1
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Burgie ES, Li H, Gannam ZTK, McLoughlin KE, Vierstra RD, Li H. The structure of Arabidopsis phytochrome A reveals topological and functional diversification among the plant photoreceptor isoforms. Nat Plants 2023; 9:1116-1129. [PMID: 37291396 PMCID: PMC10546791 DOI: 10.1038/s41477-023-01435-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 05/10/2023] [Indexed: 06/10/2023]
Abstract
Plants employ a divergent cohort of phytochrome (Phy) photoreceptors to govern many aspects of morphogenesis through reversible photointerconversion between inactive Pr and active Pfr conformers. The two most influential are PhyA whose retention of Pfr enables sensation of dim light, while the relative instability of Pfr for PhyB makes it better suited for detecting full sun and temperature. To better understand these contrasts, we solved, by cryo-electron microscopy, the three-dimensional structure of full-length PhyA as Pr. Like PhyB, PhyA dimerizes through head-to-head assembly of its C-terminal histidine kinase-related domains (HKRDs), while the remainder assembles as a head-to-tail light-responsive platform. Whereas the platform and HKRDs associate asymmetrically in PhyB dimers, these lopsided connections are absent in PhyA. Analysis of truncation and site-directed mutants revealed that this decoupling and altered platform assembly have functional consequences for Pfr stability of PhyA and highlights how plant Phy structural diversification has extended light and temperature perception.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA
- Burning Rock Dx, Irvine, CA, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO, USA.
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
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2
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Li H, Burgie ES, Gannam ZTK, Li H, Vierstra RD. Plant phytochrome B is an asymmetric dimer with unique signalling potential. Nature 2022; 604:127-133. [PMID: 35355010 PMCID: PMC9930725 DOI: 10.1038/s41586-022-04529-z] [Citation(s) in RCA: 29] [Impact Index Per Article: 14.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 02/07/2022] [Indexed: 12/24/2022]
Abstract
Many aspects of plant photoperception are mediated by the phytochrome (Phy) family of bilin-containing photoreceptors that reversibly interconvert between inactive Pr and active Pfr conformers1,2. Despite extensive biochemical studies, full understanding of plant Phy signalling has remained unclear due to the absence of relevant 3D models. Here we report a cryo-electron microscopy structure of Arabidopsis PhyB in the Pr state that reveals a topologically complex dimeric organization that is substantially distinct from its prokaryotic relatives. Instead of an anticipated parallel architecture, the C-terminal histidine-kinase-related domains (HKRDs) associate head-to-head, whereas the N-terminal photosensory regions associate head-to-tail to form a parallelogram-shaped platform with near two-fold symmetry. The platform is internally linked by the second of two internal Per/Arnt/Sim domains that binds to the photosensory module of the opposing protomer and a preceding 'modulator' loop that assembles tightly with the photosensory module of its own protomer. Both connections accelerate the thermal reversion of Pfr back to Pr, consistent with an inverse relationship between dimer assembly and Pfr stability. Lopsided contacts between the HKRDs and the platform create profound asymmetry to PhyB that might imbue distinct signalling potentials to the protomers. We propose that this unique structural dynamism creates an extensive photostate-sensitive surface for conformation-dependent interactions between plant Phy photoreceptors and their signalling partners.
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Affiliation(s)
- Hua Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA
| | - E Sethe Burgie
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Zira T K Gannam
- Department of Biology, Washington University in St Louis, St Louis, MO, USA
| | - Huilin Li
- Department of Structural Biology, Van Andel Institute, Grand Rapids, MI, USA.
| | - Richard D Vierstra
- Department of Biology, Washington University in St Louis, St Louis, MO, USA.
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3
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Burgie ES, Gannam ZTK, McLoughlin KE, Sherman CD, Holehouse AS, Stankey RJ, Vierstra RD. Differing biophysical properties underpin the unique signaling potentials within the plant phytochrome photoreceptor families. Proc Natl Acad Sci U S A 2021; 118:e2105649118. [PMID: 34039713 PMCID: PMC8179155 DOI: 10.1073/pnas.2105649118] [Citation(s) in RCA: 22] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
Many aspects of photoperception by plants and microorganisms are initiated by the phytochrome (Phy) family of photoreceptors that detect light through interconversion between red light- (Pr) and far-red light-absorbing (Pfr) states. Plants synthesize a small family of Phy isoforms (PhyA to PhyE) that collectively regulate photomorphogenesis and temperature perception through redundant and unique actions. While the selective roles of these isoforms have been partially attributed to their differing abundances, expression patterns, affinities for downstream partners, and turnover rates, we show here from analysis of recombinant Arabidopsis chromoproteins that the Phy isoforms also display distinct biophysical properties. Included are a hypsochromic shift in the Pr absorption for PhyC and varying rates of Pfr to Pr thermal reversion, part of which can be attributed to the core photosensory module in each. Most strikingly, PhyB combines strong temperature dependence of thermal reversion with an order-of-magnitude faster rate to likely serve as the main physiological thermosensor, whereby thermal reversion competes with photoconversion. In addition, comparisons of Pfr occupancies for PhyA and PhyB under a range of red- and white-light fluence rates imply that low-light environments are effectively sensed by PhyA, while high-light environments, such as full sun, are effectively sensed by PhyB. Parallel analyses of the Phy isoforms from potato and maize showed that the unique features within the Arabidopsis family are conserved, thus indicating that the distinct biophysical properties among plant Phy isoforms emerged early in Phy evolution, likely to enable full interrogation of their light and temperature environments.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Zira T K Gannam
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130
| | | | | | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, St. Louis, MO 63110
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63110
| | - Robert J Stankey
- Department of Genetics, University of Wisconsin, Madison, WI 53706
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, MO 63130;
- Department of Genetics, University of Wisconsin, Madison, WI 53706
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4
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Clinger JA, Burgie ES, Miller MD, Cohen A, Vierstra RD, Phillips Jr GN. Cryo-trapping crystal studies of photoreceptor PixJ yield new insights into its photoconversion mechanism. Acta Crystallogr A Found Adv 2019. [DOI: 10.1107/s0108767319098088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022] Open
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5
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Burgie ES, Bussell AN, Lye SH, Wang T, Hu W, McLoughlin KE, Weber EL, Li H, Vierstra RD. Photosensing and Thermosensing by Phytochrome B Require Both Proximal and Distal Allosteric Features within the Dimeric Photoreceptor. Sci Rep 2017; 7:13648. [PMID: 29057954 PMCID: PMC5651913 DOI: 10.1038/s41598-017-14037-0] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2017] [Accepted: 09/21/2017] [Indexed: 11/12/2022] Open
Abstract
Phytochromes (Phys) encompass a diverse collection of bilin-containing photoreceptors that help plants and microorganisms perceive light through photointerconversion between red light (Pr) and far-red light (Pfr)-absorbing states. In addition, Pfr reverts thermally back to Pr via a highly enthalpic process that enables temperature sensation in plants and possibly other organisms. Through domain analysis of the Arabidopsis PhyB isoform assembled recombinantly, coupled with measurements of solution size, photoconversion, and thermal reversion, we identified both proximal and distal features that influence all three metrics. Included are the downstream C-terminal histidine kinase-related domain known to promote dimerization and a conserved patch just upstream of an N-terminal Period/Arnt/Sim (PAS) domain, which upon removal dramatically accelerates thermal reversion. We also discovered that the nature of the bilin strongly influences Pfr stability. Whereas incorporation of the native bilin phytochromobilin into PhyB confers robust Pfr → Pr thermal reversion, that assembled with the cyanobacterial version phycocyanobilin, often used for optogenetics, has a dramatically stabilized Pfr state. Taken together, we conclude that Pfr acquisition and stability are impacted by a collection of opposing allosteric features that inhibit or promote photoconversion and reversion of Pfr back to Pr, thus allowing Phys to dynamically measure light, temperature, and possibly time.
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Affiliation(s)
- E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Adam N Bussell
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Shu-Hui Lye
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA.,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Tong Wang
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,CUNY Advanced Science Research Center, The City University of New York, New York, New York, 10031, USA
| | - Weiming Hu
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Katrice E McLoughlin
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA
| | - Erin L Weber
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA
| | - Huilin Li
- Department of Biology, Brookhaven National Laboratory, Upton, New York, 11973, USA.,Van Andel Research Institute, Grand Rapids, Michigan, 49503, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, 63130, USA. .,Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin, 53706, USA.
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6
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Fuller FD, Gul S, Chatterjee R, Burgie ES, Young ID, Lebrette H, Srinivas V, Brewster AS, Michels-Clark T, Clinger JA, Andi B, Ibrahim M, Pastor E, de Lichtenberg C, Hussein R, Pollock CJ, Zhang M, Stan CA, Kroll T, Fransson T, Weninger C, Kubin M, Aller P, Lassalle L, Bräuer P, Miller MD, Amin M, Koroidov S, Roessler CG, Allaire M, Sierra RG, Docker PT, Glownia JM, Nelson S, Koglin JE, Zhu D, Chollet M, Song S, Lemke H, Liang M, Sokaras D, Alonso-Mori R, Zouni A, Messinger J, Bergmann U, Boal AK, Bollinger JM, Krebs C, Högbom M, Phillips GN, Vierstra RD, Sauter NK, Orville AM, Kern J, Yachandra VK, Yano J. Drop-on-demand sample delivery for studying biocatalysts in action at X-ray free-electron lasers. Nat Methods 2017; 14:443-449. [PMID: 28250468 DOI: 10.1038/nmeth.4195] [Citation(s) in RCA: 121] [Impact Index Per Article: 17.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/19/2016] [Accepted: 01/18/2017] [Indexed: 12/22/2022]
Abstract
X-ray crystallography at X-ray free-electron laser sources is a powerful method for studying macromolecules at biologically relevant temperatures. Moreover, when combined with complementary techniques like X-ray emission spectroscopy, both global structures and chemical properties of metalloenzymes can be obtained concurrently, providing insights into the interplay between the protein structure and dynamics and the chemistry at an active site. The implementation of such a multimodal approach can be compromised by conflicting requirements to optimize each individual method. In particular, the method used for sample delivery greatly affects the data quality. We present here a robust way of delivering controlled sample amounts on demand using acoustic droplet ejection coupled with a conveyor belt drive that is optimized for crystallography and spectroscopy measurements of photochemical and chemical reactions over a wide range of time scales. Studies with photosystem II, the phytochrome photoreceptor, and ribonucleotide reductase R2 illustrate the power and versatility of this method.
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Affiliation(s)
- Franklin D Fuller
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sheraz Gul
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Ruchira Chatterjee
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - E Sethe Burgie
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Iris D Young
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Hugo Lebrette
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Vivek Srinivas
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden
| | - Aaron S Brewster
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Tara Michels-Clark
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Babak Andi
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Mohamed Ibrahim
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Ernest Pastor
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | | | - Rana Hussein
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Christopher J Pollock
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Miao Zhang
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Claudiu A Stan
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Kroll
- SSRL, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Thomas Fransson
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Clemens Weninger
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Markus Kubin
- Institute for Methods and Instrumentation on Synchrotron Radiation Research, Helmholtz Zentrum Berlin für Materialien und Energie GmbH, Berlin, Germany
| | - Pierre Aller
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Louise Lassalle
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Philipp Bräuer
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK.,Department of Biochemistry, University of Oxford, Oxford, UK
| | | | - Muhamed Amin
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Sergey Koroidov
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Christian G Roessler
- National Synchrotron Light Source II, Brookhaven National Laboratory, Upton, New York, USA
| | - Marc Allaire
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Raymond G Sierra
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Peter T Docker
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - James M Glownia
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Silke Nelson
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Jason E Koglin
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Diling Zhu
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Matthieu Chollet
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Sanghoon Song
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Henrik Lemke
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Mengning Liang
- LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | | | | | - Athina Zouni
- Institut für Biologie, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Johannes Messinger
- Institutionen för Kemi, Kemiskt Biologiskt Centrum, Umeå Universitet, Umeå, Sweden.,Department of Chemistry-Ångström, Molecular Biomimetics, Uppsala University, Uppsala, Sweden
| | - Uwe Bergmann
- Stanford PULSE Institute, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Amie K Boal
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - J Martin Bollinger
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Carsten Krebs
- Department of Chemistry, Pennsylvania State University, University Park, Pennsylvania, USA.,Department of Biochemistry and Molecular Biology, Pennsylvania State University, University Park, Pennsylvania, USA
| | - Martin Högbom
- Department of Biochemistry and Biophysics, Stockholm University, Stockholm, Sweden.,Department of Chemistry, Stanford University, Stanford, California, USA
| | - George N Phillips
- Department of BioSciences, Rice University, Houston, Texas, USA.,Department of Chemistry, Rice University, Houston, Texas, USA
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, St. Louis, Missouri, USA
| | - Nicholas K Sauter
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Allen M Orville
- Diamond Light Source Limited, Harwell Science and Innovation Campus, Didcot, UK
| | - Jan Kern
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA.,LCLS, SLAC National Accelerator Laboratory, Menlo Park, California, USA
| | - Vittal K Yachandra
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
| | - Junko Yano
- Molecular Biophysics and Integrated Bioimaging Division, Lawrence Berkeley National Laboratory, Berkeley, California, USA
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7
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Legris M, Klose C, Burgie ES, Rojas CCR, Neme M, Hiltbrunner A, Wigge PA, Schäfer E, Vierstra RD, Casal JJ. Phytochrome B integrates light and temperature signals in Arabidopsis. Science 2016; 354:897-900. [PMID: 27789798 DOI: 10.1126/science.aaf5656] [Citation(s) in RCA: 479] [Impact Index Per Article: 59.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2016] [Accepted: 09/16/2016] [Indexed: 12/19/2022]
Abstract
Ambient temperature regulates many aspects of plant growth and development, but its sensors are unknown. Here, we demonstrate that the phytochrome B (phyB) photoreceptor participates in temperature perception through its temperature-dependent reversion from the active Pfr state to the inactive Pr state. Increased rates of thermal reversion upon exposing Arabidopsis seedlings to warm environments reduce both the abundance of the biologically active Pfr-Pfr dimer pool of phyB and the size of the associated nuclear bodies, even in daylight. Mathematical analysis of stem growth for seedlings expressing wild-type phyB or thermally stable variants under various combinations of light and temperature revealed that phyB is physiologically responsive to both signals. We therefore propose that in addition to its photoreceptor functions, phyB is a temperature sensor in plants.
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Affiliation(s)
- Martina Legris
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1405 Buenos Aires, Argentina
| | - Cornelia Klose
- Institut für Biologie II, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg
| | - E Sethe Burgie
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO 63130, USA
| | - Cecilia Costigliolo Rojas Rojas
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1405 Buenos Aires, Argentina
| | - Maximiliano Neme
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1405 Buenos Aires, Argentina
| | - Andreas Hiltbrunner
- Institut für Biologie II, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schaenzlestrasse 18, 79104 Freiburg, Germany
| | - Philip A Wigge
- Sainsbury Laboratory, Cambridge University, 47 Bateman Street, Cambridge CB2 1LR, UK
| | - Eberhard Schäfer
- Institut für Biologie II, University of Freiburg, Schaenzlestrasse 1, D-79104 Freiburg.,BIOSS Centre for Biological Signaling Studies, University of Freiburg, Schaenzlestrasse 18, 79104 Freiburg, Germany
| | - Richard D Vierstra
- Department of Biology, Washington University in St. Louis, Campus Box 1137, One Brookings Drive, St. Louis, MO 63130, USA
| | - Jorge J Casal
- Fundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas (CONICET), 1405 Buenos Aires, Argentina. .,Instituto de Investigaciones Fisiológicas y Ecológicas a Vinculadas a la Agricultura (IFEVA), Facultad de Agronomía, Universidad de Buenos Aires and CONICET, Avenida San Martín 4453, 1417 Buenos Aires, Argentina
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8
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Li F, Burgie ES, Yu T, Héroux A, Schatz GC, Vierstra RD, Orville AM. X-ray radiation induces deprotonation of the bilin chromophore in crystalline D. radiodurans phytochrome. J Am Chem Soc 2015; 137:2792-5. [PMID: 25650486 DOI: 10.1021/ja510923m] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
We report that in the red light-absorbing (Pr) state, the bilin chromophore of the Deinococcus radiodurans proteobacterial phytochrome (DrBphP) is hypersensitive to X-ray photons used in typical synchrotron X-ray protein crystallography experiments. This causes the otherwise fully protonated chromophore to deprotonate without additional major structural changes. These results have major implications for our understanding of the structural and chemical characteristics of the resting and intermediate states of phytochromes and other photoreceptor proteins.
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Affiliation(s)
- Feifei Li
- Photon Sciences Directorate and ∥Biosciences Department, Brookhaven National Laboratory , Upton, New York 11973, United States
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9
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Burgie ES, Vierstra RD. Phytochromes: an atomic perspective on photoactivation and signaling. Plant Cell 2014; 26:4568-83. [PMID: 25480369 PMCID: PMC4311201 DOI: 10.1105/tpc.114.131623] [Citation(s) in RCA: 139] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/01/2014] [Revised: 10/10/2014] [Accepted: 11/14/2014] [Indexed: 05/19/2023]
Abstract
The superfamily of phytochrome (Phy) photoreceptors regulates a wide array of light responses in plants and microorganisms through their unique ability to reversibly switch between stable dark-adapted and photoactivated end states. Whereas the downstream signaling cascades and biological consequences have been described, the initial events that underpin photochemistry of the coupled bilin chromophore and the ensuing conformational changes needed to propagate the light signal are only now being understood. Especially informative has been the rapidly expanding collection of 3D models developed by x-ray crystallographic, NMR, and single-particle electron microscopic methods from a remarkably diverse array of bacterial Phys. These structures have revealed how the modular architecture of these dimeric photoreceptors engages the buried chromophore through distinctive knot, hairpin, and helical spine features. When collectively viewed, these 3D structures reveal complex structural alterations whereby photoisomerization of the bilin drives nanometer-scale movements within the Phy dimer through bilin sliding, hairpin reconfiguration, and spine deformation that ultimately impinge upon the paired signal output domains. When integrated with the recently described structure of the photosensory module from Arabidopsis thaliana PhyB, new opportunities emerge for the rational redesign of plant Phys with novel photochemistries and signaling properties potentially beneficial to agriculture and their exploitation as optogenetic reagents.
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Affiliation(s)
- E Sethe Burgie
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
| | - Richard D Vierstra
- Department of Genetics, University of Wisconsin-Madison, Madison, Wisconsin 53706
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10
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Burgie ES, Wang T, Bussell AN, Walker JM, Li H, Vierstra RD. Crystallographic and electron microscopic analyses of a bacterial phytochrome reveal local and global rearrangements during photoconversion. J Biol Chem 2014; 289:24573-87. [PMID: 25006244 DOI: 10.1074/jbc.m114.571661] [Citation(s) in RCA: 81] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Phytochromes are multidomain photoswitches that drive light perception in plants and microorganisms by coupling photoreversible isomerization of their bilin chromophore to various signaling cascades. How changes in bilin conformation affect output by these photoreceptors remains poorly resolved and might include several species-specific routes. Here, we present detailed three-dimensional models of the photosensing module and a picture of an entire dimeric photoreceptor through structural analysis of the Deinococcus radiodurans phytochrome BphP assembled with biliverdin (BV). A 1.16-Å resolution crystal structure of the bilin-binding pocket in the dark-adapted red light-absorbing state illuminated the intricate network of bilin/protein/water interactions and confirmed the protonation and ZZZssa conformation of BV. Structural and spectroscopic comparisons with the photochemically compromised D207A mutant revealed that substitutions of Asp-207 allow inclusion of cyclic porphyrins in addition to BV. A crystal structure of the entire photosensing module showed a head-to-head, twisted dimeric arrangement with bowed helical spines and a hairpin protrusion connecting the cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) and phytochrome-specific (PHY) domains. A key conserved hairpin feature is its anti-parallel, two β-strand stem, which we show by mutagenesis to be critical for BphP photochemistry. Comparisons of single particle electron microscopic images of the full-length BphP dimer in the red light-absorbing state and the photoactivated far-red light-absorbing state revealed a large scale reorientation of the PHY domain relative to the GAF domain, which alters the position of the downstream histidine kinase output module. Together, our data support a toggle model whereby bilin photoisomerization alters GAF/PHY domain interactions through conformational modification of the hairpin, which regulates signaling by impacting the relationship between sister output modules.
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Affiliation(s)
- E Sethe Burgie
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Tong Wang
- the Biology Department, Brookhaven National Laboratory, Upton, New York 11973, and
| | - Adam N Bussell
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Joseph M Walker
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706
| | - Huilin Li
- the Biology Department, Brookhaven National Laboratory, Upton, New York 11973, and the Department of Biochemistry and Cell Biology, Stony Brook University, Stony Brook, New York 11794
| | - Richard D Vierstra
- From the Department of Genetics, University of Wisconsin, Madison, Wisconsin 53706,
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11
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Cornilescu CC, Cornilescu G, Burgie ES, Markley JL, Ulijasz AT, Vierstra RD. Dynamic structural changes underpin photoconversion of a blue/green cyanobacteriochrome between its dark and photoactivated states. J Biol Chem 2013; 289:3055-65. [PMID: 24337572 DOI: 10.1074/jbc.m113.531053] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
The phytochrome superfamily of photoreceptors exploits reversible light-driven changes in the bilin chromophore to initiate a variety of signaling cascades. The nature of these alterations and how they impact the protein moiety remain poorly resolved and might include several species-specific routes. Here, we provide a detailed picture of photoconversion for the photosensing cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF) domain from Thermosynechococcus elongatus (Te) PixJ, a member of the cyanobacteriochrome clade. Solution NMR structures of the blue light-absorbing dark state Pb and green light-absorbing photoactivated state Pg, combined with paired crystallographic models, revealed that the bilin and GAF domain dynamically transition via breakage of the C10/Cys-494 thioether bond, opposite rotations of the A and D pyrrole rings, sliding of the bilin in the GAF pocket, and the appearance of an extended region of disorder that includes Cys-494. Changes in GAF domain backbone dynamics were also observed that are likely important for inter-domain signal propagation. Taken together, photoconversion of T. elongatus PixJ from Pb to Pg involves complex structural changes within the GAF domain pocket that transduce light into a mechanical signal, many aspects of which should be relevant to others within the extended phytochrome superfamily.
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Affiliation(s)
- Claudia C Cornilescu
- From the National Magnetic Resonance Facility at Madison, Department of Biochemistry and
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12
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Sethe Burgie E, Bingman CA, Makino SI, Wesenberg GE, Pan X, Fox BG, Phillips GN. Structural architecture of Galdieria sulphuraria DCN1L. Proteins 2011; 79:1329-36. [PMID: 21387409 DOI: 10.1002/prot.22937] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2010] [Revised: 10/18/2010] [Accepted: 10/21/2010] [Indexed: 11/05/2022]
Affiliation(s)
- E Sethe Burgie
- Department of Genetics, Center for Eukaryotic Structural Genomics, University of Wisconsin-Madison, Madison Wisconsin 53706-1544, USA
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13
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Burgie ES, Holden HM. Three-Dimensional Structure of DesVI from Streptomyces venezuelae: A Sugar N,N-Dimethyltransferase Required for dTDP-Desosamine Biosynthesis. Biochemistry 2008; 47:3982-8. [DOI: 10.1021/bi800063j] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Affiliation(s)
- E. Sethe Burgie
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
| | - Hazel M. Holden
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706
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14
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Abstract
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found, for example, in such macrolide antibiotics as erthyromycin, azithromycin, and clarithromycin. The efficacies of these macrolide antibiotics are markedly reduced in the absence of desosamine. In the bacterium Streptomyces venezuelae, six enzymes are required for the production of dTDP-desosamine. The focus of this X-ray crystallographic analysis is the third enzyme in the pathway, a PLP-dependent aminotransferase referred to as DesI. The structure of DesI was solved in complex with its product, dTDP-4-amino-4,6-dideoxyglucose, to a nominal resolution of 2.1 A. Each subunit of the dimeric enzyme contains 12 alpha-helices and 14 beta-strands. Three cis-peptides are observed in each subunit, Phe 330, Pro 332, and Pro 339. The two active sites of the enzyme are located in clefts at the subunit/subunit interface. Electron density corresponding to the bound product clearly demonstrates a covalent bond between the amino group of the product and C-4' of the PLP cofactor. Interestingly, there are no hydrogen-bonding interactions between the protein and the dideoxyglucosyl group of the product (within 3.2 A). The only other sugar-modifying aminotransferase whose structure is known in the presence of product is PseC from Helicobacter pylori. This enzyme, as opposed to DesI, catalyzes amino transfer to the axial position of the sugar. A superposition of the two active sites for these proteins reveals that the major differences in ligand binding occur in the orientations of the deoxyglucosyl and phosphoryl groups. Indeed, the nearly 180 degrees difference in hexose orientation explains the equatorial versus axial amino transfer exhibited by DesI and PseC, respectively.
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Affiliation(s)
| | - Hazel M. Holden
- To whom correspondence should be addressed. FAX: 608−262−1319 PHONE: 608−262−4988
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15
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Burgie ES, Thoden JB, Holden HM. Molecular architecture of DesV from Streptomyces venezuelae: a PLP-dependent transaminase involved in the biosynthesis of the unusual sugar desosamine. Protein Sci 2007; 16:887-96. [PMID: 17456741 PMCID: PMC2206644 DOI: 10.1110/ps.062711007] [Citation(s) in RCA: 29] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
Desosamine is a 3-(dimethylamino)-3,4,6-trideoxyhexose found in certain macrolide antibiotics such as the commonly prescribed erythromycin. Six enzymes are required for its biosynthesis in Streptomyces venezuelae. The focus of this article is DesV, which catalyzes the PLP-dependent replacement of a 3-keto group with an amino functionality in the fifth step of the pathway. For this study the three-dimensional structures of both the internal aldimine and the ketimine intermediate with glutamate were determined to 2.05 A resolution. DesV is a homodimer with each subunit containing 12 alpha-helical regions and 12 beta-strands that together form three layers of sheet. The structure of the internal aldimine demonstrates that the PLP-cofactor is held in place by residues contributed from both subunits (Asp 164 and Gln 167 from Subunit I and Tyr 221 and Asn 235 from Subunit II). When the ketimine intermediate is present in the active site, the loop defined by Gln 225 to Ser 228 from Subunit II closes down upon the active site. The structure of DesV is similar to another sugar-modifying enzyme referred to as PseC. This enzyme is involved in the biosynthesis of pseudaminic acid, which is a sialic acid-like nonulosonate found in the flagellin of Helicobacter pylori. In the case of PseC, however, the amino group is transferred to the C-4 rather than the C-3 position. Details concerning the structural analysis of DesV and a comparison of its molecular architecture to that of PseC are presented.
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Affiliation(s)
- E Sethe Burgie
- Department of Biochemistry, University of Wisconsin, Madison, Wisconsin 53706, USA
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Affiliation(s)
- Gary K Ackers
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, Missouri 63110, USA
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Swislocki A, Burgie ES, Rodnick KJ. Effects of ovariectomy on indices of insulin resistance, hypertension, and cardiac energy metabolism in middle-aged spontaneously hypertensive rats (SHR). Horm Metab Res 2002; 34:516-22. [PMID: 12384829 DOI: 10.1055/s-2002-34792] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
Abstract
Insulin resistance is a risk factor for coronary heart disease. The protection of young women from coronary events is sharply reduced with menopause. To assess the impact of menopause on glucose tolerance, insulin resistance, body weight gain, heart size, and cardiac energy metabolism, we studied 28-week-old female SHR and Wistar-Kyoto (WKY) rats, who were either ovariectomized (SHR(OVX) and WKY(OVX)) or sham-operated (SHR(SHAM) and WKY(SHAM)). Animals underwent blood-pressure measurement and an oral glucose tolerance test (OGTT). Hearts were weighed and assayed for metabolic enzyme activities. Female SHR were 33 % lighter and hypertensive (+ 36 mmHg), with 33 % larger hearts (when corrected for body weight differences) compared to WKY. Although ovariectomized animals of both strains were heavier overall than their sham-operated counterparts, when heart weights were corrected for body weight, both OVX strains had lighter hearts than both SHAM strains. Glucose and insulin responses during OGTT were similar between the four groups; however, free fatty acid (FFA) responses were approximately 50 % greater in SHR than WKY, although less in SHR(OVX) than SHR(SHAM). WKY(OVX) demonstrated 8 % lower ventricular hexokinase activity than WKY(SHAM), which may reflect reduced cardiac glucose utilization. We also noted 16 % higher citrate synthase activity in WKY hearts. In conclusion, the insulin resistance characteristic of younger SHR is blunted in middle-aged female rats, although FFA responses remain elevated. Ovariectomy did not alter in vivo glucose tolerance in this group; however, sex hormones may be important in maintaining normal heart size and the potential for cardiac glucose metabolism.
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Affiliation(s)
- A Swislocki
- Medical Service, VA Northern California Health Care System, Martinez, CA 94553, USA.
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