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Chretien A, Nagel MF, Botha S, de Wijn R, Brings L, Dörner K, Han H, Koliyadu JCP, Letrun R, Round A, Sato T, Schmidt C, Secareanu RC, von Stetten D, Vakili M, Wrona A, Bean R, Mancuso A, Schulz J, Pearson AR, Kottke T, Lorenzen K, Schubert R. Light-induced Trp in/Met out Switching During BLUF Domain Activation in ATP-bound Photoactivatable Adenylate Cyclase OaPAC. J Mol Biol 2024; 436:168439. [PMID: 38185322 DOI: 10.1016/j.jmb.2024.168439] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2023] [Revised: 11/28/2023] [Accepted: 01/03/2024] [Indexed: 01/09/2024]
Abstract
The understanding of signal transduction mechanisms in photoreceptor proteins is essential for elucidating how living organisms respond to light as environmental stimuli. In this study, we investigated the ATP binding, photoactivation and signal transduction process in the photoactivatable adenylate cyclase from Oscillatoria acuminata (OaPAC) upon blue light excitation. Structural models with ATP bound in the active site of native OaPAC at cryogenic as well as room temperature are presented. ATP is found in one conformation at cryogenic- and in two conformations at ambient-temperature, and is bound in an energetically unfavorable conformation for the conversion to cAMP. However, FTIR spectroscopic experiments confirm that this conformation is the native binding mode in dark state OaPAC and that transition to a productive conformation for ATP turnover only occurs after light activation. A combination of time-resolved crystallography experiments at synchrotron and X-ray Free Electron Lasers sheds light on the early events around the Flavin Adenine Dinucleotide (FAD) chromophore in the light-sensitive BLUF domain of OaPAC. Early changes involve the highly conserved amino acids Tyr6, Gln48 and Met92. Crucially, the Gln48 side chain performs a 180° rotation during activation, leading to the stabilization of the FAD chromophore. Cryo-trapping experiments allowed us to investigate a late light-activated state of the reaction and revealed significant conformational changes in the BLUF domain around the FAD chromophore. In particular, a Trpin/Metout transition upon illumination is observed for the first time in the BLUF domain and its role in signal transmission via α-helix 3 and 4 in the linker region between sensor and effector domain is discussed.
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Affiliation(s)
- Anaïs Chretien
- European XFEL GmbH, Schenefeld, Germany; Department of Chemistry, Universität Hamburg, Hamburg, Germany
| | - Marius F Nagel
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
| | - Sabine Botha
- Department of Physics, Arizona State University, Tempe, AZ 85287-1504, USA; Biodesign Center for Applied Structural Discovery, Arizona State University, Tempe, AZ 85287-5001, USA
| | | | | | | | | | | | | | | | | | | | | | - David von Stetten
- European Molecular Biology Laboratory, Hamburg Unit, Hamburg, Germany
| | | | | | | | | | | | - Arwen R Pearson
- Institute for Nanostructure and Solid-State Physics, Universität Hamburg, Hamburg, Germany
| | - Tilman Kottke
- Department of Chemistry and Medical School OWL, Bielefeld University, Bielefeld, Germany
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2
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Nakasone Y, Terazima M. Time-resolved diffusion reveals photoreactions of BLUF proteins with similar functional domains. Photochem Photobiol Sci 2022; 21:493-507. [PMID: 35391638 DOI: 10.1007/s43630-022-00214-2] [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: 02/04/2022] [Accepted: 03/21/2022] [Indexed: 11/30/2022]
Abstract
BLUF (blue light sensor using flavin) proteins are the blue light receptors that consist of flavin-binding BLUF domains and functional domains. Upon blue light excitation, the hydrogen bond network around the flavin chromophore changes, and the absorption spectrum in the visible region shifts to red. Light signal received in the BLUF domain is intramolecularly or intermolecularly transmitted to the functional region. In this review, the reactions of three BLUF proteins with similar EAL functional groups within the protein (BlrP1, and YcgF), or with a separated target protein (PapB) are described using time-resolved diffusion technique. The diffusion coefficients (D) of the BLUF domains did not significantly change upon photoexcitation, whereas those of the full-length proteins BlrP1 and YcgF and the PapB-PapA system significantly decreased. The changes in D should be due to diffusion-sensitive conformational changes (DSCC) that alter the friction of diffusion. The time constants of the major D changes of BlrP1 and PapB-PapA were similar (~ 20 ms), although the magnitude of the friction change depended on the proteins. Similarities and differences among the reactions of these proteins were clarified from the viewpoint of DSCC.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan.
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3
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Genetic Factors Affect the Survival and Behaviors of Selected Bacteria during Antimicrobial Blue Light Treatment. Int J Mol Sci 2021; 22:ijms221910452. [PMID: 34638788 PMCID: PMC8508746 DOI: 10.3390/ijms221910452] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2021] [Revised: 09/22/2021] [Accepted: 09/24/2021] [Indexed: 12/26/2022] Open
Abstract
Antimicrobial resistance is a global, mounting and dynamic issue that poses an immediate threat to human, animal, and environmental health. Among the alternative antimicrobial treatments proposed to reduce the external use of antibiotics is electromagnetic radiation, such as blue light. The prevailing mechanistic model is that blue light can be absorbed by endogenous porphyrins within the bacterial cell, inducing the production of reactive oxygen species, which subsequently inflict oxidative damages upon different cellular components. Nevertheless, it is unclear whether other mechanisms are involved, particularly those that can affect the efficacy of antimicrobial blue light treatments. In this review, we summarize evidence of inherent factors that may confer protection to a selected group of bacteria against blue light-induced oxidative damages or modulate the physiological characteristics of the treated bacteria, such as virulence and motility. These include descriptions of three major photoreceptors in bacteria, chemoreceptors, SOS-dependent DNA repair and non-SOS protective mechanisms. Future directions are also provided to assist with research efforts to increase the efficacy of antimicrobial blue light and to minimize the development of blue light-tolerant phenotypes.
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Pintér G, Hohmann K, Grün J, Wirmer-Bartoschek J, Glaubitz C, Fürtig B, Schwalbe H. Real-time nuclear magnetic resonance spectroscopy in the study of biomolecular kinetics and dynamics. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:291-320. [PMID: 37904763 PMCID: PMC10539803 DOI: 10.5194/mr-2-291-2021] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/03/2021] [Accepted: 04/07/2021] [Indexed: 11/01/2023]
Abstract
The review describes the application of nuclear magnetic resonance (NMR) spectroscopy to study kinetics of folding, refolding and aggregation of proteins, RNA and DNA. Time-resolved NMR experiments can be conducted in a reversible or an irreversible manner. In particular, irreversible folding experiments pose large requirements for (i) signal-to-noise due to the time limitations and (ii) synchronising of the refolding steps. Thus, this contribution discusses the application of methods for signal-to-noise increases, including dynamic nuclear polarisation, hyperpolarisation and photo-CIDNP for the study of time-resolved NMR studies. Further, methods are reviewed ranging from pressure and temperature jump, light induction to rapid mixing to induce rapidly non-equilibrium conditions required to initiate folding.
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Affiliation(s)
- György Pintér
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Katharina F. Hohmann
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - J. Tassilo Grün
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Julia Wirmer-Bartoschek
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Clemens Glaubitz
- Institute for Biophysical Chemistry, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemistry and Chemical Biology, Center for
Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang
Goethe-Universität Frankfurt, Frankfurt 60438, Germany
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5
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Nakasone Y, Kikukawa K, Masuda S, Terazima M. Time-Resolved Study of Interprotein Signaling Process of a Blue Light Sensor PapB–PapA Complex. J Phys Chem B 2019; 123:3210-3218. [DOI: 10.1021/acs.jpcb.9b00196] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023]
Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Koutaro Kikukawa
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
| | - Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama 226-5801, Japan
| | - Masahide Terazima
- Department of Chemistry, Graduate School of Science, Kyoto University, Oiwake, Kitashirakawa,
Sakyo-ku, Kyoto 606-8502, Japan
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6
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Park SY, Tame JRH. Seeing the light with BLUF proteins. Biophys Rev 2017; 9:169-176. [PMID: 28510088 DOI: 10.1007/s12551-017-0258-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Accepted: 03/05/2017] [Indexed: 10/19/2022] Open
Abstract
First described about 15 years ago, BLUF (Blue Light Using Flavin) domains are light-triggered switches that control enzyme activity or gene expression in response to blue light, remaining activated for seconds or even minutes after stimulation. The conserved, ferredoxin-like fold holds a flavin chromophore that captures the light and somehow triggers downstream events. BLUF proteins are found in both prokaryotes and eukaryotes and have a variety of architectures and oligomeric forms, but the BLUF domain itself seems to have a well-preserved structure and mechanism that have been the focus of intense study for a number of years. Crystallographic and NMR structures of BLUF domains have been solved, but the conflicting models have led to considerable debate about the atomic details of photo-activation. Advanced spectroscopic and computational methods have been used to analyse the early events after photon absorption, but these too have led to widely differing conclusions. New structural models are improving our understanding of the details of the mechanism and may lead to novel tailor-made tools for optogenetics.
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Affiliation(s)
- Sam-Yong Park
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan
| | - Jeremy R H Tame
- Drug Design Laboratory, Graduate School of Medical Life Science, Yokohama City University, 1-7-29 Suehiro, Tsurumi, Yokohama, 230-0045, Japan.
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Stierl M, Penzkofer A, Kennis JTM, Hegemann P, Mathes T. Key Residues for the Light Regulation of the Blue Light-Activated Adenylyl Cyclase from Beggiatoa sp. Biochemistry 2014; 53:5121-30. [DOI: 10.1021/bi500479v] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Manuela Stierl
- Institut
für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Alfons Penzkofer
- Fakultät
für Physik, Universität Regensburg, Universitätsstrasse 31, D-93053 Regensburg, Germany
| | - John T. M. Kennis
- Department
of Exact Sciences/Biophysics, Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands
| | - Peter Hegemann
- Institut
für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
| | - Tilo Mathes
- Institut
für Biologie/Experimentelle Biophysik, Humboldt Universität zu Berlin, Invalidenstrasse 42, D-10115 Berlin, Germany
- Department
of Exact Sciences/Biophysics, Vrije Universiteit, De Boelelaan 1081A, 1081 HV Amsterdam, The Netherlands
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8
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Dorn M, Jurk M, Wartenberg A, Hahn A, Schmieder P. LOV takes a pick: thermodynamic and structural aspects of the flavin-LOV-interaction of the blue-light sensitive photoreceptor YtvA from Bacillus subtilis. PLoS One 2013; 8:e81268. [PMID: 24278408 PMCID: PMC3836802 DOI: 10.1371/journal.pone.0081268] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2013] [Accepted: 10/10/2013] [Indexed: 11/29/2022] Open
Abstract
LOV domains act as versatile photochromic switches servicing multiple effector domains in a variety of blue light sensing photoreceptors abundant in a multitude of organisms from all kingdoms of life. The perception of light is realized by a flavin chromophore that upon illumination reversibly switches from the non-covalently bound dark-state to a covalently linked flavin-LOV adduct. It is usually assumed that most LOV domains preferably bind FMN, but heterologous expression frequently results in the incorporation of all natural occurring flavins, i.e. riboflavin, FMN and FAD. Over recent years, the structures, photochemical properties, activation mechanisms and physiological functions of a multitude of LOV proteins have been studied intensively, but little is known about its affinities to physiologically relevant flavins or the thermodynamics of the flavin-LOV interaction. We have investigated the interaction of the LOV domain of the well characterized bacterial photoreceptor YtvA with riboflavin, FMN and FAD by ITC experiments providing binding constants and thermodynamic profiles of these interactions. For this purpose, we have developed a protocol for the production of the apo forms of YtvA and its isolated LOV domain and we demonstrate that the latter can be used as a molecular probe for free flavins in cell lysates. Furthermore, we show here using NMR spectroscopic techniques and Analytical Ultracentrifugation that the flavin moiety stabilizes the conformation of the LOV domain and that dimerization of YtvA is caused not only by intermolecular LOV-LOV but also by STAS-STAS contacts.
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Affiliation(s)
- Matthias Dorn
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Marcel Jurk
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
| | - Anne Wartenberg
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Aaron Hahn
- Department of Chemistry and Biochemistry, Freie Universität Berlin, Berlin, Germany
| | - Peter Schmieder
- Department of Structural Biology, Leibniz-Institut für Molekulare Pharmakologie, Berlin, Germany
- * E-mail:
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9
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Tomaselli S, Giovanella U, Pagano K, Leone G, Zanzoni S, Assfalg M, Meinardi F, Molinari H, Botta C, Ragona L. Encapsulation of a Rhodamine Dye within a Bile Acid Binding Protein: Toward Water Processable Functional Bio Host–Guest Materials. Biomacromolecules 2013; 14:3549-56. [DOI: 10.1021/bm400904s] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
Affiliation(s)
- Simona Tomaselli
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Umberto Giovanella
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Katiuscia Pagano
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Giuseppe Leone
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Serena Zanzoni
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada
Le Grazie 15, 37134, Verona, Italy
| | - Michael Assfalg
- Dipartimento
di Biotecnologie, Università degli Studi di Verona, Strada
Le Grazie 15, 37134, Verona, Italy
| | - Francesco Meinardi
- Università degli Studi Milano Bicocca, Via Cozzi 53, 20125, Milano, Italy
| | - Henriette Molinari
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Chiara Botta
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
| | - Laura Ragona
- Istituto
per lo Studio delle Macromolecole, CNR, via Bassini 15, 20133 Milano, Italy
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10
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Masuda S. Light detection and signal transduction in the BLUF photoreceptors. PLANT & CELL PHYSIOLOGY 2013; 54:171-179. [PMID: 23243105 DOI: 10.1093/pcp/pcs173] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
BLUF (sensor of blue light using FAD) domain-containing proteins are one of three types of flavin-binding, blue-light-sensing proteins found in many bacteria and some algae. The other types of blue-light-sensing proteins are the cryptochromes and the light, oxygen, voltage (LOV) domain-containing proteins. BLUF proteins control a wide variety of light-dependent physiological activities including photosystem synthesis, biofilm formation and the photoavoidance response. The BLUF domain photochemical reaction is unique in that only small chromophore structural changes are involved in the light activation process, because the rigid flavin moiety is involved, rather than an isomerizable chromophore (e.g. phytochromobilin in phytochromes and retinal in rhodopsins). Recent spectroscopic, biochemical and structural studies have begun to elucidate how BLUF domains transmit the light-induced signal and identify related, subsequent changes in the domain structures. Herein, I review progress made to date concerning the physiological functions and the phototransduction mechanism of BLUF proteins.
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Affiliation(s)
- Shinji Masuda
- Center for Biological Resources and Informatics, Tokyo Institute of Technology, Yokohama, Japan.
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11
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Schlepckow K, Fürtig B, Schwalbe H. Nonequilibrium NMR Methods for Monitoring Protein and RNA Folding. Z PHYS CHEM 2011. [DOI: 10.1524/zpch.2011.0120] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractThe review introduces to time-resolved NMR spectroscopic investigations of the kinetics of protein and RNA folding. The description of the experimental investigations is discussed in the context of possible kinetic folding pathways showing the extent of information that can be gained from the various kinetic experiments. The review introduces to four different methods to initiate folding reactions in connection with time-resolved NMR experiments and discusses examples of refolding of the model proteinα-lactalbumin and of bistable RNAs.
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Affiliation(s)
- Kai Schlepckow
- Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biolo, Frankfurt a.M., Deutschland
| | - Boris Fürtig
- Johann Wolfgang Goethe University, Institute for Organic Chemistry and Chemical Biolo, Frankfurt a.M., Deutschland
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12
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Elías-Arnanz M, Padmanabhan S, Murillo FJ. Light-dependent gene regulation in nonphototrophic bacteria. Curr Opin Microbiol 2011; 14:128-35. [DOI: 10.1016/j.mib.2010.12.009] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2010] [Revised: 12/15/2010] [Accepted: 12/15/2010] [Indexed: 11/24/2022]
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13
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Losi A, Gärtner W. Old Chromophores, New Photoactivation Paradigms, Trendy Applications: Flavins in Blue Light-Sensing Photoreceptors†. Photochem Photobiol 2011; 87:491-510. [DOI: 10.1111/j.1751-1097.2011.00913.x] [Citation(s) in RCA: 120] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
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14
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Weber S, Schroeder C, Kacprzak S, Mathes T, Kowalczyk RM, Essen LO, Hegemann P, Schleicher E, Bittl R. Light-generated paramagnetic intermediates in BLUF domains. Photochem Photobiol 2011; 87:574-83. [PMID: 21198648 DOI: 10.1111/j.1751-1097.2010.00885.x] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Blue-light sensitive photoreceptory BLUF domains are flavoproteins, which regulate various, mostly stress-related processes in bacteria and eukaryotes. The photoreactivity of the flavin adenine dinucleotide (FAD) cofactor in three BLUF domains from Rhodobacter sphaeroides, Synechocystis sp. PCC 6803 and Escherichia coli have been studied at low temperature using time-resolved electron paramagnetic resonance. Photoinduced flavin triplet states and radical-pair species have been detected on a microsecond time scale. Differences in the electronic structures of the FAD cofactors as reflected by altered zero-field splitting parameters of the triplet states could be correlated with changes in the amino-acid composition of the various BLUF domains' cofactor binding pockets. For the generation of the light-induced, spin-correlated radical-pair species in the BLUF domain from Synechocystis sp. PCC 6803, a tyrosine residue near the flavin's isoalloxazine moiety plays a critical role.
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Affiliation(s)
- Stefan Weber
- Albert-Ludwigs-Universität Freiburg, Institut für Physikalische Chemie, Freiburg, Germany
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15
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Zoltowski BD, Gardner KH. Tripping the light fantastic: blue-light photoreceptors as examples of environmentally modulated protein-protein interactions. Biochemistry 2011; 50:4-16. [PMID: 21141905 PMCID: PMC3137735 DOI: 10.1021/bi101665s] [Citation(s) in RCA: 133] [Impact Index Per Article: 10.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Blue-light photoreceptors play a pivotal role in detecting the quality and quantity of light in the environment, controlling a wide range of biological responses. Several families of blue-light photoreceptors have been characterized in detail using biophysics and biochemistry, beginning with photon absorption, through intervening signal transduction, to regulation of biological activities. Here we review the light oxygen voltage, cryptochrome, and sensors of blue light using FAD families, three different groups of proteins that offer distinctly different modes of photochemical activation and signal transduction yet play similar roles in a vast array of biological responses. We cover mechanisms of light activation and propagation of conformational responses that modulate protein-protein interactions involved in biological signaling. Discovery and characterization of these processes in natural proteins are now allowing the design of photoregulatable engineered proteins, facilitating the generation of novel reagents for biochemical and cell biological research.
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Affiliation(s)
- Brian D. Zoltowski
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816 USA
| | - Kevin H. Gardner
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, TX 75390-8816 USA
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16
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Anders K, von Stetten D, Mailliet J, Kiontke S, Sineshchekov VA, Hildebrandt P, Hughes J, Essen L. Spectroscopic and Photochemical Characterization of the Red‐Light Sensitive Photosensory Module of Cph2 from Synechocystis PCC 6803. Photochem Photobiol 2011; 87:160-173. [DOI: https:/doi.org/10.1111/j.1751-1097.2010.00845.x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2023]
Abstract
AbstractCyanobacterial phytochromes are a diverse family of light receptors controlling various biological functions including phototaxis. In addition to canonical bona fide phytochromes of the well characterized Cph1/plant‐like clade, cyanobacteria also harbor phytochromes that absorb green, violet or blue light. The Synechocystis PCC 6803 Cph2 photoreceptor, a phototaxis inhibitor, is unconventional in bearing two distinct chromophore‐binding GAF domains. Whereas the C‐terminal GAF domain is most likely involved in blue‐light perception, the first two domains correspond to a Cph1‐like photosensory module lacking the PAS domain. Biochemical and spectroscopic studies show that this region switches between red (Pr) and far‐red (Pfr) absorbing states. Unlike Cph1, the Pfr state of Cph2 decays rapidly in darkness. Mutations close to the PCB chromophore further destabilize the Pfr state without drastically affecting the spectroscopic features such as the quantum efficiency of Pr→Pfr conversion, fluorescence, or the Resonance‐Raman signature of the chromophore. Overall, the PAS‐less photosensory module of Cph2 resembles Cph1 including its mode of isomerisation, but the Pfr state is unstable.
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17
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Dragnea V, Arunkumar AI, Lee CW, Giedroc DP, Bauer CE. A Q63E Rhodobacter sphaeroides AppA BLUF domain mutant is locked in a pseudo-light-excited signaling state. Biochemistry 2010; 49:10682-90. [PMID: 21082791 DOI: 10.1021/bi1002162] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The AppA BLUF photoreceptor from Rhodobacter sphaeroides contains a conserved key residue, Gln63, that is thought to undergo a shift in hydrogen-bonding interactions when a bound flavin is light excited. In this study we have characterized two substitution mutants of Gln63 (Q63E, Q63L) in the context of two constructs of the BLUF domain that have differing lengths, AppA1-126 and AppA17-133. Q63L mutations in both constructs exhibit a blue-shifted flavin absorption spectrum as well as a loss of the photocycle. Altered fluorescence emission and fluorescence quenching of the Q63L mutant indicate significant perturbations of hydrogen bonding to the flavin and surrounding amino acids which is confirmed by (1)H-(15)N HSQC NMR spectroscopy. The Q63E substitution mutant is constitutively locked in a lit signaling state as evidenced by a permanent 3 nm red shift of the flavin absorption, quenching of flavin fluorescence emission, analysis of (1)H-(15)N HSQC spectra, and the inability of full-length AppA Q63E to bind to the PpsR repressor. The significance of these findings on the mechanism of light-induced output signaling is discussed.
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Affiliation(s)
- Vladimira Dragnea
- Department of Molecular and Cellular Biochemistry, Indiana University, Bloomington, Indiana 47405, United States
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Anders K, von Stetten D, Mailliet J, Kiontke S, Sineshchekov VA, Hildebrandt P, Hughes J, Essen LO. Spectroscopic and photochemical characterization of the red-light sensitive photosensory module of Cph2 from Synechocystis PCC 6803. Photochem Photobiol 2010; 87:160-73. [PMID: 21091956 DOI: 10.1111/j.1751-1097.2010.00845.x] [Citation(s) in RCA: 38] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Cyanobacterial phytochromes are a diverse family of light receptors controlling various biological functions including phototaxis. In addition to canonical bona fide phytochromes of the well characterized Cph1/plant-like clade, cyanobacteria also harbor phytochromes that absorb green, violet or blue light. The Synechocystis PCC 6803 Cph2 photoreceptor, a phototaxis inhibitor, is unconventional in bearing two distinct chromophore-binding GAF domains. Whereas the C-terminal GAF domain is most likely involved in blue-light perception, the first two domains correspond to a Cph1-like photosensory module lacking the PAS domain. Biochemical and spectroscopic studies show that this region switches between red (P(r) ) and far-red (P(fr) ) absorbing states. Unlike Cph1, the P(fr) state of Cph2 decays rapidly in darkness. Mutations close to the PCB chromophore further destabilize the P(fr) state without drastically affecting the spectroscopic features such as the quantum efficiency of P(r) →P(fr) conversion, fluorescence, or the Resonance-Raman signature of the chromophore. Overall, the PAS-less photosensory module of Cph2 resembles Cph1 including its mode of isomerisation, but the P(fr) state is unstable.
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Affiliation(s)
- Katrin Anders
- Department of Chemistry, Philipps University, Marburg, Germany
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19
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Khrenova M, Domratcheva T, Grigorenko B, Nemukhin A. Coupling between the BLUF and EAL domains in the blue light-regulated phosphodiesterase BlrP1. J Mol Model 2010; 17:1579-86. [PMID: 20924626 DOI: 10.1007/s00894-010-0842-1] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2010] [Accepted: 08/30/2010] [Indexed: 01/13/2023]
Abstract
The first biochemical and structural characterization of the full-length active photoreceptor BlrP1 from Klebsiella pneumoniae was recently reported by Barends et al. [Nature 459:1015-1018, (2009)]. The light-regulated catalytic function of its C-terminal c-di-guanosine monophosphate phosphodiesterase, the EAL (Glu-Ala-Leu) domain, is activated by the N-terminal sensor of blue light using the flavin adenine dinucleotide (BLUF) domain. We performed molecular dynamics simulations on the dimeric BlrP1 protein in order to examine the coupling regions that are presumably involved in transmitting light-induced structural changes which occur in the BLUF domain to the EAL domain. According to the results of simulations and an analysis of the hydrogen bonding between the respective polypeptide chains, the region containing the site on the α3α4 loop of BLUF is responsible for communication between the photosensing and catalytic domains in the dimeric BlrP1 protein.
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Affiliation(s)
- Maria Khrenova
- Chemistry Department, M.V. Lomonosov Moscow State University, Leninskie Gory 1/3, Moscow 119991, Russian Federation
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20
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Nakasone Y, Ono TA, Ishii A, Masuda S, Terazima M. Temperature-sensitive reaction of a photosensor protein YcgF: possibility of a role of temperature sensor. Biochemistry 2010; 49:2288-96. [PMID: 20141167 DOI: 10.1021/bi902121z] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
The spectrally silent photoreaction of a blue light sensor protein YcgF, composed of the N-terminal BLUF domain and the C-terminal EAL domain, was investigated by the time-resolved transient grating method. Comparing photoinduced reactions of full-length YcgF with that of the BLUF-linker construct, it was found that a major conformation change after photoinduced dimerization is predominantly localized on the EAL domain. Furthermore, the photoinduced conformational change displayed significant temperature dependence. This result is explained by an equilibrium of reactive and nonreactive YcgF species, with the population of photoreactive species decreasing as the temperature is lowered in the dark state. We consider that the dimer form is the nonreactive species and it is the dominant species at lower temperatures. The temperature sensitivity of the photoreaction of YcgF suggests that this protein could have a biological function as a temperature sensor as well as behaving as a light sensor.
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Affiliation(s)
- Yusuke Nakasone
- Department of Chemistry, Graduate School of Science, Kyoto University, Kyoto 606-8502, Japan
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21
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Wu Q, Gardner KH. Structure and insight into blue light-induced changes in the BlrP1 BLUF domain. Biochemistry 2009; 48:2620-9. [PMID: 19191473 DOI: 10.1021/bi802237r] [Citation(s) in RCA: 63] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
BLUF domains (sensors of blue light using flavin adenine dinucleotide) are a group of flavin-containing blue light photosensory domains from a variety of bacterial and algal proteins. While spectroscopic studies have indicated that these domains reorganize their interactions with an internally bound chromophore upon illumination, it remains unclear how these are converted into structural and functional changes. To address this, we have solved the solution structure of the BLUF domain from Klebsiella pneumoniae BlrP1, a light-activated c-di-guanosine 5'-monophosphate phosphodiesterase which consists of a sensory BLUF and a catalytic EAL (Glu-Ala-Leu) domain [Schmidt et. al. (2008) J. Bacteriol. 187, 4774-4781]. Our dark state structure of the sensory domain shows that it adopts a standard BLUF domain fold followed by two C-terminal alpha helices which adopt a novel orientation with respect to the rest of the domain. Comparison of NMR spectra acquired under dark and light conditions suggests that residues throughout the BlrP1 BLUF domain undergo significant light-induced chemical shift changes, including sites clustered on the beta(4)beta(5) loop, beta(5) strand, and alpha(3)alpha(4) loop. Given that these changes were observed at several sites on the helical cap, over 15 A from chromophore, our data suggest a long-range signal transduction process in BLUF domains.
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Affiliation(s)
- Qiong Wu
- Department of Biochemistry, University of Texas Southwestern Medical Center, Dallas, Texas 75390-8816, USA
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22
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Minasov G, Padavattan S, Shuvalova L, Brunzelle JS, Miller DJ, Baslé A, Massa C, Collart FR, Schirmer T, Anderson WF. Crystal structures of YkuI and its complex with second messenger cyclic Di-GMP suggest catalytic mechanism of phosphodiester bond cleavage by EAL domains. J Biol Chem 2009; 284:13174-84. [PMID: 19244251 PMCID: PMC2676049 DOI: 10.1074/jbc.m808221200] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2008] [Revised: 02/05/2009] [Indexed: 12/25/2022] Open
Abstract
Cyclic di-GMP (c-di-GMP) is a ubiquitous bacterial second messenger that is involved in the regulation of cell surface-associated traits and the persistence of infections. Omnipresent GGDEF and EAL domains, which occur in various combinations with regulatory domains, catalyze c-di-GMP synthesis and degradation, respectively. The crystal structure of full-length YkuI from Bacillus subtilis, composed of an EAL domain and a C-terminal PAS-like domain, has been determined in its native form and in complex with c-di-GMP and Ca(2+). The EAL domain exhibits a triose-phosphate isomerase-barrel fold with one antiparallel beta-strand. The complex with c-di-GMP-Ca(2+) defines the active site of the putative phosphodiesterase located at the C-terminal end of the beta-barrel. The EAL motif is part of the active site with Glu-33 of the motif being involved in cation coordination. The structure of the complex allows the proposal of a phosphodiesterase mechanism, in which the divalent cation and the general base Glu-209 activate a catalytic water molecule for nucleophilic in-line attack on the phosphorus. The C-terminal domain closely resembles the PAS-fold. Its pocket-like structure could accommodate a yet unknown ligand. YkuI forms a tight dimer via EAL-EAL and trans EAL-PAS-like domain association. The possible regulatory significance of the EAL-EAL interface and a mechanism for signal transduction between sensory and catalytic domains of c-di-GMP-specific phosphodiesterases are discussed.
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Affiliation(s)
- George Minasov
- Department of Molecular Pharmacology and Biological Chemistry and Midwest Center for Structural Genomics, Northwestern Feinberg School of Medicine, Chicago, IL 60611, USA
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Tschowri N, Busse S, Hengge R. The BLUF-EAL protein YcgF acts as a direct anti-repressor in a blue-light response of Escherichia coli. Genes Dev 2009; 23:522-34. [PMID: 19240136 DOI: 10.1101/gad.499409] [Citation(s) in RCA: 143] [Impact Index Per Article: 9.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
The blue light using FAD (BLUF)-EAL protein YcgF is a known blue-light sensor of Escherichia coli, but its direct regulatory output and physiological function have remained unknown. Here, we demonstrate that unlike other EAL domain proteins, YcgF does not degrade the signaling molecule c-di-GMP, but directly binds to and releases the MerR-like repressor YcgE from its operator DNA upon blue-light irradiation. As a consequence, a distinct regulon of eight small proteins (of 71-126 amino acids) is strongly induced. These include YmgA and YmgB, which, via the RcsC/RcsD/RcsB two-component phosphorelay system, activate production of the biofilm matrix substance colanic acid as well as acid resistance genes and the biofilm-associated bdm gene and down-regulate adhesive curli fimbriae. Thus, small proteins under YcgF/YcgE control seem to act as "connectors" that provide additional signal input into a two-component signaling pathway. Moreover, we found ycgF and ycgE expression to be strongly activated at low temperature, and we elucidate how blue light, cold, and starvation signals are integrated in the expression and activity of the YcgF/YcgE/small protein signaling pathway. In conclusion, this pathway may modulate biofilm formation via the two-component network when E. coli has to survive in an extrahost aquatic environment.
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Affiliation(s)
- Natalia Tschowri
- Institut für Biologie-Mikrobiologie, Freie Universität Berlin, 14195 Berlin, Germany
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Mathes T, Vogl C, Stolz J, Hegemann P. In Vivo Generation of Flavoproteins with Modified Cofactors. J Mol Biol 2009; 385:1511-8. [DOI: 10.1016/j.jmb.2008.11.001] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2008] [Revised: 10/31/2008] [Accepted: 11/03/2008] [Indexed: 10/21/2022]
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