobutane thymine dimer that was shown to be sensitive to weak magnetic fields has been of interest. In this work, we investigated the directional magnetosensitivity of these radical pairs to a weak magnetic field by spin dynamics simulations. We find significant reduction in the magnetosensitivity by inclusion of dipolar and exchange interactions, which can be mitigated by a scavenging radical, as demonstrated for the [FAD•- TyrD•] radical pair in CraCRY, but not for the [FADH• T□T•-] radical pair because of the large exchange coupling. The directional magnetosensitivity of the ClCRY4 [FAD•- TyrE•] radical pair can survive this adverse effect even without the scavenging reaction, possibly motivating further experimental exploration.
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Affiliation(s)
- Gongyi Hong
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Ohio, 45433, USA
| | - Ruth Pachter
- Air Force Research Laboratory, Materials and Manufacturing Directorate, Wright-Patterson Air Force Base, Ohio, 45433, USA.
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22
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Pažėra G, Benjamin P, Mouritsen H, Hore PJ. Isotope Substitution Effects on the Magnetic Compass Properties of Cryptochrome-Based Radical Pairs: A Computational Study. J Phys Chem B 2023; 127:838-845. [PMID: 36669149 PMCID: PMC9900586 DOI: 10.1021/acs.jpcb.2c05335] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
The biophysical mechanism of the magnetic compass sense of migratory songbirds is thought to rely on the photochemical reactions of flavin-containing radical pairs in cryptochrome proteins located in the birds' eyes. A consequence of this hypothesis is that the effect of the Earth's magnetic field on the quantum yields of reaction products should be sensitive to isotopic substitutions that modify the hyperfine interactions in the radicals. In this report, we use spin dynamics simulations to explore the effects of 1H → 2H, 12C → 13C, and 14N → 15N isotopic substitutions on the functioning of cryptochrome 4a as a magnetic direction sensor. Two main conclusions emerge. (1) Uniform deuteration of the flavin chromophore appears to be the best way to boost the anisotropy of the magnetic field effect and to change its symmetry. (2) 13C substitution of three of the 12 flavin carbons, in particular C4, C4a, and C8α, seems to be the best recipe for attenuating the anisotropy. These predictions should give insight into the factors that control the magnetic sensitivity once spectroscopic techniques are available for measuring magnetic field effects on oriented protein samples.
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Affiliation(s)
| | - Philip Benjamin
- Department
of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K.
| | - Henrik Mouritsen
- Institut
für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany,Research
Centre for Neurosensory Science, University
of Oldenburg, Oldenburg 26111, Germany
| | - P. J. Hore
- Department
of Chemistry, University of Oxford, Oxford OX1 3QZ, U.K.,
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23
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Wong SY, Benjamin P, Hore PJ. Magnetic field effects on radical pair reactions: estimation of B1/2 for flavin-tryptophan radical pairs in cryptochromes. Phys Chem Chem Phys 2023; 25:975-982. [PMID: 36519379 PMCID: PMC9811481 DOI: 10.1039/d2cp03793a] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
Magnetic field effects on the yields of radical pair reactions are often characterised by the "half-field" parameter, B1/2, which encodes useful information on spin relaxation, radical recombination kinetics and electron-electron couplings as well as electron-nuclear hyperfine interactions. Here we use a variety of spin dynamics simulation methods to estimate the hyperfine-only values of B1/2 for the flavin-tryptophan radical pair, [FAD˙- TrpH˙+], thought to be the detector in the magnetic compass sense of migratory songbirds. The main findings are: (a) in the absence of fast recombination and spin relaxation, [FAD˙- TrpH˙+] radical pairs in solution and in the putative magnetoreceptor protein, cryptochrome, have B1/2 ≈ 1.89 mT and 2.46 mT, respectively. (b) The widely used expression for B1/2 due to Weller et al. (Chem. Phys. Lett, 1983, 96, 24-27) is only applicable to small, short-lived (∼5 ns), rapidly tumbling radical pairs in solution, and is quantitatively unreliable in the context of magnetoreception. (c) In the absence of molecular tumbling, the low-field effect for [FAD˙- TrpH˙+] is predicted to be abolished by the anisotropic components of the hyperfine interactions. Armed with the 2.46 mT "base value" for cryptochrome, measurements of B1/2 can be used to understand the impact of spin relaxation on its performance as a magnetic compass sensor.
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Affiliation(s)
- Siu Ying Wong
- Institut für Physik, Carl-von-Ossietzky Universität OldenburgOldenburg 26111Germany
| | - Philip Benjamin
- Department of Chemistry, University of OxfordOxfordOX1 3QZUK
| | - P. J. Hore
- Department of Chemistry, University of OxfordOxfordOX1 3QZUK
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24
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Schuhmann F, Ryvkin L, McLaren JD, Gerhards L, Solov'yov IA. Across atoms to crossing continents: Application of similarity measures to biological location data. PLoS One 2023; 18:e0284736. [PMID: 37186599 PMCID: PMC10184918 DOI: 10.1371/journal.pone.0284736] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2022] [Accepted: 04/06/2023] [Indexed: 05/17/2023] Open
Abstract
Biological processes involve movements across all measurable scales. Similarity measures can be applied to compare and analyze these movements but differ in how differences in movement are aggregated across space and time. The present study reviews frequently-used similarity measures, such as the Hausdorff distance, Fréchet distance, Dynamic Time Warping, and Longest Common Subsequence, jointly with several measures less used in biological applications (Wasserstein distance, weak Fréchet distance, and Kullback-Leibler divergence), and provides computational tools for each of them that may be used in computational biology. We illustrate the use of the selected similarity measures in diagnosing differences within two extremely contrasting sets of biological data, which, remarkably, may both be relevant for magnetic field perception by migratory birds. Specifically, we assess and discuss cryptochrome protein conformational dynamics and extreme migratory trajectories of songbirds between Alaska and Africa. We highlight how similarity measures contrast regarding computational complexity and discuss those which can be useful in noise elimination or, conversely, are sensitive to spatiotemporal scales.
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Affiliation(s)
- Fabian Schuhmann
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Leonie Ryvkin
- Department of Mathematics & Computer Science, Technische Universiteit Eindhoven, Eindhoven, Netherlands
- Department of Computer Science, Ruhr-Universität Bochum, Bochum, Germany
| | - James D McLaren
- Institute of Chemistry and Marine Biology, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Luca Gerhards
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Research Centre for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Oldenburg, Germany
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25
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Li N, Xue L, Mai X, Wang P, Zhu C, Han X, Xie Y, Wang B, Ge Y, Zhang Y, Sun J. Transfection of clMagR/clCry4 imparts MR-T 2 imaging contrast properties to living organisms ( E. coli) in the presence of Fe 3+ by endogenous formation of iron oxide nanoparticles. Front Mol Biosci 2023; 10:1119356. [PMID: 36876047 PMCID: PMC9981785 DOI: 10.3389/fmolb.2023.1119356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2022] [Accepted: 01/30/2023] [Indexed: 02/19/2023] Open
Abstract
Rapid development of medical imaging, such as cellular tracking, has increased the demand for "live" contrast agents. This study provides the first experimental evidence demonstrating that transfection of the clMagR/clCry4 gene can impart magnetic resonance imaging (MRI) T2-contrast properties to living prokaryotic Escherichia coli (E. coli) in the presence of Fe3+ through the endogenous formation of iron oxide nanoparticles. The transfected clMagR/clCry4 gene markedly promoted uptake of exogenous iron by E. coli, achieving an intracellular co-precipitation condition and formation of iron oxide nanoparticles. This study will stimulate further exploration of the biological applications of clMagR/clCry4 in imaging studies.
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Affiliation(s)
- Nuan Li
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China.,Jiangsu Key Laboratory of Biomaterials and Devices, Southeast University, Nanjing, China
| | - Le Xue
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China.,Jiangsu Key Laboratory of Biomaterials and Devices, Southeast University, Nanjing, China
| | - Xiaoli Mai
- Department of Radiology, The Affiliated Drum Tower Hospital of Nanjing University, Nanjing, China
| | - Peng Wang
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China.,Jiangsu Key Laboratory of Biomaterials and Devices, Southeast University, Nanjing, China.,Department of Sports Medicine and Adult Reconstructive Surgery, The Affiliated Drum Tower Hospital of Nanjing University, Nanjing, China
| | - Chenzhuo Zhu
- Southeast University-Monash University Joint Graduate School, Southeast University, Suzhou, China
| | - Xiaofeng Han
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China
| | - Yuanyuan Xie
- Clinical Stem Cell Center, The Affiliated Drum Tower Hospital of Nanjing University, Nanjing, China
| | - Bin Wang
- Clinical Stem Cell Center, The Affiliated Drum Tower Hospital of Nanjing University, Nanjing, China
| | - Yuqing Ge
- State Key Laboratory of Transducer Technology, Shanghai Institute of Microsystem and Information Technology, Chinese Academy of Sciences, Shanghai, China
| | - Yewei Zhang
- The Hepatopancreatobiliary Center, The Second Affiliated Hospital of Nanjing Medical University, Nanjing, China
| | - Jianfei Sun
- State Key Laboratory of Bioelectronics, School of Biological Sciences and Medical Engineering, Southeast University, Nanjing, China.,Jiangsu Key Laboratory of Biomaterials and Devices, Southeast University, Nanjing, China
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26
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Grüning G, Wong SY, Gerhards L, Schuhmann F, Kattnig DR, Hore PJ, Solov’yov IA. Effects of Dynamical Degrees of Freedom on Magnetic Compass Sensitivity: A Comparison of Plant and Avian Cryptochromes. J Am Chem Soc 2022; 144:22902-22914. [DOI: 10.1021/jacs.2c06233] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Affiliation(s)
- Gesa Grüning
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Siu Ying Wong
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Luca Gerhards
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Fabian Schuhmann
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
| | - Daniel R. Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, Exeter EX4 4QD, U.K
| | - P. J. Hore
- Department of Chemistry, Physical and Theoretical Chemistry Laboratory, University of Oxford, Oxford OX1 3QZ, U.K
| | - Ilia A. Solov’yov
- Department of Physics, Carl von Ossietzky University, Carl-von-Ossietzky-Street 9-11, 26129 Oldenburg, Germany
- Research Center for Neurosensory Science, Carl von Ossietzky Universität Oldenburg, 26111 Oldenburg, Germany
- Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Institut für Physik, Ammerländer Heerstreet 114-118, 26129 Oldenburg, Germany
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27
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Tiwari Y, Poonia VS. Role of chiral-induced spin selectivity in the radical pair mechanism of avian magnetoreception. Phys Rev E 2022; 106:064409. [PMID: 36671157 DOI: 10.1103/physreve.106.064409] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2022] [Accepted: 12/11/2022] [Indexed: 06/17/2023]
Abstract
In this paper, we investigate the effect of chiral-induced spin selectivity (CISS) on the radical pair mechanism of avian magnetoreception. We examine the impact of spin selectivity on the avian compass sensitivity. In this analysis, we also consider the dipolar and exchange interactions and observe their interplay with CISS. We find that CISS results in a multifold increase in avian compass sensitivity. Interestingly, we also observe that CISS can counter the deleterious effect of dipolar interaction and increase system sensitivity. The analysis has been performed for the toy model (only one nucleus) and a more general case where we consider up to six nuclei from the cryptochrome radical pair system. We observe that the CISS allows the radical pair model to have more realistic recombination rates with good sensitivity. We also do an analysis of the functional window of the avian compass reported in behavioral experiments in the functional window. We could not find a parameter set where a functional window can be observed along with CISS. We also show the effect of spin relaxation on the system and show that under relaxation, CISS shows increased compass sensitivity compared to no CISS case.
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Affiliation(s)
- Yash Tiwari
- Department of Electronics and Communication, Indian Institute of Technology, Roorkee, Uttrakhand 247667, India
| | - Vishvendra Singh Poonia
- Department of Electronics and Communication, Indian Institute of Technology, Roorkee, Uttrakhand 247667, India
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28
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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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29
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Morphology, biochemistry and connectivity of Cluster N and the hippocampal formation in a migratory bird. Brain Struct Funct 2022; 227:2731-2749. [DOI: 10.1007/s00429-022-02566-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2022] [Accepted: 09/05/2022] [Indexed: 11/02/2022]
Abstract
AbstractThe exceptional navigational capabilities of migrating birds are based on the perception and integration of a variety of natural orientation cues. The “Wulst” in the forebrain of night-migratory songbirds contains a brain area named “Cluster N”, which is involved in processing directional navigational information derived from the Earth´s magnetic field. Cluster N is medially joined by the hippocampal formation, known to retrieve and utilise navigational information. To investigate the connectivity and neurochemical characteristics of Cluster N and the hippocampal formation of migratory birds, we performed morphological and histochemical analyses based on the expression of calbindin, calretinin, parvalbumin, glutamate receptor type 1 and early growth response protein-1 in the night-migratory Garden warbler (Sylvia borin) and mapped their mutual connections using neuronal tract tracing. The resulting expression patterns revealed regionally restricted neurochemical features, which mapped well onto the hippocampal and hyperpallial substructures known from other avian species. Magnetic field-induced neuronal activation covered caudal parts of the hyperpallium and the medially adjacent hippocampal dorsomedial/dorsolateral subdivisions. Neuronal tract tracings revealed connections between Cluster N and the hippocampal formation with the vast majority originating from the densocellular hyperpallium, either directly or indirectly via the area corticoidea dorsolateralis. Our data indicate that the densocellular hyperpallium could represent a central relay for the transmission of magnetic compass information to the hippocampal formation where it might be integrated with other navigational cues in night-migratory songbirds.
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30
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Deppisch P, Helfrich-Förster C, Senthilan PR. The Gain and Loss of Cryptochrome/Photolyase Family Members during Evolution. Genes (Basel) 2022; 13:genes13091613. [PMID: 36140781 PMCID: PMC9498864 DOI: 10.3390/genes13091613] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2022] [Revised: 09/02/2022] [Accepted: 09/05/2022] [Indexed: 11/20/2022] Open
Abstract
The cryptochrome/photolyase (CRY/PL) family represents an ancient group of proteins fulfilling two fundamental functions. While photolyases repair UV-induced DNA damages, cryptochromes mainly influence the circadian clock. In this study, we took advantage of the large number of already sequenced and annotated genes available in databases and systematically searched for the protein sequences of CRY/PL family members in all taxonomic groups primarily focusing on metazoans and limiting the number of species per taxonomic order to five. Using BLASTP searches and subsequent phylogenetic tree and motif analyses, we identified five distinct photolyases (CPDI, CPDII, CPDIII, 6-4 photolyase, and the plant photolyase PPL) and six cryptochrome subfamilies (DASH-CRY, mammalian-type MCRY, Drosophila-type DCRY, cnidarian-specific ACRY, plant-specific PCRY, and the putative magnetoreceptor CRY4. Manually assigning the CRY/PL subfamilies to the species studied, we have noted that over evolutionary history, an initial increase of various CRY/PL subfamilies was followed by a decrease and specialization. Thus, in more primitive organisms (e.g., bacteria, archaea, simple eukaryotes, and in basal metazoans), we find relatively few CRY/PL members. As species become more evolved (e.g., cnidarians, mollusks, echinoderms, etc.), the CRY/PL repertoire also increases, whereas it appears to decrease again in more recent organisms (humans, fruit flies, etc.). Moreover, our study indicates that all cryptochromes, although largely active in the circadian clock, arose independently from different photolyases, explaining their different modes of action.
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31
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Alachkar A. Aromatic patterns: Tryptophan aromaticity as a catalyst for the emergence of life and rise of consciousness. Phys Life Rev 2022; 42:93-114. [PMID: 35905538 DOI: 10.1016/j.plrev.2022.07.002] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2022] [Accepted: 07/12/2022] [Indexed: 11/28/2022]
Abstract
Sunlight held the key to the origin of life on Earth. The earliest life forms, cyanobacteria, captured the sunlight to generate energy through photosynthesis. Life on Earth evolved in accordance with the circadian rhythms tied to sensitivity to sunlight patterns. A unique feature of cyanobacterial photosynthetic proteins and circadian rhythms' molecules, and later of nearly all photon-sensing molecules throughout evolution, is that the aromatic amino acid tryptophan (Trp) resides at the center of light-harvesting active sites. In this perspective, I review the literature and integrate evidence from different scientific fields to explore the role Trp plays in photon-sensing capabilities of living organisms through its resonance delocalization of π-electrons. The observations presented here are the product of apparently unrelated phenomena throughout evolution, but nevertheless share consistent patterns of photon-sensing by Trp-containing and Trp-derived molecules. I posit the unique capacity to transfer electrons during photosynthesis in the earliest life forms is conferred to Trp due to its aromaticity. I propose this ability evolved to assume more complex functions, serving as a host for mechanisms underlying mental aptitudes - a concept which provides a theoretical basis for defining the neural correlates of consciousness. The argument made here is that Trp aromaticity may have allowed for the inception of the mechanistic building blocks used to fabricate complexity in higher forms of life. More specifically, Trp aromatic non-locality may have acted as a catalyst for the emergence of consciousness by instigating long-range synchronization and stabilizing the large-scale coherence of neural networks, which mediate functional brain activity. The concepts proposed in this perspective provide a conceptual foundation that invites further interdisciplinary dialogue aimed at examining and defining the role of aromaticity (beyond Trp) in the emergence of life and consciousness.
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Affiliation(s)
- Amal Alachkar
- Department of Pharmaceutical Sciences, School of Pharmacy and Pharmaceutical Sciences, University of California, Irvine, CA 92697, USA; UC Irvine Center for the Neurobiology of Learning and Memory, University of California-Irvine, Irvine, CA 92697, USA; Institute for Genomics and Bioinformatics, School of Information and Computer Sciences, University of California, Irvine, CA 92697, USA.
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32
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Deviers J, Cailliez F, Gutiérrez BZ, Kattnig DR, de la Lande A. Ab initio derivation of flavin hyperfine interactions for the protein magnetosensor cryptochrome. Phys Chem Chem Phys 2022; 24:16784-16798. [PMID: 35775941 DOI: 10.1039/d1cp05804e] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
The radicals derived from flavin adenine dinucleotide (FAD) are a corner stone of recent hypotheses about magnetoreception, including the compass of migratory songbirds. These models attribute a magnetic sense to coherent spin dynamics in radical pairs within the flavo-protein cryptochrome. The primary determinant of sensitivity and directionality of this process are the hyperfine interactions of the involved radicals. Here, we present a comprehensive computational study of the hyperfine couplings in the protonated and unprotonated FAD radicals in cryptochrome 4 from C. livia. We combine long (800 ns) molecular dynamics trajectories to accurate quantum chemistry calculations. Hyperfine parameters are derived using auxiliary density functional theory applied to cluster and hybrid QM/MM (Quantum Mechanics/Molecular Mechanics) models comprising the FAD and its significant surrounding environment, as determined by a detailed sensitivity analysis. Thanks to this protocol we elucidate the sensitivity of the hyperfine interaction parameters to structural fluctuations and the polarisation effect of the protein environment. We find that the ensemble-averaged hyperfine interactions are predominantly governed by thermally induced geometric distortions of the flavin. We discuss our results in view of the expected performance of these radicals as part of a magnetoreceptor. Our data could be used to parametrize spin Hamiltonians including not only average values but also standard deviations.
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Affiliation(s)
- Jean Deviers
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK.,Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Fabien Cailliez
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
| | - Bernardo Zúñiga Gutiérrez
- Departamento de Química, Universidad de Guadalajara, Blvd. Marcelino García Barragán 1421, C. P. 44430, Guadalajara Jal, Mexico
| | - Daniel R Kattnig
- Living Systems Institute and Department of Physics, University of Exeter, Stocker Road, Exeter, Devon, EX4 4QD, UK
| | - Aurélien de la Lande
- Institut de Chimie Physique, CNRS UMR 8000, Université Paris-Saclay, 91405 Orsay, France.
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33
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Hanić M, Schuhmann F, Frederiksen A, Langebrake C, Manthey G, Liedvogel M, Xu J, Mouritsen H, Solov'yov IA. Computational Reconstruction and Analysis of Structural Models of Avian Cryptochrome 4. J Phys Chem B 2022; 126:4623-4635. [PMID: 35704801 DOI: 10.1021/acs.jpcb.2c00878] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
A recent study by Xu et al. (Nature, 2021, 594, 535-540) provided strong evidence that cryptochrome 4 (Cry4) is a key protein to endow migratory birds with the magnetic compass sense. The investigation compared the magnetic field response of Cry4 from migratory and nonmigratory bird species and suggested that a difference in magnetic sensitivity could exist. This finding prompted an in-depth investigation into Cry4 protein differences on the structural and dynamic levels. In the present study, the pigeon Cry4 (ClCry4) crystal structure was used to reconstruct the missing avian Cry4 protein structures via homology modeling for carefully selected bird species. The reconstructed Cry4 structure from European robin, Eurasian blackcap, zebra finch, chicken, and pigeon were subsequently simulated dynamically and analyzed. The studied avian Cry4 structures show flexibility in analogous regions pointing to similar activation mechanisms and/or signaling interaction partners. It can be concluded that the experimentally recorded difference in the magnetic field sensitivity of Cry4 from different birds is unlikely to be due to solely intrinsic dynamics of the proteins but requires additional factors that have not yet been identified.
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Affiliation(s)
- Maja Hanić
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Fabian Schuhmann
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Anders Frederiksen
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Corinna Langebrake
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Georg Manthey
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany
| | - Miriam Liedvogel
- Institute of Avian Research, An der Vogelwarte 21, Wilhelmshaven 26386, Germany.,Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,MPRG Behavioural Genomics, Max Planck Institute for Evolutionary Biology, Plön 24306, Germany
| | - Jingjing Xu
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Henrik Mouritsen
- Department of Biology and Environmental Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany
| | - Ilia A Solov'yov
- Department of Physics, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Research Center for Neurosensory Sciences, Carl von Ossietzky University of Oldenburg, Carl-von-Ossietzky Straße 9-11, Oldenburg 26129, Germany.,Center for Nanoscale Dynamics (CENAD), Carl von Ossietzky Universität Oldenburg, Institut für Physik, Ammerländer Heerstr. 114-118, 26129 Oldenburg, Germany
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Direct Interaction of Avian Cryptochrome 4 with a Cone Specific G-Protein. Cells 2022; 11:cells11132043. [PMID: 35805127 PMCID: PMC9265643 DOI: 10.3390/cells11132043] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2022] [Revised: 06/23/2022] [Accepted: 06/24/2022] [Indexed: 02/04/2023] Open
Abstract
Background: Night-migratory birds sense the Earth’s magnetic field by an unknown molecular mechanism. Theoretical and experimental evidence support the hypothesis that the light-induced formation of a radical-pair in European robin cryptochrome 4a (ErCry4a) is the primary signaling step in the retina of the bird. In the present work, we investigated a possible route of cryptochrome signaling involving the α-subunit of the cone-secific heterotrimeric G protein from European robin. Methods: Protein–protein interaction studies include surface plasmon resonance, pulldown affinity binding and Förster resonance energy transfer. Results: Surface plasmon resonance studies showed direct interaction, revealing high to moderate affinity for binding of non-myristoylated and myristoylated G protein to ErCry4a, respectively. Pulldown affinity experiments confirmed this complex formation in solution. We validated these in vitro data by monitoring the interaction between ErCry4a and G protein in a transiently transfected neuroretinal cell line using Förster resonance energy transfer. Conclusions: Our results suggest that ErCry4a and the G protein also interact in living cells and might constitute the first biochemical signaling step in radical-pair-based magnetoreception.
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35
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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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36
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Arai S, Shimizu R, Adachi M, Hirai M. Magnetic field effects on the structure and molecular behavior of pigeon iron–sulfur protein. Protein Sci 2022; 31:e4313. [DOI: 10.1002/pro.4313] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 03/31/2022] [Accepted: 04/02/2022] [Indexed: 11/10/2022]
Affiliation(s)
- Shigeki Arai
- Institute for Quantum Life Science National Institutes for Quantum Science and Technology Tokai Ibaraki Japan
| | - Rumi Shimizu
- Institute for Quantum Life Science National Institutes for Quantum Science and Technology Tokai Ibaraki Japan
| | - Motoyasu Adachi
- Institute for Quantum Life Science National Institutes for Quantum Science and Technology Tokai Ibaraki Japan
| | - Mitsuhiro Hirai
- Graduate School of Science and Technology Gunma University Maebashi Gunma Japan
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37
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Chetverikova R, Dautaj G, Schwigon L, Dedek K, Mouritsen H. Double cones in the avian retina form an oriented mosaic which might facilitate magnetoreception and/or polarized light sensing. J R Soc Interface 2022; 19:20210877. [PMID: 35414212 PMCID: PMC9006000 DOI: 10.1098/rsif.2021.0877] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
To navigate between breeding and wintering grounds, night-migratory songbirds are aided by a light-dependent magnetic compass sense and maybe also by polarized light vision. Although the underlying mechanisms for magnetoreception and polarized light sensing remain unclear, double cone photoreceptors in the avian retina have been suggested to represent the primary sensory cells. To use these senses, birds must be able to separate the directional information from the Earth's magnetic field and/or light polarization from variations in light intensity. Theoretical considerations suggest that this could be best achieved if neighbouring double cones were oriented in an ordered pattern. Therefore, we investigate the orientation patterns of double cones in European robins (Erithacus rubecula) and domestic chickens (Gallus gallus domesticus). We used whole-mounted retinas labelled with double cone markers to quantify the orientations of individual double cones in relation to their nearest neighbours. In both species, our data show that the double cone array is highly ordered: the angles between neighbouring double cones were more likely to be 90°/-90° in the central retina and 180°/0° in the peripheral retina, respectively. The observed regularity in double cone orientation could aid the cells' putative function in light-dependent magnetoreception and/or polarized light sensing.
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Affiliation(s)
- Raisa Chetverikova
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Glen Dautaj
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Leonard Schwigon
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany
| | - Karin Dedek
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany.,Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
| | - Henrik Mouritsen
- Animal Navigation/Neurosensorics Group, Institute for Biology and Environmental Sciences, University of Oldenburg, Oldenburg, Germany.,Research Center Neurosensory Science, University of Oldenburg, Oldenburg, Germany
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38
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Krylov VV, Izvekov EI, Pavlova VV, Pankova NA, Osipova EA. Magnetic Fluctuations Entrain the Circadian Rhythm of Locomotor Activity in Zebrafish: Can Cryptochrome Be Involved? BIOLOGY 2022; 11:biology11040591. [PMID: 35453790 PMCID: PMC9025847 DOI: 10.3390/biology11040591] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/24/2022] [Revised: 04/05/2022] [Accepted: 04/11/2022] [Indexed: 12/16/2022]
Abstract
Simple Summary Most physiological processes are subject to biological circadian rhythms maintained by a complex cascade of biochemical events. The circadian rhythmicity of behavior allows organisms to use energy and resources optimally under changing environmental conditions. To that end, endogenous circadian rhythms are synchronized with external pacemakers (zeitgebers), especially daily changes in illumination. In the 1960s, it was assumed that, in addition to this primary photic cue, animals can use diurnal geomagnetic variation as a secondary zeitgeber. Earlier research found that slow magnetic fluctuations can affect some behavioral endpoints of circadian rhythms by modulating an organism’s physiological state. However, no direct experiments to test such an entrainment of biological clocks by artificial magnetic fields were performed due to the technical difficulty of eliminating natural geomagnetic variation. For the first time, we carried out such tests in a fully controlled magnetic environment using zebrafish as a research model. The experimental treatments included various light/dark cycles and continuous illumination coupled with pre-recorded natural geomagnetic variations. The obtained results indicate that slow magnetic fluctuations can entrain endogenous rhythmical activity in vertebrates. Probably, cryptochromes play a key role in this process. This research provides promising opportunities for the magnetic control of circadian processes, e.g., correcting circadian dysfunctions. Abstract In the 1960s, it was hypothesized that slow magnetic fluctuations could be a secondary zeitgeber for biological circadian rhythms. However, no comprehensive experimental research has been carried out to test the entrainment of free-running circadian rhythms by this zeitgeber. We studied the circadian patterns of the locomotor activity of zebrafish (Danio rerio) under different combinations of light regimes and slow magnetic fluctuations, based on a record of natural geomagnetic variation. A rapid synchronization of activity rhythms to an unusual 24:12 light/dark cycle was found under magnetic fluctuations with a period of 36 h. Under constant illumination, significant locomotor activity rhythms with 26.17 h and 33.07 h periods were registered in zebrafish exposed to magnetic fluctuations of 26.8 h and 33.76 h, respectively. The results reveal the potential of magnetic fluctuations for entrainment of circadian rhythms in zebrafish and genuine prospects to manipulate circadian oscillators via magnetic fields. The putative mechanisms responsible for the entrainment are discussed, including the possible role of cryptochromes.
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Affiliation(s)
- Viacheslav V. Krylov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; (E.I.I.); (V.V.P.); (N.A.P.); (E.A.O.)
- Scientific and Technological Center of Unique Instrumentation, Russian Academy of Sciences, 117342 Moscow, Russia
- Correspondence:
| | - Evgeny I. Izvekov
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; (E.I.I.); (V.V.P.); (N.A.P.); (E.A.O.)
| | - Vera V. Pavlova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; (E.I.I.); (V.V.P.); (N.A.P.); (E.A.O.)
| | - Natalia A. Pankova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; (E.I.I.); (V.V.P.); (N.A.P.); (E.A.O.)
| | - Elena A. Osipova
- Papanin Institute for Biology of Inland Waters, Russian Academy of Sciences, 152742 Borok, Russia; (E.I.I.); (V.V.P.); (N.A.P.); (E.A.O.)
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39
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Limited solvation of an electron donating tryptophan stabilizes a photoinduced charge-separated state in plant (6-4) photolyase. Sci Rep 2022; 12:5084. [PMID: 35332186 PMCID: PMC8948257 DOI: 10.1038/s41598-022-08928-0] [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: 11/30/2021] [Accepted: 03/15/2022] [Indexed: 11/08/2022] Open
Abstract
(6-4) Photolyases ((6-4) PLs) are ubiquitous photoenzymes that use the energy of sunlight to catalyze the repair of carcinogenic UV-induced DNA lesions, pyrimidine(6-4)pyrimidone photoproducts. To repair DNA, (6-4) PLs must first undergo so-called photoactivation, in which their excited flavin adenine dinucleotide (FAD) cofactor is reduced in one or two steps to catalytically active FADH- via a chain of three or four conserved tryptophan residues, transiently forming FAD•-/FADH- ⋯ TrpH•+ pairs separated by distances of 15 to 20 Å. Photolyases and related photoreceptors cryptochromes use a plethora of tricks to prevent charge recombination of photoinduced donor-acceptor pairs, such as chain branching and elongation, rapid deprotonation of TrpH•+ or protonation of FAD•-. Here, we address Arabidopsis thaliana (6-4) PL (At64) photoactivation by combining molecular biology, in vivo survival assays, static and time-resolved spectroscopy and computational methods. We conclude that At64 photoactivation is astonishingly efficient compared to related proteins-due to two factors: exceptionally low losses of photoinduced radical pairs through ultrafast recombination and prevention of solvent access to the terminal Trp3H•+, which significantly extends its lifetime. We propose that a highly conserved histidine residue adjacent to the 3rd Trp plays a key role in Trp3H•+ stabilization.
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40
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Chen E, Chen Z, Chen L, Hu X. The biological effects of geomagnetic field exhibit an important potential for cancer and vascular diseases. Cell Biol Int 2022; 46:878-882. [PMID: 35233872 DOI: 10.1002/cbin.11785] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 02/08/2022] [Accepted: 02/25/2022] [Indexed: 11/11/2022]
Abstract
Xu et al. recently demonstrated that cryptochrome 4 (CRY4) protein, as a light-dependent magnetic receptor, can sense geomagnetic fields to guide night-migratory songbirds' navigation and evolution by the formation of composite radical pairs and electron transport. We aim to comment on CRY4 through radical pairs and electron transport for magnetic sensitive in night-migratory songbirds' migration and evolution. Additionally, we find that the role of magnetic fields is deeply concerning to the scientific community and very enlightening for the diagnosis and treatment of cancer and vascular disease. We believe that this commentary makes a significant contribution to the literature because it elaborates on the importance of the geomagnetic field to night-migratory songbirds and extends the diagnostic and therapeutic value to cancer and vascular disease. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Enlin Chen
- Department of anesthesiology, The First Affiliated Hospital Of University of South China,, Hengyang, 421001, Hunan, China
| | - Zhe Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Basic Medical Science, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Linxi Chen
- Institute of Pharmacy and Pharmacology, Hunan Provincial Key Laboratory of tumor microenvironment responsive drug research, Hunan Province Cooperative Innovation Center for Molecular Target New Drug Study, College of Basic Medical Science, Hengyang Medical School, University of South China, Hengyang, 421001, Hunan, China
| | - Xiaoling Hu
- Department of anesthesiology, The First Affiliated Hospital Of University of South China,, Hengyang, 421001, Hunan, China
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41
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Deviers J, Cailliez F, de la Lande A, Kattnig DR. Anisotropic magnetic field effects in the re-oxidation of cryptochrome in the presence of scavenger radicals. J Chem Phys 2022; 156:025101. [PMID: 35032990 DOI: 10.1063/5.0078115] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
The avian compass and many other of nature's magnetoreceptive traits are widely ascribed to the protein cryptochrome. There, magnetosensitivity is thought to emerge as the spin dynamics of radicals in the applied magnetic field enters in competition with their recombination. The first and dominant model makes use of a radical pair. However, recent studies have suggested that magnetosensitivity could be markedly enhanced for a radical triad, the primary radical pair of which undergoes a spin-selective recombination reaction with a third radical. Here, we test the practicality of this supposition for the reoxidation reaction of the reduced FAD cofactor in cryptochrome, which has been implicated with light-independent magnetoreception but appears irreconcilable with the classical radical pair mechanism (RPM). Based on the available realistic cryptochrome structures, we predict the magnetosensitivity of radical triad systems comprising the flavin semiquinone, the superoxide, and a tyrosine or ascorbyl scavenger radical. We consider many hyperfine-coupled nuclear spins, the relative orientation and placement of the radicals, their coupling by the electron-electron dipolar interaction, and spin relaxation in the superoxide radical in the limit of instantaneous decoherence, which have not been comprehensively considered before. We demonstrate that these systems can provide superior magnetosensitivity under realistic conditions, with implications for dark-state cryptochrome magnetoreception and other biological magneto- and isotope-sensitive radical recombination reactions.
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Affiliation(s)
- Jean Deviers
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
| | - Fabien Cailliez
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Aurélien de la Lande
- Institut de Chimie Physique, Université Paris Saclay, CNRS (UMR 8000), 15 avenue Jean Perrin, 91405 Orsay, France
| | - Daniel R Kattnig
- Department of Physics and Living Systems Institute, University of Exeter, Stocker Road, EX4 4QD Exeter, United Kingdom
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42
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Broadband 75-85 MHz radiofrequency fields disrupt magnetic compass orientation in night-migratory songbirds consistent with a flavin-based radical pair magnetoreceptor. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2022; 208:97-106. [PMID: 35019998 PMCID: PMC8918455 DOI: 10.1007/s00359-021-01537-8] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 12/15/2021] [Accepted: 12/17/2021] [Indexed: 12/20/2022]
Abstract
The light-dependent magnetic compass sense of night-migratory songbirds can be disrupted by weak radiofrequency fields. This finding supports a quantum mechanical, radical-pair-based mechanism of magnetoreception as observed for isolated cryptochrome 4, a protein found in birds’ retinas. The exact identity of the magnetically sensitive radicals in cryptochrome is uncertain in vivo, but their formation seems to require a bound flavin adenine dinucleotide chromophore and a chain of four tryptophan residues within the protein. Resulting from the hyperfine interactions of nuclear spins with the unpaired electrons, the sensitivity of the radicals to radiofrequency magnetic fields depends strongly on the number of magnetic nuclei (hydrogen and nitrogen atoms) they contain. Quantum-chemical calculations suggested that electromagnetic noise in the frequency range 75–85 MHz could give information about the identity of the radicals involved. Here, we show that broadband 75–85 MHz radiofrequency fields prevent a night-migratory songbird from using its magnetic compass in behavioural experiments. These results indicate that at least one of the components of the radical pair involved in the sensory process of avian magnetoreception must contain a substantial number of strong hyperfine interactions as would be the case if a flavin–tryptophan radical pair were the magnetic sensor.
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43
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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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44
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Babcock N, Kattnig DR. Radical Scavenging Could Answer the Challenge Posed by Electron-Electron Dipolar Interactions in the Cryptochrome Compass Model. JACS AU 2021; 1:2033-2046. [PMID: 34841416 PMCID: PMC8611662 DOI: 10.1021/jacsau.1c00332] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2021] [Indexed: 06/13/2023]
Abstract
Many birds are endowed with a visual magnetic sense that may exploit magnetosensitive radical recombination processes in the protein cryptochrome. In this widely accepted but unproven model, geomagnetic sensitivity is suggested to arise from variations in the recombination rate of a pair of radicals, whose unpaired electron spins undergo coherent singlet-triplet interconversion in the geomagnetic field by coupling to nuclear spins via hyperfine interactions. However, simulations of this conventional radical pair mechanism (RPM) predicted only tiny magnetosensitivities for realistic conditions because the RPM's directional sensitivity is strongly suppressed by the intrinsic electron-electron dipolar (EED) interactions, casting doubt on its viability as a magnetic sensor. We show how this RPM-suppression problem is overcome in a three-radical system in which a third "scavenger" radical reacts with one member of the primary pair. We use this finding to predict substantial magnetic field effects that exceed those of the RPM in the presence of EED interactions in animal cryptochromes.
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Affiliation(s)
- Nathan
Sean Babcock
- Quantum
Biology Laboratory, Howard University, 2400 Sixth Street NW, Washington District of Columbia, 20059, United States of America
- Living
Systems Institute and Department of Physics University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
| | - Daniel R. Kattnig
- Living
Systems Institute and Department of Physics University of Exeter, Stocker Road, Exeter, EX4 4QD, United Kingdom
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45
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Ozturk N. Light-dependent reactions of animal circadian photoreceptor cryptochrome. FEBS J 2021; 289:6622-6639. [PMID: 34750956 DOI: 10.1111/febs.16273] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2021] [Revised: 10/21/2021] [Accepted: 11/08/2021] [Indexed: 11/29/2022]
Abstract
Circadian rhythms are endogenous autonomous 24-h oscillations that are generated by a transcription-translation feedback loop (TTFL). In the positive arm of the TTFL, two transcription factors activate the expression of two genes of the negative arm as well as circadian clock-regulated genes. The circadian clocks are reset through photoreceptor proteins by sunlight in the early morning to keep synchrony with the geological clock. Among animal circadian photoreceptors, Drosophila Cryptochrome (DmCRY) has some unique properties because Drosophila has a single cryptochrome (CRY) that appears to have functions which are specific to organs or tissues, or even to a subset of cells. In mammals, CRYs are not photoreceptors but function in the TTFL, while insects have a light-insensitive mammalian-like CRY or a Drosophila-like photoreceptor CRY (or both). Here, we postulate that as being just one CRY in Drosophila, DmCRY might play different roles in different tissues/organs in a context-dependent manner. In addition to being a circadian photoreceptor/protein, attributing also a magnetoreception function to DmCRY has increased its workload. Considering that DmCRY senses photons as a photoreceptor but also can regulate many different events in a light-dependent manner, differential protein-protein interactions (PPIs) of DmCRY might play a critical role in the generation of such diverse outputs. Therefore, we need to add novel approaches in addition to the current ones to study multiple and context-dependent functions of DmCRY by adopting recently developed techniques. Successful identification of transient/fast PPIs on a scale of minutes would enhance our understanding of light-dependent and/or magnetoreception-associated reactions.
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Affiliation(s)
- Nuri Ozturk
- Molecular Biology and Genetics, Gebze Technical University, Turkey
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46
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Wong SY, Wei Y, Mouritsen H, Solov'yov IA, Hore PJ. Cryptochrome magnetoreception: four tryptophans could be better than three. J R Soc Interface 2021; 18:20210601. [PMID: 34753309 PMCID: PMC8580466 DOI: 10.1098/rsif.2021.0601] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 10/14/2021] [Indexed: 12/28/2022] Open
Abstract
The biophysical mechanism of the magnetic compass sensor in migratory songbirds is thought to involve photo-induced radical pairs formed in cryptochrome (Cry) flavoproteins located in photoreceptor cells in the eyes. In Cry4a-the most likely of the six known avian Crys to have a magnetic sensing function-four radical pair states are formed sequentially by the stepwise transfer of an electron along a chain of four tryptophan residues to the photo-excited flavin. In purified Cry4a from the migratory European robin, the third of these flavin-tryptophan radical pairs is more magnetically sensitive than the fourth, consistent with the smaller separation of the radicals in the former. Here, we explore the idea that these two radical pair states of Cry4a could exist in rapid dynamic equilibrium such that the key magnetic and kinetic properties are weighted averages. Spin dynamics simulations suggest that the third radical pair is largely responsible for magnetic sensing while the fourth may be better placed to initiate magnetic signalling particularly if the terminal tryptophan radical can be reduced by a nearby tyrosine. Such an arrangement could have allowed independent optimization of the essential sensing and signalling functions of the protein. It might also rationalize why avian Cry4a has four tryptophans while Crys from plants have only three.
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Affiliation(s)
- Siu Ying Wong
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - Yujing Wei
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
| | - Henrik Mouritsen
- Institut für Biologie und Umweltwissenschaften, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
- Research Centre for Neurosensory Science, University of Oldenburg, Oldenburg 26111, Germany
| | - Ilia A. Solov'yov
- Institut für Physik, Carl-von-Ossietzky Universität Oldenburg, Oldenburg 26111, Germany
| | - P. J. Hore
- Department of Chemistry, University of Oxford, Oxford OX1 3QZ, UK
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Einwich A, Seth PK, Bartölke R, Bolte P, Feederle R, Dedek K, Mouritsen H. Localisation of cryptochrome 2 in the avian retina. J Comp Physiol A Neuroethol Sens Neural Behav Physiol 2021; 208:69-81. [PMID: 34677638 PMCID: PMC8918457 DOI: 10.1007/s00359-021-01506-1] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 08/13/2021] [Accepted: 08/19/2021] [Indexed: 12/12/2022]
Abstract
Cryptochromes are photolyase-related blue-light receptors acting as core components of the mammalian circadian clock in the cell nuclei. One or more members of the cryptochrome protein family are also assumed to play a role in avian magnetoreception, but the primary sensory molecule in the retina of migratory birds that mediates light-dependent magnetic compass orientation has still not been identified. The mRNA of cryptochrome 2 (Cry2) has been reported to be located in the cell nuclei of the retina, but Cry2 localisation has not yet been demonstrated at the protein level. Here, we provide evidence that Cry2 protein is located in the photoreceptor inner segments, the outer nuclear layer, the inner nuclear layer and the ganglion cell layer in the retina of night-migratory European robins, homing pigeons and domestic chickens. At the subcellular level, we find Cry2 both in the cytoplasm and the nucleus of cells residing in these layers. This broad nucleic expression rather points to a role for avian Cry2 in the circadian clock and is consistent with a function as a transcription factor, analogous to mammalian Cry2, and speaks against an involvement in magnetoreception.
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Affiliation(s)
- Angelika Einwich
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Pranav Kumar Seth
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Rabea Bartölke
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Petra Bolte
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Regina Feederle
- Helmholtz Zentrum München, German Research Center for Environmental Health, Institute for Diabetes and Obesity, Monoclonal Antibody Core Facility, Neuherberg, Germany
| | - Karin Dedek
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.,Research Centre for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany
| | - Henrik Mouritsen
- Institute for Biology and Environmental Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany. .,Research Centre for Neurosensory Sciences, Carl von Ossietzky University Oldenburg, Oldenburg, Germany.
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Balay SD, Hochstoeger T, Vilceanu A, Malkemper EP, Snider W, Dürnberger G, Mechtler K, Schuechner S, Ogris E, Nordmann GC, Ushakova L, Nimpf S, Keays DA. The expression, localisation and interactome of pigeon CRY2. Sci Rep 2021; 11:20293. [PMID: 34645873 PMCID: PMC8514597 DOI: 10.1038/s41598-021-99207-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 09/13/2021] [Indexed: 11/18/2022] Open
Abstract
Cryptochromes (CRY) are highly conserved signalling molecules that regulate circadian rhythms and are candidate radical pair based magnetoreceptors. Birds have at least four cryptochromes (CRY1a, CRY1b, CRY2, and CRY4), but few studies have interrogated their function. Here we investigate the expression, localisation and interactome of clCRY2 in the pigeon retina. We report that clCRY2 has two distinct transcript variants, clCRY2a, and a previously unreported splice isoform, clCRY2b which is larger in size. We show that clCRY2a mRNA is expressed in all retinal layers and clCRY2b is enriched in the inner and outer nuclear layer. To define the localisation and interaction network of clCRY2 we generated and validated a monoclonal antibody that detects both clCRY2 isoforms. Immunohistochemical studies revealed that clCRY2a/b is present in all retinal layers and is enriched in the outer limiting membrane and outer plexiform layer. Proteomic analysis showed clCRY2a/b interacts with typical circadian molecules (PER2, CLOCK, ARTNL), cell junction proteins (CTNNA1, CTNNA2) and components associated with the microtubule motor dynein (DYNC1LI2, DCTN1, DCTN2, DCTN3) within the retina. Collectively these data show that clCRY2 is a component of the avian circadian clock and unexpectedly associates with the microtubule cytoskeleton.
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Affiliation(s)
- Spencer D Balay
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Tobias Hochstoeger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Alexandra Vilceanu
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - E Pascal Malkemper
- Max Planck Research Group Neurobiology of Magnetoreception, Center of Advanced European Studies and Research (Caesar), Ludwig-Erhard-Allee 2, 53175, Bonn, Germany
| | - William Snider
- Department of Neuroscience, Johns Hopkins University School of Medicine, Baltimore, USA
| | - Gerhard Dürnberger
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Karl Mechtler
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria.,Institute of Molecular Biotechnology of the Austrian Academy of Sciences (IMBA), Vienna Biocenter (VBC), Dr. Bohr-Gasse 3, 1030, Vienna, Austria
| | - Stefan Schuechner
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Egon Ogris
- Monoclonal Antibody Facility, Max Perutz Labs, Medical University of Vienna, Dr. Bohr-Gasse 9, 1030, Vienna, Austria
| | - Gregory C Nordmann
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria.,Vienna BioCenter PhD Program, Doctoral School of the University of Vienna and Medical University of Vienna, 1030, Vienna, Austria
| | - Lyubov Ushakova
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - Simon Nimpf
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria
| | - David A Keays
- Research Institute of Molecular Pathology (IMP), Vienna Biocenter (VBC), Campus Vienna Biocenter 1, 1030, Vienna, Austria. .,Department of Anatomy and Neuroscience, University of Melbourne, Parkville, Australia. .,Division of Neurobiology, Department Biology II, Ludwig-Maximilians-University Munich, Planegg-Martinsried, 82152, Munich, Germany.
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49
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Hamada M, Iwata T, Fuki M, Kandori H, Weber S, Kobori Y. Orientations and water dynamics of photoinduced secondary charge-separated states for magnetoreception by cryptochrome. Commun Chem 2021; 4:141. [PMID: 36697801 PMCID: PMC9814139 DOI: 10.1038/s42004-021-00573-4] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 09/02/2021] [Indexed: 01/28/2023] Open
Abstract
In the biological magnetic compass, blue-light photoreceptor protein of cryptochrome is thought to conduct the sensing of the Earth's magnetic field by photoinduced sequential long-range charge-separation (CS) through a cascade of tryptophan residues, WA(H), WB(H) and WC(H). Mechanism of generating the weak-field sensitive radical pair (RP) is poorly understood because geometries, electronic couplings and their modulations by molecular motion have not been investigated in the secondary CS states generated prior to the terminal RP states. In this study, water dynamics control of the electronic coupling is revealed to be a key concept for sensing the direction of weak magnetic field. Geometry and exchange coupling (singlet-triplet energy gap: 2J) of photoinduced secondary CS states composed of flavin adenine dinucleotide radical anion (FAD-•) and radical cation WB(H)+• in the cryptochrome DASH from Xenopus laevis were clarified by time-resolved electron paramagnetic resonance. We found a time-dependent energetic disorder in 2J and was interpreted by a trap CS state capturing one reorientated water molecule at 120 K. Enhanced electron-tunneling by water-libration was revealed for the terminal charge-separation event at elevated temperature. This highlights importance of optimizing the electronic coupling for regulation of the anisotropic RP yield on the possible magnetic compass senses.
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Affiliation(s)
- Misato Hamada
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Tatsuya Iwata
- grid.265050.40000 0000 9290 9879Department of Pharmaceutical Sciences, Toho University, Funabashi, Chiba 274‒8510 Japan
| | - Masaaki Fuki
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
| | - Hideki Kandori
- grid.47716.330000 0001 0656 7591Department of Life Science and Applied Chemistry, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan ,grid.47716.330000 0001 0656 7591OptoBioTechnology Research Center, Nagoya Institute of Technology, Showa-ku, Nagoya 466-8555 Japan
| | - Stefan Weber
- grid.5963.9Institute of Physical Chemistry, Albert-Ludwigs-Universität Freiburg, 79104 Freiburg, Germany
| | - Yasuhiro Kobori
- grid.31432.370000 0001 1092 3077Department of Chemistry, Graduate School of Science, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan ,grid.31432.370000 0001 1092 3077Molecular Photoscience Research Center, Kobe University, 1‒1 Rokkodai‒cho, Nada‒ku, Kobe, 657‒8501 Japan
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Dybus A, Kulig H, Yu YH, Lanckriet R, Proskura W, Cheng YH. CRY1 Gene Polymorphism and Racing Performance of Homing Pigeons. Animals (Basel) 2021; 11:2632. [PMID: 34573598 PMCID: PMC8466513 DOI: 10.3390/ani11092632] [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: 08/24/2021] [Revised: 09/03/2021] [Accepted: 09/06/2021] [Indexed: 11/16/2022] Open
Abstract
Cryptochromes (CRY) are the family of proteins proposed as the putative magnetoreceptor molecules. In birds, among others in pigeons, CRY1 is widely expressed in a retina. Homing pigeons are known for their navigational abilities, and pigeon racing is a popular sport. So, the purpose of this study was to analyze the variability of the nucleotide sequence of the homing pigeon CRY1 gene, spanning the region coding the two amino acids W320 and W374 of Trp-triad, and estimate the relationship between genotypes and the racing performance. Investigations were carried out on 129 pigeons. Analysis of sequencing results indicated the AG to TT change within the seventh intron of CRY1 gene. Genotypes were determined by the forced PCR-RFLP method. The influence of detected polymorphism on the results of racing pigeons in 100-400 km flights was shown. The AG/TT individuals achieved significantly higher (p ≤ 0.05) mean values of ace points (AP) than the AG/AG ones. Regarding the detected nucleotide change localization, the polymorphism may be involved in CRY1 gene expression modulation. The AG to TT change in CRY1 gene may be considered as a potential genetic marker of racing performance in homing pigeons.
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Affiliation(s)
- Andrzej Dybus
- Department of Genetics, West Pomeranian University of Technology, 70-311 Szczecin, Poland;
| | - Hanna Kulig
- Department of Genetics, West Pomeranian University of Technology, 70-311 Szczecin, Poland;
| | - Yu-Hsiang Yu
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (Y.-H.Y.); (Y.-H.C.)
| | | | - Witold Proskura
- Faculty of Biotechnology and Animal Husbandry, West Pomeranian University of Technology in Szczecin, 71-270 Szczecin, Poland;
| | - Yeong-Hsiang Cheng
- Department of Biotechnology and Animal Science, National Ilan University, Yilan 26047, Taiwan; (Y.-H.Y.); (Y.-H.C.)
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