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Elkurdi A, Guigas G, Hourani-Alsharafat L, Scheerer P, Nienhaus GU, Krauß N, Lamparter T. Time-resolved fluorescence anisotropy with Atto 488-labeled phytochrome Agp1 from Agrobacterium fabrum. Photochem Photobiol 2024; 100:561-572. [PMID: 37675785 DOI: 10.1111/php.13851] [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: 06/13/2023] [Revised: 07/20/2023] [Accepted: 08/17/2023] [Indexed: 09/08/2023]
Abstract
Phytochromes are photoreceptor proteins with a bilin chromophore that undergo photoconversion between two spectrally different forms, Pr and Pfr. Three domains, termed PAS, GAF, and PHY domains, constitute the N-terminal photosensory chromophore module (PCM); the C-terminus is often a histidine kinase module. In the Agrobacterium fabrum phytochrome Agp1, the autophosphorylation activity of the histidine kinase is high in the Pr and low in the Pfr form. Crystal structure analyses of PCMs suggest flexibility around position 308 in the Pr but not in the Pfr form. Here, we performed time-resolved fluorescence anisotropy measurements with different Agp1 mutants, each with a single cysteine residue at various positions. The fluorophore label Atto-488 was attached to each mutant, and time-resolved fluorescence anisotropy was measured in the Pr and Pfr forms. Fluorescence anisotropy curves were fitted with biexponential functions. Differences in the amplitude A2 of the second component between the PCM and the full-length variant indicate a mechanical coupling between position 362 and the histidine kinase. Pr-to-Pfr photoconversion induced no significant changes in the time constant t2 at any position. An intermediate t2 value at position 295, which is located in a compact environment, suggests flexibility around the nearby position 308 in Pr and in Pfr.
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Affiliation(s)
- Afaf Elkurdi
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Gernot Guigas
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | | | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Structural Biology of Cellular Signaling, Berlin, Germany
| | - Gerd Ulrich Nienhaus
- Institute of Applied Physics, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
- Institute of Biological and Chemical Systems, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Institute of Nanotechnology, Karlsruhe Institute of Technology, Eggenstein-Leopoldshafen, Germany
- Department of Physics, University of Illinois at Urbana-Champaign, Urbana, Illinois, USA
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology (KIT), Karlsruhe, Germany
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2
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Multamäki E, Nanekar R, Morozov D, Lievonen T, Golonka D, Wahlgren WY, Stucki-Buchli B, Rossi J, Hytönen VP, Westenhoff S, Ihalainen JA, Möglich A, Takala H. Comparative analysis of two paradigm bacteriophytochromes reveals opposite functionalities in two-component signaling. Nat Commun 2021; 12:4394. [PMID: 34285211 PMCID: PMC8292422 DOI: 10.1038/s41467-021-24676-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/10/2020] [Accepted: 06/30/2021] [Indexed: 02/06/2023] Open
Abstract
Bacterial phytochrome photoreceptors usually belong to two-component signaling systems which transmit environmental stimuli to a response regulator through a histidine kinase domain. Phytochromes switch between red light-absorbing and far-red light-absorbing states. Despite exhibiting extensive structural responses during this transition, the model bacteriophytochrome from Deinococcus radiodurans (DrBphP) lacks detectable kinase activity. Here, we resolve this long-standing conundrum by comparatively analyzing the interactions and output activities of DrBphP and a bacteriophytochrome from Agrobacterium fabrum (Agp1). Whereas Agp1 acts as a conventional histidine kinase, we identify DrBphP as a light-sensitive phosphatase. While Agp1 binds its cognate response regulator only transiently, DrBphP does so strongly, which is rationalized at the structural level. Our data pinpoint two key residues affecting the balance between kinase and phosphatase activities, which immediately bears on photoreception and two-component signaling. The opposing output activities in two highly similar bacteriophytochromes suggest the use of light-controllable histidine kinases and phosphatases for optogenetics.
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Affiliation(s)
- Elina Multamäki
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Rahul Nanekar
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Dmitry Morozov
- grid.9681.60000 0001 1013 7965Department of Chemistry, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Topias Lievonen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - David Golonka
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Weixiao Yuan Wahlgren
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Brigitte Stucki-Buchli
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Jari Rossi
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland
| | - Vesa P. Hytönen
- grid.502801.e0000 0001 2314 6254Faculty of Medicine and Health Technology, BioMediTech, Tampere University, Tampere, Finland ,grid.511163.10000 0004 0518 4910Fimlab Laboratories, Tampere, Finland
| | - Sebastian Westenhoff
- grid.8761.80000 0000 9919 9582Department of Chemistry and Molecular Biology, University of Gothenburg, Gothenburg, Sweden
| | - Janne A. Ihalainen
- grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
| | - Andreas Möglich
- grid.7384.80000 0004 0467 6972Lehrstuhl für Biochemie, Universität Bayreuth, Bayreuth, Germany
| | - Heikki Takala
- grid.7737.40000 0004 0410 2071Faculty of Medicine, Anatomy, University of Helsinki, Helsinki, Finland ,grid.9681.60000 0001 1013 7965Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Jyvaskyla, Finland
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3
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Takala H, Edlund P, Ihalainen JA, Westenhoff S. Tips and turns of bacteriophytochrome photoactivation. Photochem Photobiol Sci 2021; 19:1488-1510. [PMID: 33107538 DOI: 10.1039/d0pp00117a] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/27/2022]
Abstract
Phytochromes are ubiquitous photosensor proteins, which control the growth, reproduction and movement in plants, fungi and bacteria. Phytochromes switch between two photophysical states depending on the light conditions. In analogy to molecular machines, light absorption induces a series of structural changes that are transduced from the bilin chromophore, through the protein, and to the output domains. Recent progress towards understanding this structural mechanism of signal transduction has been manifold. We describe this progress with a focus on bacteriophytochromes. We describe the mechanism along three structural tiers, which are the chromophore-binding pocket, the photosensory module, and the output domains. We discuss possible interconnections between the tiers and conclude by presenting future directions and open questions. We hope that this review may serve as a compendium to guide future structural and spectroscopic studies designed to understand structural signaling in phytochromes.
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Affiliation(s)
- Heikki Takala
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland. and Department of Anatomy, Faculty of Medicine, University of Helsinki, Box 63, 00014 Helsinki, Finland
| | - Petra Edlund
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
| | - Janne A Ihalainen
- Department of Biological and Environmental Science, Nanoscience Center, University of Jyvaskyla, Box 35, 40014 Jyvaskyla, Finland.
| | - Sebastian Westenhoff
- Department of Chemistry and Molecular Biology, University of Gothenburg, Box 462, 40530 Gothenburg, Sweden.
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4
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Ultrafast proton release reaction and primary photochemistry of phycocyanobilin in solution observed with fs-time-resolved mid-IR and UV/Vis spectroscopy. Photochem Photobiol Sci 2021; 20:715-732. [PMID: 34002345 DOI: 10.1007/s43630-021-00045-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2021] [Accepted: 04/16/2021] [Indexed: 12/27/2022]
Abstract
Deactivation processes of photoexcited (λex = 580 nm) phycocyanobilin (PCB) in methanol were investigated by means of UV/Vis and mid-IR femtosecond (fs) transient absorption (TA) as well as static fluorescence spectroscopy, supported by density-functional-theory calculations of three relevant ground state conformers, PCBA, PCBB and PCBC, their relative electronic state energies and normal mode vibrational analysis. UV/Vis fs-TA reveals time constants of 2.0, 18 and 67 ps, describing decay of PCBB*, of PCBA* and thermal re-equilibration of PCBA, PCBB and PCBC, respectively, in line with the model by Dietzek et al. (Chem Phys Lett 515:163, 2011) and predecessors. Significant substantiation and extension of this model is achieved first via mid-IR fs-TA, i.e. identification of molecular structures and their dynamics, with time constants of 2.6, 21 and 40 ps, respectively. Second, transient IR continuum absorption (CA) is observed in the region above 1755 cm-1 (CA1) and between 1550 and 1450 cm-1 (CA2), indicative for the IR absorption of highly polarizable protons in hydrogen bonding networks (X-H…Y). This allows to characterize chromophore protonation/deprotonation processes, associated with the electronic and structural dynamics, on a molecular level. The PCB photocycle is suggested to be closed via a long living (> 1 ns), PCBC-like (i.e. deprotonated), fluorescent species.
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5
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Lamparter T, Xue P, Elkurdi A, Kaeser G, Sauthof L, Scheerer P, Krauß N. Phytochromes in Agrobacterium fabrum. FRONTIERS IN PLANT SCIENCE 2021; 12:642801. [PMID: 33995441 PMCID: PMC8117939 DOI: 10.3389/fpls.2021.642801] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/16/2020] [Accepted: 03/18/2021] [Indexed: 05/31/2023]
Abstract
The focus of this review is on the phytochromes Agp1 and Agp2 of Agrobacterium fabrum. These are involved in regulation of conjugation, gene transfer into plants, and other effects. Since crystal structures of both phytochromes are known, the phytochrome system of A. fabrum provides a tool for following the entire signal transduction cascade starting from light induced conformational changes to protein interaction and the triggering of DNA transfer processes.
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Affiliation(s)
- Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Afaf Elkurdi
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
| | - Luisa Sauthof
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Patrick Scheerer
- Charité – Universitätsmedizin Berlin, Corporate Member of Freie Universität Berlin and Humboldt-Universität zu Berlin, Institute of Medical Physics and Biophysics, Group Protein X-ray Crystallography and Signal Transduction, Berlin, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology KIT, Karlsruhe, Germany
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6
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Ebid AA, Alhammad RM, Alhendi RT, Alqarhi BA, Baweyan EM, Alfadli LH, Alzahrani MA, Alotaibi MF, Alaidrous NA, Alzahrani RA, Alqurashi RM, Alharbi SS, Azhar SJ. Immediate effect of pulsed high-intensity neodymium-doped yttrium aluminum garnet (Nd: YAG) laser on staphylococcus aureus and pseudomonas aeruginosa growth: an experimental study. J Phys Ther Sci 2019; 31:925-930. [PMID: 31871379 PMCID: PMC6879417 DOI: 10.1589/jpts.31.925] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2019] [Accepted: 08/14/2019] [Indexed: 01/11/2023] Open
Abstract
[Purpose] The aim of this study was to evaluate the effect of pulsed high intensity
neodymium-doped yttrium aluminum garnet (Nd: YAG) laser on staphylococcus aureus (S.
aureus) and pseudomonas aeruginosa (P. aeruginosa) bacterial growth, which cause many
health problems and establish which doses are effective in bacterial inhibition.
[Materials and Methods] Five samples of S. aureus and five samples of P. aeruginosa were
prepared in the microbiology lab, one used as control sample and the other 4 samples acted
as experimental samples. The experimental samples received pulsed high intensity Nd: YAG
laser with a total dose of 500, 600, 700 and 800 joules. The primary measures are colony
count and the percentage decrease in colony count, the colony count was assessed at
baseline and after 24 h of laser application. [Result] There was significant decrease in
colony count and the percentage decrease in colony count after pulsed high intensity Nd:
YAG laser application in all experimental samples of S. aureus and P. aeruginosa after 24
h of application for all doses (500, 600, 700 and 800 j) as compared with the control
sample, with the most effect in higher doses of pulsed high intensity Nd: YAG laser than
lower doses in both types of bacteria. [Conclusion] pulsed high intensity Nd: YAG laser
was found to be an effective modality for inhibition of S. aureus and P. aeruginosa growth
after a single application.
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Affiliation(s)
- Anwar Abdelgayed Ebid
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia.,Department of Physical Therapy, Faculty of Physical Therapy, Cairo University, Egypt
| | - Raniah M Alhammad
- Department of Microbiology, Faculty of Medicine, Umm AlQura University, Saudi Arabia
| | - Rania T Alhendi
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Bushra A Alqarhi
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Elaf M Baweyan
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Luluh H Alfadli
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mashael A Alzahrani
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Mawaddah F Alotaibi
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Nawal A Alaidrous
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Raghad A Alzahrani
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Rafaa M Alqurashi
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shouq S Alharbi
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
| | - Shuruq J Azhar
- Department of Physical Therapy, Faculty of Applied Medical Sciences, Umm AlQura University: PO Box 715, Postal Code 21421, Umm Al-Qura University, Makkah, Saudi Arabia
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7
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Takeda K, Terazima M. Dynamics of Conformational Changes in Full-Length Phytochrome from Cyanobacterium Synechocystis sp. PCC6803 (Cph1) Monitored by Time-Resolved Translational Diffusion Detection. Biochemistry 2019; 58:2720-2729. [DOI: 10.1021/acs.biochem.9b00081] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- Kimitoshi Takeda
- 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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8
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Xue P, El Kurdi A, Kohler A, Ma H, Kaeser G, Ali A, Fischer R, Krauß N, Lamparter T. Evidence for weak interaction between phytochromes Agp1 and Agp2 from Agrobacterium fabrum. FEBS Lett 2019; 593:926-941. [PMID: 30941759 DOI: 10.1002/1873-3468.13376] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2018] [Revised: 03/25/2019] [Accepted: 03/28/2019] [Indexed: 11/09/2022]
Abstract
During bacterial conjugation, plasmid DNA is transferred from cell to cell. In Agrobacterium fabrum, conjugation is regulated by the phytochrome photoreceptors Agp1 and Agp2. Both contribute equally to this regulation. Agp1 and Agp2 are histidine kinases, but, for Agp2, we found no autophosphorylation activity. A clear autophosphorylation signal, however, was obtained with mutants in which the phosphoaccepting Asp of the C-terminal response regulator domain is replaced. Thus, the Agp2 histidine kinase differs from the classical transphosphorylation pattern. We performed size exclusion, photoconversion, dark reversion, autophosphorylation, chromophore assembly kinetics and fluorescence resonance energy transfer measurements on mixed Agp1/Agp2 samples. These assays pointed to an interaction between both proteins. This could partially explain the coaction of both phytochromes in the cell.
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Affiliation(s)
- Peng Xue
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Afaf El Kurdi
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Anja Kohler
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Hongju Ma
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Gero Kaeser
- Botanical Institute, Karlsruhe Institute of Technology, Germany
| | - Arin Ali
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Reinhard Fischer
- Institute for Applied Biosciences, Karlsruhe Institute of Technology, Germany
| | - Norbert Krauß
- Botanical Institute, Karlsruhe Institute of Technology, Germany
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9
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Takeda K, Terazima M. Photoinduced Orientation Change of the Dimer Structure of the Pr-I State of Cph1Δ2. Biochemistry 2018; 57:5058-5071. [DOI: 10.1021/acs.biochem.8b00605] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Kimitoshi Takeda
- 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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10
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Lamparter T, Krauß N, Scheerer P. Phytochromes from Agrobacterium fabrum. Photochem Photobiol 2017; 93:642-655. [DOI: 10.1111/php.12761] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2016] [Accepted: 02/22/2017] [Indexed: 01/24/2023]
Affiliation(s)
- Tilman Lamparter
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Norbert Krauß
- Karlsruhe Institute of Technology (KIT); Botanical Institute; Karlsruhe Germany
| | - Patrick Scheerer
- Charité - Universitätsmedizin Berlin; Institute of Medical Physics and Biophysics (CC2); Group Protein X-ray Crystallography and Signal Transduction; Berlin Germany
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11
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Kacprzak S, Njimona I, Renz A, Feng J, Reijerse E, Lubitz W, Krauss N, Scheerer P, Nagano S, Lamparter T, Weber S. Intersubunit distances in full-length, dimeric, bacterial phytochrome Agp1, as measured by pulsed electron-electron double resonance (PELDOR) between different spin label positions, remain unchanged upon photoconversion. J Biol Chem 2017; 292:7598-7606. [PMID: 28289094 DOI: 10.1074/jbc.m116.761882] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2016] [Revised: 03/10/2017] [Indexed: 11/06/2022] Open
Abstract
Bacterial phytochromes are dimeric light-regulated histidine kinases that convert red light into signaling events. Light absorption by the N-terminal photosensory core module (PCM) causes the proteins to switch between two spectrally distinct forms, Pr and Pfr, thus resulting in a conformational change that modulates the C-terminal histidine kinase region. To provide further insights into structural details of photoactivation, we investigated the full-length Agp1 bacteriophytochrome from the soil bacterium Agrobacterium fabrum using a combined spectroscopic and modeling approach. We generated seven mutants suitable for spin labeling to enable application of pulsed EPR techniques. The distances between attached spin labels were measured using pulsed electron-electron double resonance spectroscopy to probe the arrangement of the subunits within the dimer. We found very good agreement of experimental and calculated distances for the histidine-kinase region when both subunits are in a parallel orientation. However, experimental distance distributions surprisingly showed only limited agreement with either parallel- or antiparallel-arranged dimer structures when spin labels were placed into the PCM region. This observation indicates that the arrangements of the PCM subunits in the full-length protein dimer in solution differ significantly from that in the PCM crystals. The pulsed electron-electron double resonance data presented here revealed either no or only minor changes of distance distributions upon Pr-to-Pfr photoconversion.
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Affiliation(s)
- Sylwia Kacprzak
- From the Albert-Ludwigs-Universität Freiburg, Institut für Physikalische Chemie, 79104 Freiburg, Germany,
| | - Ibrahim Njimona
- the Karlsruhe Institute of Technology, Botanical Institute I, 76131 Karlsruhe, Germany
| | - Anja Renz
- From the Albert-Ludwigs-Universität Freiburg, Institut für Physikalische Chemie, 79104 Freiburg, Germany
| | - Juan Feng
- the Karlsruhe Institute of Technology, Botanical Institute I, 76131 Karlsruhe, Germany
| | - Edward Reijerse
- the Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Wolfgang Lubitz
- the Max Planck Institute for Chemical Energy Conversion, 45470 Mülheim an der Ruhr, Germany
| | - Norbert Krauss
- the Karlsruhe Institute of Technology, Botanical Institute I, 76131 Karlsruhe, Germany
| | - Patrick Scheerer
- the Institut für Medizinische Physik und Biophysik (CC2), Group Protein X-ray Crystallography & Signal Transduction, Charité-Universitätsmedizin Berlin, 10117 Berlin, Germany, and
| | - Soshichiro Nagano
- the Justus-Liebig-Universität Giessen, Institut für Pflanzenphysiologie, 35390 Giessen, Germany
| | - Tilman Lamparter
- the Karlsruhe Institute of Technology, Botanical Institute I, 76131 Karlsruhe, Germany
| | - Stefan Weber
- From the Albert-Ludwigs-Universität Freiburg, Institut für Physikalische Chemie, 79104 Freiburg, Germany
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12
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Nagano S, Scheerer P, Zubow K, Michael N, Inomata K, Lamparter T, Krauß N. The Crystal Structures of the N-terminal Photosensory Core Module of Agrobacterium Phytochrome Agp1 as Parallel and Anti-parallel Dimers. J Biol Chem 2016; 291:20674-91. [PMID: 27466363 DOI: 10.1074/jbc.m116.739136] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2016] [Indexed: 11/06/2022] Open
Abstract
Agp1 is a canonical biliverdin-binding bacteriophytochrome from the soil bacterium Agrobacterium fabrum that acts as a light-regulated histidine kinase. Crystal structures of the photosensory core modules (PCMs) of homologous phytochromes have provided a consistent picture of the structural changes that these proteins undergo during photoconversion between the parent red light-absorbing state (Pr) and the far-red light-absorbing state (Pfr). These changes include secondary structure rearrangements in the so-called tongue of the phytochrome-specific (PHY) domain and structural rearrangements within the long α-helix that connects the cGMP-specific phosphodiesterase, adenylyl cyclase, and FhlA (GAF) and the PHY domains. We present the crystal structures of the PCM of Agp1 at 2.70 Å resolution and of a surface-engineered mutant of this PCM at 1.85 Å resolution in the dark-adapted Pr states. Whereas in the mutant structure the dimer subunits are in anti-parallel orientation, the wild-type structure contains parallel subunits. The relative orientations between the PAS-GAF bidomain and the PHY domain are different in the two structures, due to movement involving two hinge regions in the GAF-PHY connecting α-helix and the tongue, indicating pronounced structural flexibility that may give rise to a dynamic Pr state. The resolution of the mutant structure enabled us to detect a sterically strained conformation of the chromophore at ring A that we attribute to the tight interaction with Pro-461 of the conserved PRXSF motif in the tongue. Based on this observation and on data from mutants where residues in the tongue region were replaced by alanine, we discuss the crucial roles of those residues in Pr-to-Pfr photoconversion.
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Affiliation(s)
- Soshichiro Nagano
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Patrick Scheerer
- the Institute of Medical Physics and Biophysics (CC2), Group Protein X-ray Crystallography and Signal Transduction, Charité-Universitätsmedizin Berlin, Charitéplatz 1, D-10117 Berlin, Germany
| | - Kristina Zubow
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom
| | - Norbert Michael
- the Institut für Chemie, Technische Universität Berlin, Sekretariat PC 14, Straße des 17. Juni 135, D-10623 Berlin, Germany
| | - Katsuhiko Inomata
- the Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa, 920-1192, Japan, and
| | - Tilman Lamparter
- the Botanical Institute, Karlsruhe Institute of Technology (KIT), Kaiserstraße 2, D-76131 Karlsruhe, Germany
| | - Norbert Krauß
- From the School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, United Kingdom, the Botanical Institute, Karlsruhe Institute of Technology (KIT), Kaiserstraße 2, D-76131 Karlsruhe, Germany
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13
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Takala H, Björling A, Linna M, Westenhoff S, Ihalainen JA. Light-induced Changes in the Dimerization Interface of Bacteriophytochromes. J Biol Chem 2015; 290:16383-92. [PMID: 25971964 DOI: 10.1074/jbc.m115.650127] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2015] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are dimeric photoreceptor proteins that sense red light levels in plants, fungi, and bacteria. The proteins are structurally divided into a light-sensing photosensory module consisting of PAS, GAF, and PHY domains and a signaling output module, which in bacteriophytochromes typically is a histidine kinase (HK) domain. Existing structural data suggest that two dimerization interfaces exist between the GAF and HK domains, but their functional roles remain unclear. Using mutational, biochemical, and computational analyses of the Deinococcus radiodurans phytochrome, we demonstrate that two dimerization interfaces between sister GAF and HK domains stabilize the dimer with approximately equal contributions. The existence of both dimerization interfaces is critical for thermal reversion back to the resting state. We also find that a mutant in which the interactions between the GAF domains were removed monomerizes under red light. This implies that the interactions between the HK domains are significantly altered by photoconversion. The results suggest functional importance of the dimerization interfaces in bacteriophytochromes.
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Affiliation(s)
- Heikki Takala
- From the University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, SE-40530 Sweden and University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Sciences, Jyväskylä, FI-40014 Finland
| | - Alexander Björling
- From the University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, SE-40530 Sweden and
| | - Marko Linna
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Sciences, Jyväskylä, FI-40014 Finland
| | - Sebastian Westenhoff
- From the University of Gothenburg, Department of Chemistry and Molecular Biology, Gothenburg, SE-40530 Sweden and
| | - Janne A Ihalainen
- University of Jyvaskyla, Nanoscience Center, Department of Biological and Environmental Sciences, Jyväskylä, FI-40014 Finland
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14
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Takala H, Lehtivuori H, Hammarén H, Hytönen VP, Ihalainen JA. Connection between Absorption Properties and Conformational Changes in Deinococcus radiodurans Phytochrome. Biochemistry 2014; 53:7076-85. [DOI: 10.1021/bi501180s] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Affiliation(s)
- Heikki Takala
- Nanoscience
Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
- Department
of Chemistry and Molecular Biology, University of Gothenburg, 40530 Gothenburg, Sweden
| | - Heli Lehtivuori
- Nanoscience
Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
- Nanoscience
Center, Department of Physics, University of Jyväskylä, 40014 Jyväskylä, Finland
| | - Henrik Hammarén
- School
of Medicine, University of Tampere and Tampere University Hospital, 33520 Tampere, Finland
| | - Vesa P. Hytönen
- BioMediTech, University of Tampere, 33520 Tampere, Finland
- Fimlab Laboratories, 33520 Tampere, Finland
| | - Janne A. Ihalainen
- Nanoscience
Center, Department of Biological and Environmental Science, University of Jyväskylä, 40014 Jyväskylä, Finland
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15
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Njimona I, Yang R, Lamparter T. Temperature effects on bacterial phytochrome. PLoS One 2014; 9:e109794. [PMID: 25289638 PMCID: PMC4188573 DOI: 10.1371/journal.pone.0109794] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/14/2014] [Accepted: 09/12/2014] [Indexed: 02/01/2023] Open
Abstract
Bacteriophytochromes (BphPs) are light-sensing regulatory proteins encoded in photosynthetic and non-photosynthetic bacteria. This protein class incorporate bilin as their chromophore, with majority of them bearing a light- regulated His kinase or His kinase related module in the C-terminal. We studied the His kinase actives in the temperature range of 5°C to 40°C on two BphPs, Agp1 from Agrobacterium tumefaciens and Cph1 from cyanobacterium Synechocystis PCC 6803. As reported, the phosphorylation activities of the far red (FR) irradiated form of the holoprotein is stronger than that of the red (R) irradiated form in both phytochromes. We observed for the apoprotein and FR irradiated holoprotein of Agp1 an increase in the phosphorylation activities from 5°C to 25°C and a decrease from 25°C to 40°C. At 5°C the activities of the apoprotein were significantly lower than those of the FR irradiated holoprotein, which was opposite at 40°C. A similar temperature pattern was observed for Cph1, but the maximum of the apoprotein was at 20°C while the maximum of the FR irradiated holoprotein was at 10°C. At 40°C, prolonged R irradiation leads to an irreversible bleaching of Cph1, an effect which depends on the C-terminal His kinase module. A more prominent and reversible temperature effect on spectral properties of Agp1, mediated by the His kinase, has been reported before. His kinases in phytochromes could therefore share similar temperature characteristics. We also found that phytochrome B mutants of Arabidopsis have reduced hypocotyl growth at 37°C in darkness, suggesting that this phytochrome senses the temperature or mediates signal transduction of temperature effects.
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Affiliation(s)
- Ibrahim Njimona
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
| | - Rui Yang
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
| | - Tilman Lamparter
- Karlsruhe Institute of Technology KIT, Botanical Institute, Karlsruhe, Germany
- * E-mail:
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16
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Song C, Rohmer T, Tiersch M, Zaanen J, Hughes J, Matysik J. Solid-State NMR Spectroscopy to Probe Photoactivation in Canonical Phytochromes. Photochem Photobiol 2013; 89:259-73. [DOI: 10.1111/php.12029] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2012] [Accepted: 11/28/2012] [Indexed: 01/17/2023]
Affiliation(s)
| | - Thierry Rohmer
- Leids Instituut voor Chemisch Onderzoek; Universiteit Leiden; Leiden; The Netherlands
| | | | - Jan Zaanen
- Instituut-Lorentz for Theoretical Physics; Universiteit Leiden; Leiden; The Netherlands
| | - Jon Hughes
- Pflanzenphysiologie; Justus-Liebig-Universität; Giessen; Germany
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17
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Sides CR, Liyanage R, Lay JO, Philominathan STL, Matsushita O, Sakon J. Probing the 3-D structure, dynamics, and stability of bacterial collagenase collagen binding domain (apo- versus holo-) by limited proteolysis MALDI-TOF MS. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2012; 23:505-519. [PMID: 22207568 PMCID: PMC3389352 DOI: 10.1007/s13361-011-0309-3] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/05/2011] [Revised: 11/23/2011] [Accepted: 11/26/2011] [Indexed: 05/31/2023]
Abstract
Pairing limited proteolysis and matrix-assisted laser desorption/ionization-time of flight mass spectrometry (MALDI-TOF MS) to probe clostridial collagenase collagen binding domain (CBD) reveals the solution dynamics and stability of the protein, as these factors are crucial to CBD effectiveness as a drug-delivery vehicle. MS analysis of proteolytic digests indicates initial cleavage sites, thereby specifying the less stable and highly accessible regions of CBD. Modulation of protein structure and stability upon metal binding is shown through MS analysis of calcium-bound and cobalt-bound CBD proteolytic digests. Previously determined X-ray crystal structures illustrate that calcium binding induces secondary structure transformation in the highly mobile N-terminal arm and increases protein stability. MS-based detection of exposed residues confirms protein flexibility, accentuates N-terminal dynamics, and demonstrates increased global protein stability exported by calcium binding. Additionally, apo- and calcium-bound CBD proteolysis sites correlate well with crystallographic B-factors, accessibility, and enzyme specificity. MS-observed cleavage sites with no clear correlations are explained either by crystal contacts of the X-ray crystal structures or by observed differences between Molecules A and B in the X-ray crystal structures. The study newly reveals the absence of the βA strand and thus the very dynamic N-terminal linker, as corroborated by the solution X-ray scattering results. Cobalt binding has a regional effect on the solution phase stability of CBD, as limited proteolysis data implies the capture of an intermediate-CBD solution structure when cobalt is bound.
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Affiliation(s)
- Cynthia R. Sides
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
| | - Rohana Liyanage
- Arkansas Statewide Mass Spectrometry Facility, University of Arkansas, Fayetteville, Arkansas, USA
| | - Jackson O. Lay
- Arkansas Statewide Mass Spectrometry Facility, University of Arkansas, Fayetteville, Arkansas, USA
| | | | - Osamu Matsushita
- Department of Microbiology, Kitasato University Medical School, Kanagawa 228-8555, Japan
| | - Joshua Sakon
- Department of Chemistry and Biochemistry, University of Arkansas, Fayetteville, Arkansas, USA
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18
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Inomata K. Syntheses of Bilin Chromophores Toward the Investigation of Structure and Function of Phytochromes. HETEROCYCLES 2012. [DOI: 10.3987/rev-12-750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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19
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Njimona I, Lamparter T. Temperature effects on Agrobacterium phytochrome Agp1. PLoS One 2011; 6:e25977. [PMID: 22043299 PMCID: PMC3197147 DOI: 10.1371/journal.pone.0025977] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2011] [Accepted: 09/14/2011] [Indexed: 01/18/2023] Open
Abstract
Phytochromes are widely distributed biliprotein photoreceptors with a conserved N-terminal chromophore-binding domain. Most phytochromes bear a light-regulated C-terminal His kinase or His kinase-like region. We investigated the effects of light and temperature on the His kinase activity of the phytochrome Agp1 from Agrobacterium tumefaciens. As in earlier studies, the phosphorylation activity of the holoprotein after far-red irradiation (where the red-light absorbing Pr form dominates) was stronger than that of the holoprotein after red irradiation (where the far red-absorbing Pfr form dominates). Phosphorylation activities of the apoprotein, far red-irradiated holoprotein, and red-irradiated holoprotein decreased when the temperature increased from 25°C to 35°C; at 40°C, almost no kinase activity was detected. The activity of a holoprotein sample incubated at 40°C was nearly completely restored when the temperature returned to 25°C. UV/visible spectroscopy indicated that the protein was not denatured up to 45°C. At 50°C, however, Pfr denatured faster than the dark-adapted sample containing the Pr form of Agp1. The Pr visible spectrum was unaffected by temperatures of 20–45°C, whereas irradiated samples exhibited a clear temperature effect in the 30–40°C range in which prolonged irradiation resulted in the photoconversion of Pfr into a new spectral species termed Prx. Pfr to Prx photoconversion was dependent on the His-kinase module of Agp1; normal photoconversion occurred at 40°C in the mutant Agp1-M15, which lacks the C-terminal His-kinase module, and in a domain-swap mutant in which the His-kinase module of Agp1 is replaced by the His-kinase/response regulator module of the other A. tumefaciens phytochrome, Agp2. The temperature-dependent kinase activity and spectral properties in the physiological temperature range suggest that Agp1 serves as an integrated light and temperature sensor in A. tumefaciens.
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Affiliation(s)
- Ibrahim Njimona
- Botanical Institute, Karlsruhe Institute of Technology (KIT) Campus South, Karlsruhe, Germany
| | - Tilman Lamparter
- Botanical Institute, Karlsruhe Institute of Technology (KIT) Campus South, Karlsruhe, Germany
- * E-mail:
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20
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Two ground state isoforms and a chromophore D-ring photoflip triggering extensive intramolecular changes in a canonical phytochrome. Proc Natl Acad Sci U S A 2011; 108:3842-7. [PMID: 21325055 DOI: 10.1073/pnas.1013377108] [Citation(s) in RCA: 149] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Phytochrome photoreceptors mediate light responses in plants and in many microorganisms. Here we report studies using (1)H-(13)C magic-angle spinning NMR spectroscopy of the sensor module of cyanobacterial phytochrome Cph1. Two isoforms of the red-light absorbing Pr ground state are identified. Conclusive evidence that photoisomerization occurs at the C15-methine bridge leading to a β-facial disposition of the ring D is presented. In the far-red-light absorbing Pfr state, strong hydrogen-bonding interactions of the D-ring carbonyl group to Tyr-263 and of N24 to Asp-207 hold the chromophore in a tensed conformation. Signaling is triggered when Asp-207 is released from its salt bridge to Arg-472, probably inducing conformational changes in the tongue region. A second signal route is initiated by partner swapping of the B-ring propionate between Arg-254 and Arg-222.
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21
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Scheerer P, Michael N, Park JH, Nagano S, Choe HW, Inomata K, Borucki B, Krauß N, Lamparter T. Light-Induced Conformational Changes of the Chromophore and the Protein in Phytochromes: Bacterial Phytochromes as Model Systems. Chemphyschem 2010; 11:1090-105. [DOI: 10.1002/cphc.200900913] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023]
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22
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Sharda S, Koay MST, Kim YJ, Engelhard M, Gärtner W. A non-hydrolyzable ATP derivative generates a stable complex in a light-inducible two-component system. J Biol Chem 2009; 284:33999-4004. [PMID: 19808667 DOI: 10.1074/jbc.m109.017772] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Isothermal calorimetry (ITC) measurements yielded the binding constants during complex formation of light-inducible histidine kinases (HK) and their cognate CheY-type response regulators (RR). HK-RR interactions represent the core function of the bacterial two-component system, which is also present in many bacterial phytochromes. Here, we have studied the recombinant forms of phytochromes CphA and CphB from the cyanobacterium Tolypothrix PCC7601 and their cognate RRs RcpA and RcpB. The interaction between the two reaction partners (HK and RR) was studied in the presence and absence of ATP. A complex formation was observable in the presence of ATP, but specific interactions were only found when a non-hydrolyzable ATP derivative was added to the mixture. Also, the incubation of the HK domain alone (expressed as a recombinant protein) with the RR did not yield specific interactions, indicating that the HK domain is only active as a component of the full-length phytochrome. Considering also previous studies on the same proteins (Hübschmann, T., Jorissen, H. J. M. M., Börner, T., Gärtner, W., and de Marsac, N. (2001) Eur. J. Biochem. 268, 3383-3389) we now conclude that the HK domains of these phytochromes are active only when the chromophore domain is in its Pr form. The formerly documented phosphate transfer between the HK domain and the RR takes place via a transiently formed protein-protein complex, which becomes detectable by ITC in the presence of a non-hydrolyzable ATP derivative. This finding is of interest also in relation to the function of some (blue light-sensitive) photoreceptors that carry the HK domain and the RR fused together in one single protein.
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Affiliation(s)
- Shivani Sharda
- Max Planck Institute for Bioinorganic Chemistry, 45413 Mülheim, Germany
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23
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Yang X, Kuk J, Moffat K. Conformational differences between the Pfr and Pr states in Pseudomonas aeruginosa bacteriophytochrome. Proc Natl Acad Sci U S A 2009; 106:15639-44. [PMID: 19720999 PMCID: PMC2747172 DOI: 10.1073/pnas.0902178106] [Citation(s) in RCA: 118] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2009] [Indexed: 11/18/2022] Open
Abstract
Phytochromes are red-light photoreceptors that regulate light responses in plants, fungi, and bacteria by means of reversible photoconversion between red (Pr) and far-red (Pfr) light-absorbing states. Here, we report the crystal structure of the Q188L mutant of Pseudomonas aeruginosa bacteriophytochrome (PaBphP) photosensory core module, which exhibits altered photoconversion behavior and different crystal packing from wild type. We observe two distinct chromophore conformations in the Q188L crystal structure that we identify with the Pfr and Pr states. The Pr/Pfr compositions, varying from crystal to crystal, seem to correlate with light conditions under which the Q188L crystals are cryoprotected. We also compare all known Pr and Pfr structures. Using site-directed mutagenesis, we identify residues that are involved in stabilizing the 15Ea (Pfr) and 15Za (Pr) configurations of the biliverdin chromophore. Specifically, Ser-261 appears to be essential to form a stable Pr state in PaBphP, possibly by means of its interaction with the propionate group of ring C. We propose a "flip-and-rotate" model that summarizes the major conformational differences between the Pr and Pfr states of the chromophore and its binding pocket.
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Affiliation(s)
- Xiaojing Yang
- Department of Biochemistry and Molecular Biology and
| | - Jane Kuk
- Department of Biochemistry and Molecular Biology and
| | - Keith Moffat
- Department of Biochemistry and Molecular Biology and
- Institute for Biophysical Dynamics, University of Chicago, 929 East 57th Street, Chicago, IL 60637
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24
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Krieger A, Molina I, Oberpichler I, Michael N, Lamparter T. Spectral properties of phytochrome Agp2 from Agrobacterium tumefaciens are specifically modified by a compound of the cell extract. JOURNAL OF PHOTOCHEMISTRY AND PHOTOBIOLOGY B-BIOLOGY 2008; 93:16-22. [DOI: 10.1016/j.jphotobiol.2008.07.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2008] [Revised: 05/24/2008] [Accepted: 07/04/2008] [Indexed: 11/29/2022]
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25
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The structure of a complete phytochrome sensory module in the Pr ground state. Proc Natl Acad Sci U S A 2008; 105:14709-14. [PMID: 18799745 DOI: 10.1073/pnas.0806477105] [Citation(s) in RCA: 322] [Impact Index Per Article: 20.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/01/2023] Open
Abstract
Phytochromes are red/far-red photochromic biliprotein photoreceptors, which in plants regulate seed germination, stem extension, flowering time, and many other light effects. However, the structure/functional basis of the phytochrome photoswitch is still unclear. Here, we report the ground state structure of the complete sensory module of Cph1 phytochrome from the cyanobacterium Synechocystis 6803. Although the phycocyanobilin (PCB) chromophore is attached to Cys-259 as expected, paralleling the situation in plant phytochromes but contrasting to that in bacteriophytochromes, the ZZZssa conformation does not correspond to that expected from Raman spectroscopy. We show that the PHY domain, previously considered unique to phytochromes, is structurally a member of the GAF (cGMP phosphodiesterase/adenylyl cyclase/FhlA) family. Indeed, the tandem-GAF dumbbell revealed for phytochrome sensory modules is remarkably similar to the regulatory domains of cyclic nucleotide (cNMP) phosphodiesterases and adenylyl cyclases. A unique feature of the phytochrome structure is a long, tongue-like protrusion from the PHY domain that seals the chromophore pocket and stabilizes the photoactivated far-red-absorbing state (Pfr). The tongue carries a conserved PRxSF motif, from which an arginine finger points into the chromophore pocket close to ring D forming a salt bridge with a conserved aspartate residue. The structure that we present provides a framework for light-driven signal transmission in phytochromes.
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26
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Ulijasz AT, Cornilescu G, von Stetten D, Kaminski S, Mroginski MA, Zhang J, Bhaya D, Hildebrandt P, Vierstra RD. Characterization of two thermostable cyanobacterial phytochromes reveals global movements in the chromophore-binding domain during photoconversion. J Biol Chem 2008; 283:21251-66. [PMID: 18480055 PMCID: PMC3258942 DOI: 10.1074/jbc.m801592200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2008] [Revised: 04/30/2008] [Indexed: 11/06/2022] Open
Abstract
Photointerconversion between the red light-absorbing (Pr) form and the far-red light-absorbing (Pfr) form is the central feature that allows members of the phytochrome (Phy) superfamily to act as reversible switches in light perception. Whereas the chromophore structure and surrounding binding pocket of Pr have been described, those for Pfr have remained enigmatic for various technical reasons. Here we describe a novel pair of Phys from two thermophilic cyanobacteria, Synechococcus sp. OS-A and OS-B', that overcome several of these limitations. Like other cyanobacterial Phys, SyA-Cph1 and SyB-Cph1 covalently bind the bilin phycocyanobilin via their cGMP phosphodiesterase/adenyl cyclase/FhlA (GAF) domains and then assume the photointerconvertible Pr and Pfr states with absorption maxima at 630 and 704 nm, respectively. However, they are naturally missing the N-terminal Per/Arndt/Sim domain common to others in the Phy superfamily. Importantly, truncations containing only the GAF domain are monomeric, photochromic, and remarkably thermostable. Resonance Raman and NMR spectroscopy show that all four pyrrole ring nitrogens of phycocyanobilin are protonated both as Pr and following red light irradiation, indicating that the GAF domain by itself can complete the Pr to Pfr photocycle. (1)H-(15)N two-dimensional NMR spectra of isotopically labeled preparations of the SyB-Cph1 GAF domain revealed that a number of amino acids change their environment during photoconversion of Pr to Pfr, which can be reversed by subsequent photoconversion back to Pr. Through three-dimensional NMR spectroscopy before and after light photoexcitation, it should now be possible to define the movements of the chromophore and binding pocket during photoconversion. We also generated a series of strongly red fluorescent derivatives of SyB-Cph1, which based on their small size and thermostability may be useful as cell biological reporters.
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Affiliation(s)
- Andrew T. Ulijasz
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Gabriel Cornilescu
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - David von Stetten
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Steve Kaminski
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Maria Andrea Mroginski
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Junrui Zhang
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Devaki Bhaya
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Peter Hildebrandt
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
| | - Richard D. Vierstra
- Department of Genetics and
National Magnetic Resonance Facility,
University of Wisconsin, Madison, Wisconsin 53706, the
Technische Universität, D-10623
Berlin, Germany, and the Department of
Plant Biology, Carnegie Institution of Washington, Stanford, California
94305
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27
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Pal A, Chu UB, Ramachandran S, Grawoig D, Guo LW, Hajipour AR, Ruoho AE. Juxtaposition of the steroid binding domain-like I and II regions constitutes a ligand binding site in the sigma-1 receptor. J Biol Chem 2008; 283:19646-56. [PMID: 18467334 PMCID: PMC2443669 DOI: 10.1074/jbc.m802192200] [Citation(s) in RCA: 49] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2008] [Revised: 04/23/2008] [Indexed: 11/06/2022] Open
Abstract
sigma-1 receptors represent unique binding sites that are capable of interacting with a wide range of compounds to mediate different cellular events. The composition of the ligand binding site of this receptor is unclear, since no NMR or crystal structures are available. Recent studies in our laboratory using radiolabeled photoreactive ligands suggested that the steroid binding domain-like I (SBDLI) (amino acids 91-109) and the steroid binding domain-like II (SBDLII) (amino acids 176-194) regions are involved in forming the ligand binding site(s) ( Chen, Y., Hajipour, A. R., Sievert, M. K., Arbabian, M., and Ruoho, A. E. (2007) Biochemistry 46, 3532-3542 ; Pal, A., Hajipour, A. R., Fontanilla, D., Ramachandran, S., Chu, U. B., Mavlyutov, T., and Ruoho, A. E. (2007) Mol. Pharmacol. 72, 921-933 ). In this report, we have further addressed this issue by utilizing our previously developed sulfhydryl-reactive, cleavable, radioiodinated photocross-linking reagent: methanesulfonothioic acid, S-((4-(4-amino-3-[125I]iodobenzoyl) phenyl)methyl) ester (Guo, L. W., Hajipour, A. R., Gavala, M. L., Arbabian, M., Martemyanov, K. A., Arshavsky, V. Y., and Ruoho, A. E. (2005) Bioconjugate Chem. 16, 685-693). This photoprobe was shown to derivatize the single cysteine residues as mixed disulfides at position 94 in the SBDLI region of the wild type guinea pig sigma-1 receptor (Cys94) and at position 190 in the SBDLII region of a mutant guinea pig sigma-1 receptor (C94A,V190C), both in a sigma-ligand (haloperidol or (+)-pentazocine)-sensitive manner. Significantly, photocross-linking followed by Endo Lys-C cleavage under reducing conditions and intramolecular radiolabel transfer from the SBDLI to the SBDLII region in the wild type receptor and, conversely, from the SBDLII to the SBDLI region in the mutant receptor were observed. These data support a model in which the SBDLI and SBDLII regions are juxtaposed to form, at least in part, a ligand binding site of the sigma-1 receptor.
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Affiliation(s)
- Arindam Pal
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - Uyen B. Chu
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - Subramaniam Ramachandran
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - David Grawoig
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - Lian-Wang Guo
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - Abdol R. Hajipour
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
| | - Arnold E. Ruoho
- Department of Pharmacology,
University of Wisconsin School of Medicine and Public Health, Madison,
Wisconsin 53705 and the
Pharmaceutical Research Laboratory,
College of Chemistry, Isfahan University of Technology, Isfahan 84156,
Iran
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Tao L, Kiefer SE, Xie D, Bryson JW, Hefta SA, Doyle ML. Time-resolved limited proteolysis of mitogen-activated protein kinase-activated protein kinase-2 determined by LC/MS only. JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY 2008; 19:841-854. [PMID: 18400511 DOI: 10.1016/j.jasms.2008.02.014] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2008] [Revised: 02/21/2008] [Accepted: 02/21/2008] [Indexed: 05/26/2023]
Abstract
Mass spectrometry has gained prominence in limited proteolysis studies largely due to its unparalleled precision in determining protein molecular mass. However, proteolytic fragments usually cannot be identified through direct mass measurement, since multiple subsequences of a protein can frequently be matched to observed masses of proteolytic fragments. Therefore, additional information from N-terminal sequencing is often needed. Here we demonstrate that mass spectrometry analysis of the time course of limited proteolysis reactions provides new information that is self-sufficient to identify all proteolytic fragments. The method uses a non-specific protease like subtilisin and exploits information contained in the time-resolved dataset such as: increased likelihood of identifying larger fragments generated during initial proteolysis solely by their masses, additivity of the masses of two mutually exclusive sequence regions that generate the full-length molecule (or an already assigned subfragment), and analyses of the proteolytic subfragment patterns that are facilitated by having established the initial cleavage sites. We show that the identities of the observed proteolytic fragments can be determined by LC/MS alone because enough constraints exist in the time-resolved dataset. For a medium-sized protein, it takes about 8 h to complete the study, a significant improvement over the traditional SDS-PAGE and N-terminal sequencing method, which usually takes several days. We illustrate this method with application to the catalytic domain of mitogen-activated protein kinase-activated protein kinase-2, and compare the results with N-terminal sequencing data and the known X-ray crystal structure.
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Affiliation(s)
- Li Tao
- Department of Gene Expression and Protein Biochemistry, Bristol-Myers Squibb Research and Development, Princeton, New Jersey 08534, USA.
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The PHY domain is required for conformational stability and spectral integrity of the bacteriophytochrome from Deinococcus radiodurans. Biochem Biophys Res Commun 2008; 369:1120-4. [PMID: 18331835 DOI: 10.1016/j.bbrc.2008.03.001] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2008] [Accepted: 03/01/2008] [Indexed: 11/23/2022]
Abstract
Bacteriophytochrome from Deinococcus radiodurans (DrBphP) is a plant phytochrome homolog. To investigate the interaction of chromophore and protein structure, we purified recombinant DrBphP and performed biochemical analyses. Differences of apo- and holo-protein in electrophoretic properties in native gels and their susceptibility to trypsin indicate changes in both the conformation and surface topography of this protein as a result of chromophore assembly. Furthermore, proteolysis to Pr and Pfr conformers displayed distinctive cleavage patterns with a noticeable Pr-specific tryptic fragment. Of interest, a prolonged tryptic digestion showed a more severe impact upon the Pfr form. Most importantly, when we assessed the extent of dark reversion to evaluate the role of the cleaved part, a rapidly accelerated reversion was observed upon cleavage at residues 329-505 corresponding to the PHY domain. Our data thus show that the PHY domain is necessary for the Pfr stabilization and spectral integrity of DrBphP.
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30
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Lee J, Tomchick DR, Brautigam CA, Machius M, Kort R, Hellingwerf KJ, Gardner KH. Changes at the KinA PAS-A dimerization interface influence histidine kinase function. Biochemistry 2008; 47:4051-64. [PMID: 18324779 DOI: 10.1021/bi7021156] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
The Bacillus subtilis KinA protein is a histidine protein kinase that controls the commitment of this organism to sporulate in response to nutrient deprivation and several other conditions. Prior studies indicated that the N-terminal Per-ARNT-Sim domain (PAS-A) plays a critical role in the catalytic activity of this enzyme, as demonstrated by the significant decrease of the autophosphorylation rate of a KinA protein lacking this domain. On the basis of the environmental sensing role played by PAS domains in a wide range of proteins, including other bacterial sensor kinases, it has been suggested that the PAS-A domain plays an important regulatory role in KinA function. We have investigated this potential by using a combination of biophysical and biochemical methods to examine PAS-A structure and function, both in isolation and within the intact protein. Here, we present the X-ray crystal structure of the KinA PAS-A domain, showing that it crystallizes as a homodimer using beta-sheet/beta-sheet packing interactions as observed for several other PAS domain complexes. Notably, we observed two dimers with tertiary and quaternary structure differences in the crystalline lattice, indicating significant structural flexibility in these domains. To confirm that KinA PAS-A also forms dimers in solution, we used a combination of NMR spectroscopy, gel filtration chromatography, and analytical ultracentrifugation, the results of which are all consistent with the crystallographic results. We experimentally tested the importance of several residues at the dimer interface using site-directed mutagenesis, finding changes in the PAS-A domain that significantly alter KinA enzymatic activity in vitro and in vivo. These results support the importance of PAS domains within KinA and other histidine kinases and suggest possible routes for natural or artificial regulation of kinase activity.
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Affiliation(s)
- James Lee
- Department of Biochemistry, UT Southwestern Medical Center, 5323 Harry Hines Blvd., Dallas, Texas 75390-8816, USA
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31
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Inomata K. Studies on the Structure and Function of Phytochromes as Photoreceptors Based on Synthetic Organic Chemistry. BULLETIN OF THE CHEMICAL SOCIETY OF JAPAN 2008. [DOI: 10.1246/bcsj.81.25] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/18/2023]
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Noack S, Lamparter T. Light modulation of histidine-kinase activity in bacterial phytochromes monitored by size exclusion chromatography, crosslinking, and limited proteolysis. Methods Enzymol 2008; 423:203-21. [PMID: 17609133 DOI: 10.1016/s0076-6879(07)23009-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/16/2023]
Abstract
Phytochromes are photoreceptors that have been found in plants, bacteria, and fungi. Most bacterial and fungal phytochromes are histidine kinases and, for several bacterial phytochromes, light regulation of kinase activity has been demonstrated. Typical histidine kinases are homodimeric proteins in which one subunit phosphorylates the substrate histidine residue of the other subunit; dimerization is an intrinsic property of the histidine kinase itself. Truncated phytochromes which lack the histidine kinase can also form dimers, but the interaction between subunits is modulated by light. This light-dependent dimerization can give a clue to the intramolecular signal transduction of phytochromes which modulates the histidine kinase activity. Size exclusion chromatography, limited proteolysis, and protein crosslinking can be used to study light-induced conformational changes and the interaction of subunits within the homodimer.
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Affiliation(s)
- Steffi Noack
- Freie Universität Berlin, Pflanzenphysiologie, Berlin, Germany
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Rohmer T, Strauss H, Hughes J, de Groot H, Gärtner W, Schmieder P, Matysik J. 15N MAS NMR studies of cph1 phytochrome: Chromophore dynamics and intramolecular signal transduction. J Phys Chem B 2007; 110:20580-5. [PMID: 17034247 DOI: 10.1021/jp062454+] [Citation(s) in RCA: 47] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Solid-state nuclear magnetic resonance (NMR) is applied for the first time to the photoreceptor phytochrome. The two stable states, Pr and Pfr, of the 59-kDa N-terminal module of the cyanobacterial phytochrome Cph1 from Synechocystis sp. PCC 6803 containing a uniformly 15N-labeled phycocyanobilin cofactor are explored by 15N cross-polarization (CP) magic-angle spinning (MAS) NMR. As recently shown by 15N solution-state NMR using chemical shifts [Strauss, H. M.; Hughes, J.; Schmieder, P. Biochemistry 2005, 44, 8244], all four nitrogens are protonated in both states. CP/MAS NMR provides two additional independent lines of evidence for the protonation of the nitrogens. Apparent loss of mobility during photoactivation, indicated by the decrease of line width, demonstrates strong tension of the entire chromophore in the Pfr state, which is in clear contrast to a more relaxed Pr state. The outer rings (A and D) of the chromophore are significantly affected by the phototransformation, as indicated by both change of chemical shift and line width. On the other hand, on the inner rings (B and C) only minor changes of chemical shifts are detected, providing evidence for a conserved environment during phototransformation. In a mechanical model, the phototransformation is understood in terms of rotations between the A-B and C-D methine bridges, allowing for intramolecular signal transduction to the protein surface by a unit composed of the central rings B and C and its tightly linked protein surroundings during the highly energetic Pfr state.
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Affiliation(s)
- Thierry Rohmer
- Leiden Institute of Chemistry, Gorlaeus Laboratoria, Leiden University, PO Box 9502, 2300 RA Leiden, The Netherlands
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Sharda S, Shah R, Gärtner W. Domain interaction in cyanobacterial phytochromes as a prerequisite for spectral integrity. EUROPEAN BIOPHYSICS JOURNAL: EBJ 2007; 36:815-21. [PMID: 17522854 DOI: 10.1007/s00249-007-0171-1] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/11/2007] [Revised: 04/20/2007] [Accepted: 04/24/2007] [Indexed: 11/24/2022]
Abstract
Two phytochromes, CphA and CphB, from the cyanobacterium Calothrix PCC7601, with similar size (768 and 766 amino acids) and domain structure, were investigated for the essential length of their protein moiety required to maintain the spectral integrity. Both proteins fold into PAS-, GAF-, PHY-, and Histidine-kinase (HK) domains. CphA binds a phycocyanobilin (PCB) chromophore at a "canonical" cysteine within the GAF domain, identically as in plant phytochromes. CphB binds biliverdin IXalpha at cysteine24, positioned in the N-terminal PAS domain. The C-terminally located HK and PHY domains, present in both proteins, were removed subsequently by introducing stop-codons at the corresponding DNA positions. The spectral properties of the resulting proteins were investigated. The full-length proteins absorb at (CphA) 663 and 707 nm (red-, far red-absorbing P (r) and P (fr) forms of phytochromes) and at (CphB) 704 and 750 nm. Removal of the HK domains had no effect on the absorbance maxima of the resulting PAS-GAF-PHY constructs (CphA: 663/707 nm, CphB: 704/750 nm, P (r)/P (fr), respectively). Further deletion of the "PHY" domains caused a blue-shift of the P (r) and P (fr) absorption of CphA (lambda (max): 658/698 nm) and increased the amount of unproperly folded apoprotein, seen by a reduced capability to bind the chromophore in photoconvertible manner. In CphB, however, it practically impaired the formation of P (fr), i.e., showing a very low oscillator strength absorption band, whereas the P (r) form remains unchanged (702 nm). This finding clearly indicates a different interaction between domains in the "typical", PCB binding and in the biliverdin-binding phytochromes, and demonstrates a loss of oscillator strength for the latter, most probably due to a strong conformational distortion of the chromophore in the CphB P (fr) form.
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Affiliation(s)
- S Sharda
- Max-Planck-Institute for Bioinorganic Chemistry, Mulheim, Germany
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35
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Wagner JR, Zhang J, Brunzelle JS, Vierstra RD, Forest KT. High resolution structure of Deinococcus bacteriophytochrome yields new insights into phytochrome architecture and evolution. J Biol Chem 2007; 282:12298-309. [PMID: 17322301 DOI: 10.1074/jbc.m611824200] [Citation(s) in RCA: 199] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are red/far red light photochromic photoreceptors that direct many photosensory behaviors in the bacterial, fungal, and plant kingdoms. They consist of an N-terminal domain that covalently binds a bilin chromophore and a C-terminal region that transmits the light signal, often through a histidine kinase relay. Using x-ray crystallography, we recently solved the first three-dimensional structure of a phytochrome, using the chromophore-binding domain of Deinococcus radiodurans bacterial phytochrome assembled with its chromophore, biliverdin IXalpha. Now, by engineering the crystallization interface, we have achieved a significantly higher resolution model. This 1.45A resolution structure helps identify an extensive buried surface between crystal symmetry mates that may promote dimerization in vivo. It also reveals that upon ligation of the C3(2) carbon of biliverdin to Cys(24), the chromophore A-ring assumes a chiral center at C2, thus becoming 2(R),3(E)-phytochromobilin, a chemistry more similar to that proposed for the attached chromophores of cyanobacterial and plant phytochromes than previously appreciated. The evolution of bacterial phytochromes to those found in cyanobacteria and higher plants must have involved greater fitness using more reduced bilins, such as phycocyanobilin, combined with a switch of the attachment site from a cysteine near the N terminus to one conserved within the cGMP phosphodiesterase/adenyl cyclase/FhlA domain. From analysis of site-directed mutants in the D. radiodurans phytochrome, we show that this bilin preference was partially driven by the change in binding site, which ultimately may have helped photosynthetic organisms optimize shade detection. Collectively, these three-dimensional structural results better clarify bilin/protein interactions and help explain how higher plant phytochromes evolved from prokaryotic progenitors.
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Affiliation(s)
- Jeremiah R Wagner
- Departments of Genetics and Bacteriology, University of Wisconsin, Madison, Wisconsin 53706, USA
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Tarutina M, Ryjenkov DA, Gomelsky M. An unorthodox bacteriophytochrome from Rhodobacter sphaeroides involved in turnover of the second messenger c-di-GMP. J Biol Chem 2006; 281:34751-8. [PMID: 16968704 DOI: 10.1074/jbc.m604819200] [Citation(s) in RCA: 118] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Bacteriophytochromes are bacterial photoreceptors that sense red/far red light using the biliverdin chromophore. Most bacteriophytochromes work as photoactivated protein kinases. The Rhodobacter sphaeroides bacteriophytochrome BphG1 is unconventional in that it has GGDEF and EAL output domains, which are involved, respectively, in synthesis (diguanylate cyclase) and degradation (phosphodiesterase) of the bacterial second messenger c-di-GMP. The GGDEF-EAL proteins studied to date displayed either diguanylate cyclase or phosphodiesterase activity but not both. To elucidate the function of BphG1, the holoprotein was purified from an Escherichia coli overexpression system designed to produce biliverdin. The holoprotein contained covalently bound biliverdin and interconverted between the red (dark) and far red (light-activated) forms. BphG1 had c-di-GMP-specific phosphodiesterase activity. Unexpectedly for a photochromic protein, this activity was essentially light-independent. BphG1 expressed in E. coli was found to undergo partial cleavage into two species. The smaller species was identified as the EAL domain of BphG1. It possessed c-di-GMP phosphodiesterase activity. Surprisingly, the larger species lacking EAL possessed diguanylate cyclase activity, which was dependent on biliverdin and strongly activated by light. BphG1 therefore is the first phytochrome with a non-kinase photoactivated enzymatic activity. This shows that the photosensory modules of phytochromes can transmit light signals to various outputs. BphG1 is potentially the first "bifunctional" enzyme capable of both c-di-GMP synthesis and hydrolysis. A model for the regulation of the "opposite" activities of BphG1 is presented.
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Affiliation(s)
- Marina Tarutina
- Department of Molecular Biology, University of Wyoming, Laramie, Wyoming 82071, USA
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37
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Ashby M, Houmard J. Cyanobacterial two-component proteins: structure, diversity, distribution, and evolution. Microbiol Mol Biol Rev 2006; 70:472-509. [PMID: 16760311 PMCID: PMC1489541 DOI: 10.1128/mmbr.00046-05] [Citation(s) in RCA: 108] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/22/2022] Open
Abstract
A survey of the already characterized and potential two-component protein sequences that exist in the nine complete and seven partially annotated cyanobacterial genome sequences available (as of May 2005) showed that the cyanobacteria possess a much larger repertoire of such proteins than most other bacteria. By analysis of the domain structure of the 1,171 potential histidine kinases, response regulators, and hybrid kinases, many various arrangements of about thirty different modules could be distinguished. The number of two-component proteins is related in part to genome size but also to the variety of physiological properties and ecophysiologies of the different strains. Groups of orthologues were defined, only a few of which have representatives with known physiological functions. Based on comparisons with the proposed phylogenetic relationships between the strains, the orthology groups show that (i) a few genes, some of them clustered on the genome, have been conserved by all species, suggesting their very ancient origin and an essential role for the corresponding proteins, and (ii) duplications, fusions, gene losses, insertions, and deletions, as well as domain shuffling, occurred during evolution, leading to the extant repertoire. These mechanisms are put in perspective with the different genetic properties that cyanobacteria have to achieve genome plasticity. This review is designed to serve as a basis for orienting further research aimed at defining the most ancient regulatory mechanisms and understanding how evolution worked to select and keep the most appropriate systems for cyanobacteria to develop in the quite different environments that they have successfully colonized.
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Affiliation(s)
- Mark
K. Ashby
- Department
of Basic Medical Sciences, Biochemistry Section, University of the West
Indies, Mona Campus, Kingston 7,
Jamaica, Ecole Normale
Supérieure, CNRS UMR 8541, Génétique
Moléculaire, 46 rue d'Ulm, 75230 Paris Cedex 05,
France
| | - Jean Houmard
- Department
of Basic Medical Sciences, Biochemistry Section, University of the West
Indies, Mona Campus, Kingston 7,
Jamaica, Ecole Normale
Supérieure, CNRS UMR 8541, Génétique
Moléculaire, 46 rue d'Ulm, 75230 Paris Cedex 05,
France
- Corresponding
author. Mailing address: Ecole Normale Supérieure, CNRS UMR 8541,
Génétique Moléculaire, 46 rue d'Ulm, 75230 Paris
Cedex 05, France. Phone: 33 1 44 32 35 19. Fax: 33 1 44 96 53 60.
E-mail:
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Jawhara S, Mordon S. Monitoring of bactericidal action of laser by in vivo imaging of bioluminescent E. coli in a cutaneous wound infection. Lasers Med Sci 2006; 21:153-9. [PMID: 16897111 DOI: 10.1007/s10103-006-0388-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2006] [Accepted: 04/25/2006] [Indexed: 10/24/2022]
Abstract
The worldwide rise in antibiotic resistance necessitates the development of novel antimicrobial strategies. This study aimed to evaluate the bactericidal action of an 810-nm diode laser in a cutaneous wound infection. An Escherichia coli strain was transformed with a shuttle vector (pRB474) containing firefly luciferase gene from Photinus pyralis resulting in a bioluminescent phenotype. Because firefly luciferase is an enzyme and as such is prone to inactivation at elevated temperature, the first phase has consisted in evaluating in vitro the effect of temperature elevation (30, 40, 50, and 60 degrees C for 2 min) on bacteria bioluminescence. The second phase was performed in vivo. Two full-thickness circular, 14-mm diameter wounds (control and laser-irradiated) were induced on rats. Wound infection was carried out using a suspension (50 microl PBS) containing 5 x 10(7) cells of bioluminescent E. coli (10(9) cells/ml). Thirty minutes later, light irradiation was performed with an 810-nm diode laser (P = 10 W, psi = 1.4 cm, fluence: 130, 195, and 260 J/cm2). Temperature was measured within each wound with a noncontact infrared thermometer. Light emission of the bioluminescent bacteria was monitored in vivo by a bioluminescence imaging system before and at 4, 8, 24, and 48 h after laser irradiation. In vitro, bacteria bioluminescence is not affected when temperature is maintained at 50 degrees C for 2 min. In vivo, bioluminescence imaging showed that at 4 h, the viability of E. coli was reduced when compared to the control (CTRL) group (p < 0.01). This observation was confirmed at 8 h (p < 0.001), at 24 h (p < 0.001), and finally at 48 h (p < 0.001). Loss of viability of E. coli depends on laser fluence. At 48 h, bioluminescent bacteria were not detected (100% loss of viability) in the wound irradiated at 260 J/cm2. For this fluence, the temperature reached 45 degrees C at the end of the irradiation. This study confirms previous observations on the bactericidal effect of diode lasers. Because a progressive desiccation of the superficial dermis is usually observed when using laser irradiation, the hypothesis that laser irradiation dries out the wound making the wound an inhospitable place for bacteria is much more relevant than a direct effect of infrared light on chromophores inside bacteria. This is confirmed by the fact that in this latter case, one would expect an immediate drop in luminescence followed by an increase as the surviving bacteria started to divide and repopulate the wound. However, the exact mechanism deserves further studies. This study points out the advantage of using bioluminescence imaging to evaluate laser for the treatment of acute infections in vivo, nondestructively, and noninvasively.
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Affiliation(s)
- Samir Jawhara
- UPRES EA 2689-INSERM (French National Institute of Health and Medical Research) IFR 114, Pavillon Vancostenobel, Lille University Hospital, 59037, Lille, Cedex, France
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Abstract
Phytochromes are a widespread family of red/far-red responsive photoreceptors first discovered in plants, where they constitute one of the three main classes of photomorphogenesis regulators. All phytochromes utilize covalently attached bilin chromophores that enable photoconversion between red-absorbing (P(r)) and far-red-absorbing (P(fr)) forms. Phytochromes are thus photoswitchable photosensors; canonical phytochromes have a conserved N-terminal photosensory core and a C-terminal regulatory region, which typically includes a histidine-kinase-related domain. The discovery of new bacterial and cyanobacterial members of the phytochrome family within the last decade has greatly aided biochemical and structural characterization of this family, with the first crystal structure of a bacteriophytochrome photosensory core appearing in 2005. This structure and other recent biochemical studies have provided exciting new insights into the structure of phytochrome, the photoconversion process that is central to light sensing, and the mechanism of signal transfer by this important family of photoreceptors.
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Affiliation(s)
- Nathan C. Rockwell
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - Yi-Shin Su
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616
| | - J. Clark Lagarias
- Section of Molecular and Cellular Biology, University of California, Davis, CA 95616
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Scheerer P, Michael N, Park JH, Noack S, Förster C, Hammam MAS, Inomata K, Choe HW, Lamparter T, Krauss N. Crystallization and preliminary X-ray crystallographic analysis of the N-terminal photosensory module of phytochrome Agp1, a biliverdin-binding photoreceptor from Agrobacterium tumefaciens. J Struct Biol 2005; 153:97-102. [PMID: 16377207 DOI: 10.1016/j.jsb.2005.11.002] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2005] [Accepted: 11/02/2005] [Indexed: 11/19/2022]
Abstract
Phytochromes are photochromic photoreceptors with a bilin chromophore that have been found in plants and bacteria. Typical bacterial phytochromes are composed of an N-terminal photosensory chromophore module and a C-terminal protein kinase. The former contains the chromophore, which allows phytochromes to adopt the two interconvertible spectral forms, Pr and Pfr. The N-terminal photosensory module of Agrobacterium phytochrome Agp1, Agp1-M15, was used for crystallization studies. The protein was either assembled with the natural chromophore biliverdin or a sterically locked synthetic biliverdin-derivative, termed 15Za. The last-named adduct does not undergo photoisomerization due to an additional carbon chain between the rings C and D of the chromophore. Both adducts could be crystallized, but the resolution was largely improved by the use of 15Za. Crystals of biliverdin-Agp1-M15 diffract to 6A resolution and belong to the tetragonal space group I422 with unit cell dimensions a = b = 171 Angstroms, c = 81 Angstroms, crystals of 15Za-Agp1-M15 belong to the same space group with similar unit cell dimensions a = b = 174 Angstroms, c = 80 Angstroms, but diffract to 3.4 Angstroms resolution. Assuming the asymmetric unit to be occupied by one monomer of 55kDa, the unit cell contains 54-55% solvent with a crystal volume per protein mass, V(m), of 2.7 Angstroms(3) Da(-1).
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Affiliation(s)
- Patrick Scheerer
- Charité-Universitätsmedizin Berlin, Institut für Biochemie, Proteinstrukturforschung, Campus Charité-Mitte, Germany
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Inomata K, Hammam MAS, Kinoshita H, Murata Y, Khawn H, Noack S, Michael N, Lamparter T. Sterically locked synthetic bilin derivatives and phytochrome Agp1 from Agrobacterium tumefaciens form photoinsensitive Pr- and Pfr-like adducts. J Biol Chem 2005; 280:24491-7. [PMID: 15878872 DOI: 10.1074/jbc.m504710200] [Citation(s) in RCA: 85] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochrome photoreceptors undergo reversible photoconversion between the red-absorbing form, Pr, and the far-red-absorbing form, Pfr. The first step in the conversion from Pr to Pfr is a Z to E isomerization around the C15=C16 double bond of the bilin chromophore. We prepared four synthetic biliverdin (BV) derivatives in which rings C and D are sterically locked by cyclizing with an additional carbon chain. In these chromophores, which are termed 15Za, 15Zs, 15Ea, and 15Es, the C15=C16 double bond is in either the Z or E configuration and the C14-C15 single bond in either the syn or anti conformation. The chromophores were assembled with Agrobacterium phytochrome Agp1, which incorporates BV as natural chromophore. All locked BV derivatives bound covalently to the protein and formed adducts with characteristic spectral properties. The 15Za adduct was spectrally similar to the Pr form and the 15Ea adduct similar to the Pfr form of the BV adduct. Thus, the chromophore of Agp1 adopts a C15=C16 Z configuration and a C14-C15 anti conformation in the Pr form and a C15=C16 E configuration and a C14-C15 anti conformation in the Pfr form. Both the 15Zs and the 15Es adducts absorbed only in the blue region of the visible spectra. All chromophore adducts were analyzed by size exclusion chromatography and histidine kinase activity to probe for protein conformation. In either case, the 15Za adduct behaved like the Pr and the 15Ea adduct like the Pfr form of Agp1. Replacing the natural chromophore by a locked 15Ea derivative can thus bring phytochrome holoprotein in the Pfr form in darkness. In this way, physiological action of Pfr can be studied in vivo and separated from Pr/Pfr cycling and other light effects.
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Affiliation(s)
- Katsuhiko Inomata
- Division of Material Sciences, Graduate School of Natural Science and Technology, Kanazawa University, Kakuma, Kanazawa, Ishikawa 920-1192, Japan.
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Jacobi PA, Adel Odeh IM, Buddhu SC, Cai G, Rajeswari S, Fry D, Zheng W, DeSimone RW, Guo J, Coutts LD, Hauck SI, Leung SH, Ghosh I, Pippin. D. Synthetic Studies in Phytochrome Chemistry. Synlett 2005; 19:2861-2885. [PMID: 18633455 PMCID: PMC2467512 DOI: 10.1055/s-2005-918956] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
An account is given of the author's several approaches to the synthesis of the parent chromophore of phytochrome (1), a protein-bound linear tetrapyrrole derivative that controls photomorphogenesis in higher plants. These studies culminated in enantioselective syntheses of both 2R- and 2S-phytochromobilin (4), as well as several (13)C-labeled derivatives designed to probe the site of Z,E-isomerization during photoexcitation. When reacted in vitro, synthetic 2R-4 and recombinant-derived phytochrome apoprotein N-C produced a protein-bound chromophore with identical difference spectra to naturally occurring 1.
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Affiliation(s)
- Peter A. Jacobi
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Imad M. Adel Odeh
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Subhas C. Buddhu
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Guolin Cai
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Sundaramoorthi Rajeswari
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Douglas Fry
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Wanjun Zheng
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Robert W. DeSimone
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Jiasheng Guo
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Lisa D. Coutts
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Sheila I. Hauck
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Sam H. Leung
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Indranath Ghosh
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
| | - Douglas Pippin.
- Department of Chemistry, Dartmouth College, Hanover, New Hampshire 03755, USA. Fax: 603 646 3946
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