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Park E, Kim Y, Choi G. Phytochrome B Requires PIF Degradation and Sequestration to Induce Light Responses across a Wide Range of Light Conditions. THE PLANT CELL 2018; 30:1277-1292. [PMID: 29764986 PMCID: PMC6048787 DOI: 10.1105/tpc.17.00913] [Citation(s) in RCA: 65] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2017] [Revised: 03/23/2018] [Accepted: 05/10/2018] [Indexed: 05/04/2023]
Abstract
Phytochrome B (phyB) inhibits the function of phytochrome-interacting factors (PIFs) by inducing their degradation and sequestration, but the relative physiological importance of these two phyB activities is unclear. In an analysis of published Arabidopsis thaliana phyB mutations, we identified a point mutation in the N-terminal half of phyB (phyBG111D) that abolishes its PIF sequestration activity without affecting its PIF degradation activity. We also identified a point mutation in the phyB C-terminal domain, which, when combined with a deletion of the C-terminal end (phyB990G767R), does the opposite; it blocks PIF degradation without affecting PIF sequestration. The resulting phyB proteins, phyB990G767R and phyBG111D, are equally capable of inducing light responses under continuous red light. However, phyBG111D, which exhibits only the PIF degradation activity, induces stronger light responses than phyB990G767R under white light with prolonged dark periods (i.e., diurnal cycles). In contrast, phyB990G767R, which exhibits only the PIF sequestration activity, induces stronger light responses in flickering light (a condition that mimics sunflecks). Together, our results indicate that both of these separable phyB activities are required for light responses in varying light conditions.
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Affiliation(s)
- Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Yeojae Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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52
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Qiu Y, Pasoreck EK, Reddy AK, Nagatani A, Ma W, Chory J, Chen M. Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017. [PMID: 29199270 DOI: 10.1038/s41467-107-02062-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/12/2023] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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Affiliation(s)
- Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | | | - Amit K Reddy
- Department of Biology, Duke University, Durham, NC, 27708, USA
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502, Japan
| | - Wenxiu Ma
- Department of Statistics, University of California, Riverside, CA, 92521, USA
| | - Joanne Chory
- Howard Hughes Medical Institute, Plant Biology Laboratory, The Salk Institute for Biological Studies, La Jolla, CA, 92037, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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53
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Mechanism of early light signaling by the carboxy-terminal output module of Arabidopsis phytochrome B. Nat Commun 2017; 8:1905. [PMID: 29199270 PMCID: PMC5712524 DOI: 10.1038/s41467-017-02062-6] [Citation(s) in RCA: 55] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 11/03/2017] [Indexed: 11/08/2022] Open
Abstract
Plant phytochromes are thought to transduce light signals by mediating the degradation of phytochrome-interacting transcription factors (PIFs) through the N-terminal photosensory module, while the C-terminal module, including a histidine kinase-related domain (HKRD), does not participate in signaling. Here we show that the C-terminal module of Arabidopsis phytochrome B (PHYB) is sufficient to mediate the degradation of PIF3 specifically and to activate photosynthetic genes in the dark. The HKRD is a dimerization domain for PHYB homo and heterodimerization. A D1040V mutation, which disrupts the dimerization of HKRD and the interaction between C-terminal module and PIF3, abrogates PHYB nuclear accumulation, photobody biogenesis, and PIF3 degradation. By contrast, disrupting the interaction between PIF3 and PHYB's N-terminal module has little effect on PIF3 degradation. Together, this study demonstrates that the dimeric form of the C-terminal module plays important signaling roles by targeting PHYB to subnuclear photobodies and interacting with PIF3 to trigger its degradation.
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54
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Viczián A, Klose C, Ádám É, Nagy F. New insights of red light-induced development. PLANT, CELL & ENVIRONMENT 2017; 40:2457-2468. [PMID: 27943362 DOI: 10.1111/pce.12880] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 05/14/2023]
Abstract
The red/far-red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever-changing environment. Our understanding of how absorption of a red/far-red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light-grown plants. We discuss how its light-independent inactivation (termed dark/thermal reversion), post-translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light-controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor.
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Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology2/Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
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55
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Affiliation(s)
- Karen J Halliday
- SynthSys, School of Biological Sciences, CH Waddington Building, University of Edinburgh, Edinburgh EH9 3BF, UK.
| | - Seth J Davis
- Department of Biology, University of York, York YO10 5DD, UK.
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56
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Abstract
The eukaryotic nucleus is enclosed by the nuclear envelope, which is perforated by the nuclear pores, the gateways of macromolecular exchange between the nucleoplasm and cytoplasm. The nucleoplasm is organized in a complex three-dimensional fashion that changes over time and in response to stimuli. Within the cell, the nucleus must be viewed as an organelle (albeit a gigantic one) that is a recipient of cytoplasmic forces and capable of morphological and positional dynamics. The most dramatic reorganization of this organelle occurs during mitosis and meiosis. Although many of these aspects are less well understood for the nuclei of plants than for those of animals or fungi, several recent discoveries have begun to place our understanding of plant nuclei firmly into this broader cell-biological context.
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Affiliation(s)
- Iris Meier
- Department of Molecular Genetics, The Ohio State University, Columbus, Ohio 43210;
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
| | | | - David E Evans
- Department of Biological and Medical Sciences, Oxford Brookes University, Oxford OX3 0BP, United Kingdom;
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57
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Nevarez PA, Qiu Y, Inoue H, Yoo CY, Benfey PN, Schnell DJ, Chen M. Mechanism of Dual Targeting of the Phytochrome Signaling Component HEMERA/pTAC12 to Plastids and the Nucleus. PLANT PHYSIOLOGY 2017; 173:1953-1966. [PMID: 28232584 PMCID: PMC5373053 DOI: 10.1104/pp.16.00116] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/02/2017] [Accepted: 02/21/2017] [Indexed: 05/20/2023]
Abstract
HEMERA (HMR) is a nuclear and plastidial dual-targeted protein. While it functions in the nucleus as a transcriptional coactivator in phytochrome signaling to regulate a distinct set of light-responsive, growth-relevant genes, in plastids it is known as pTAC12, which associates with the plastid-encoded RNA polymerase, and is essential for inducing the plastomic photosynthetic genes and initiating chloroplast biogenesis. However, the mechanism of targeting HMR to the nucleus and plastids is still poorly understood. Here, we show that HMR can be directly imported into chloroplasts through a transit peptide residing in the N-terminal 50 amino acids. Upon cleavage of the transit peptide and additional proteolytic processing, mature HMR, which begins from Lys-58, retains its biochemical properties in phytochrome signaling. Unexpectedly, expression of mature HMR failed to rescue not only the plastidial but also the nuclear defects of the hmr mutant. This is because the predicted nuclear localization signals of HMR are nonfunctional, and therefore mature HMR is unable to accumulate in either plastids or the nucleus. Surprisingly, fusing the transit peptide of the small subunit of Rubisco with mature HMR rescues both its plastidial and nuclear localization and functions. These results, combined with the observation that the nuclear form of HMR has the same reduced molecular mass as plastidial HMR, support a retrograde protein translocation mechanism in which HMR is targeted first to plastids, processed to the mature form, and then relocated to the nucleus.
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Affiliation(s)
- P Andrew Nevarez
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Yongjian Qiu
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Hitoshi Inoue
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Philip N Benfey
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Danny J Schnell
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.)
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, California 92521 (Y.Q., C.Y., M.C.);
- Department of Biology, Duke University, Durham, North Carolina 27708 (P.A.N., Y.Q., C.Y., P.N.B., M.C.); and
- Department of Plant Biology, Michigan State University, East Lansing, Michigan 48824 (H.I., D.J.S.)
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58
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Smith RW, Helwig B, Westphal AH, Pel E, Hörner M, Beyer HM, Samodelov SL, Weber W, Zurbriggen MD, Borst JW, Fleck C. Unearthing the transition rates between photoreceptor conformers. BMC SYSTEMS BIOLOGY 2016; 10:110. [PMID: 27884151 PMCID: PMC5123409 DOI: 10.1186/s12918-016-0368-y] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/13/2016] [Accepted: 11/07/2016] [Indexed: 12/04/2022]
Abstract
Background Obtaining accurate estimates of biological or enzymatic reaction rates is critical in understanding the design principles of a network and how biological processes can be experimentally manipulated on demand. In many cases experimental limitations mean that some enzymatic rates cannot be measured directly, requiring mathematical algorithms to estimate them. Here, we describe a methodology that calculates rates at which light-regulated proteins switch between conformational states. We focus our analysis on the phytochrome family of photoreceptors found in cyanobacteria, plants and many optogenetic tools. Phytochrome proteins change between active (PA) and inactive (PI) states at rates that are proportional to photoconversion cross-sections and influenced by light quality, light intensity, thermal reactions and dimerisation. This work presents a method that can accurately calculate these photoconversion cross-sections in the presence of multiple non-light regulated reactions. Results Our approach to calculating the photoconversion cross-sections comprises three steps: i) calculate the thermal reversion reaction rate(s); ii) develop search spaces from which all possible sets of photoconversion cross-sections exist, and; iii) estimate extinction coefficients that describe our absorption spectra. We confirm that the presented approach yields accurate results through the use of simulated test cases. Our test cases were further expanded to more realistic scenarios where noise, multiple thermal reactions and dimerisation are considered. Finally, we present the photoconversion cross-sections of an Arabidopsis phyB N-terminal fragment commonly used in optogenetic tools. Conclusions The calculation of photoconversion cross-sections has implications for both photoreceptor and synthetic biologists. Our method allows, for the first time, direct comparisons of photoconversion cross-sections and response speeds of photoreceptors in different cellular environments and synthetic tools. Due to the generality of our procedure, as shown by the application to multiple test cases, the photoconversion cross-sections and quantum yields of any photoreceptor might now, in principle, be obtained. Electronic supplementary material The online version of this article (doi:10.1186/s12918-016-0368-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Robert W Smith
- Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.,LifeGlimmer GmbH, Markelstrasse 38, Berlin, 12163, Germany
| | - Britta Helwig
- Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.,Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands
| | - Adrie H Westphal
- Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands
| | - Eran Pel
- Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.,Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands
| | - Maximilian Hörner
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.,Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
| | - Hannes M Beyer
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.,Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
| | - Sophia L Samodelov
- Spemann Graduate School of Biology and Medicine, University of Freiburg, Albertstrasse 19A, Freiburg, 79104, Germany.,Institute of Synthetic Biology, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
| | - Wilfried Weber
- Faculty of Biology & BioSS, University of Freiburg, Schänzlestrasse 18, Freiburg, 79104, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology, Heinrich Heine University, Universitätsstrasse 1, Düsseldorf, 40225, Germany
| | - Jan Willem Borst
- Laboratory of Biochemistry, PO Box 8128, Wageningen, 6700ET, The Netherlands
| | - Christian Fleck
- Laboratory of Systems & Synthetic Biology, Wageningen UR, PO Box 8033, Wageningen, 6700EJ, The Netherlands.
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59
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Kim J, Song K, Park E, Kim K, Bae G, Choi G. Epidermal Phytochrome B Inhibits Hypocotyl Negative Gravitropism Non-Cell-Autonomously. THE PLANT CELL 2016; 28:2770-2785. [PMID: 27758895 PMCID: PMC5155346 DOI: 10.1105/tpc.16.00487] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2016] [Revised: 09/27/2016] [Accepted: 10/06/2016] [Indexed: 05/20/2023]
Abstract
Seedling hypocotyls display negative gravitropism in the dark but agravitropism in the light. The Arabidopsis thaliana pif quadruple mutant (pifQ), which lacks four PHYTOCHROME-INTERACTING FACTORS (PIFs), is agravitropic in the dark. Endodermis-specific expression of PIF1 rescues gravitropism in pifQ mutant seedlings. Since phytochromes induce light responses by inhibiting PIFs and the COP1-SPA ubiquitin E3 ligase complex in the nucleus, we asked whether phyB can cell autonomously inhibit hypocotyl negative gravitropism in the endodermis. We found that while epidermis-specific expression of PHYB rescues hypocotyl negative gravitropism and all other phyB mutant phenotypes, endodermis-specific expression of PHYB does not. Epidermal phyB induces the phosphorylation and degradation of endodermal PIFs in response to red light. This induces a global gene expression pattern similar to that induced by red light treatment of seedlings expressing PHYB under the control of its own endogenous promoter. Our results imply that epidermal phyB generates an unidentified mobile signal that travels to the endodermis where it promotes PIF degradation and inhibits hypocotyl negative gravitropism.
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Affiliation(s)
- Jaewook Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Kijong Song
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Eunae Park
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Keunhwa Kim
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Gabyong Bae
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
| | - Giltsu Choi
- Department of Biological Sciences, KAIST, Daejeon 34141, Korea
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60
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Yue J, Qin Q, Meng S, Jing H, Gou X, Li J, Hou S. TOPP4 Regulates the Stability of PHYTOCHROME INTERACTING FACTOR5 during Photomorphogenesis in Arabidopsis. PLANT PHYSIOLOGY 2016; 170:1381-97. [PMID: 26704640 PMCID: PMC4775132 DOI: 10.1104/pp.15.01729] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2015] [Accepted: 12/23/2015] [Indexed: 05/18/2023]
Abstract
In plants, photoreceptors transfer light signals to phytochrome-interacting factors (PIFs), inducing the rapid phosphorylation and degradation of PIFs to promote photomorphogenesis. However, the phosphatase responsible for PIF dephosphorylation remains unknown. In this study, we identified a type 1 protein phosphatase, TOPP4, that is essential for PIF5 protein stability in Arabidopsis (Arabidopsis thaliana). Compared with the wild type, the dominant-negative mutant, topp4-1, displayed reduced hypocotyl length and larger apical hook and cotyledon opening angle under red light. Overexpression of topp4-1 in the wild type led to defects that were similar to those in the topp4-1 mutant. Red light induced phytochrome B (phyB)-dependent TOPP4 expression in hypocotyls. The topp4-1 mutation weakened the closed cotyledon angle of phyB-9 and phyA-211 phyB-9, while overexpression of TOPP4 significantly repressed the short hypocotyls of phyB-green fluorescent protein seedlings, indicating that TOPP4 and phyB function in an antagonistic way during photomorphogenesis. Protein interaction assays and phosphorylation studies demonstrate that TOPP4 interacts directly with PIF5 and dephosphorylates it. Furthermore, TOPP4 inhibits the red light-induced ubiquitination and degradation of PIF5. These findings demonstrate that dephosphorylation of PIF5 by TOPP4 inhibits its ubiquitin-mediated degradation during photomorphogenesis. These data outline a novel phytochrome signaling mechanism by which TOPP4-mediated dephosphorylation of PIF5 attenuates phytochrome-dependent light responses.
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Affiliation(s)
- Jing Yue
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Qianqian Qin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Siyuan Meng
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Huiting Jing
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Xiaoping Gou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Suiwen Hou
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
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61
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Huang H, Yoo CY, Bindbeutel R, Goldsworthy J, Tielking A, Alvarez S, Naldrett MJ, Evans BS, Chen M, Nusinow DA. PCH1 integrates circadian and light-signaling pathways to control photoperiod-responsive growth in Arabidopsis. eLife 2016; 5:e13292. [PMID: 26839287 PMCID: PMC4755757 DOI: 10.7554/elife.13292] [Citation(s) in RCA: 59] [Impact Index Per Article: 7.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 01/13/2016] [Indexed: 01/06/2023] Open
Abstract
Plants react to seasonal change in day length through altering physiology and development. Factors that function to harmonize growth with photoperiod are poorly understood. Here we characterize a new protein that associates with both circadian clock and photoreceptor components, named PHOTOPERIODIC CONTROL OF HYPOCOTYL1 (PCH1). pch1 seedlings have overly elongated hypocotyls specifically under short days while constitutive expression of PCH1 shortens hypocotyls independent of day length. PCH1 peaks at dusk, binds phytochrome B (phyB) in a red light-dependent manner, and co-localizes with phyB into photobodies. PCH1 is necessary and sufficient to promote the biogenesis of large photobodies to maintain an active phyB pool after light exposure, potentiating red-light signaling and prolonging memory of prior illumination. Manipulating PCH1 alters PHYTOCHROME INTERACTING FACTOR 4 levels and regulates light-responsive gene expression. Thus, PCH1 is a new factor that regulates photoperiod-responsive growth by integrating the clock with light perception pathways through modulating daily phyB-signaling. DOI:http://dx.doi.org/10.7554/eLife.13292.001 Most living things possess an internal “circadian” clock that synchronizes many behaviors, such as eating, resting or growing, with the day-night cycle. With the help of proteins that can detect light, known as photoreceptors, the clock also coordinates these behaviors as the number of daylight hours changes during the year. However, it is not known how the clock and photoreceptors are able to work together. The circadian clocks of animals and plants have evolved separately and use different proteins. In plants, a photoreceptor called phytochrome B responds to red light and regulates the ability of plants to grow. Most plants harness sunlight during the day, but grow fastest in the dark just before dawn. In 2015, researchers identified a new protein in a plant called Arabidopsis that is associated with several plant clock proteins and photoreceptors, including phytochrome B. However, the role of this new protein was not clear. Now, Huang et al. – including many of the researchers from the 2015 work – studied the new protein, named PCH1, in more detail. The experiments show that PCH1 is a critical link that regulates the daily growth of Arabidopsis plants in response to the number of daylight hours. PCH1 stabilizes the structure of phytochrome B so that it remains active, even in the dark. This prolonged activity acts as a molecular memory of prior exposure to light and helps to prevent plants from growing too much in the winter when there are fewer hours of daylight. Since PCH1 is also found in other species of plants, it may play the same role in regulating growth of major crop plants. The next challenge is to understand how the binding of PCH1 to phytochrome B alters the photoreceptor’s activity. In the future, Huang et al. hope to find out if manipulating the activity of PCH1 can improve the growth of crops in places where there is a large change in day length across the seasons. DOI:http://dx.doi.org/10.7554/eLife.13292.002
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Affiliation(s)
- He Huang
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Chan Yul Yoo
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, United States
| | | | | | - Allison Tielking
- Mary Institute and Saint Louis Country Day School, St. Louis, United States
| | - Sophie Alvarez
- Donald Danforth Plant Science Center, St. Louis, United States
| | | | - Bradley S Evans
- Donald Danforth Plant Science Center, St. Louis, United States
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute of Integrative Genome Biology, University of California at Riverside, Riverside, United States
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62
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Montgomery BL. Spatiotemporal Phytochrome Signaling during Photomorphogenesis: From Physiology to Molecular Mechanisms and Back. FRONTIERS IN PLANT SCIENCE 2016; 7:480. [PMID: 27148307 PMCID: PMC4826876 DOI: 10.3389/fpls.2016.00480] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/17/2016] [Accepted: 03/24/2016] [Indexed: 05/21/2023]
Abstract
Light exposure results in distinct responses in specific seedling tissues during photomorphogenesis. Light promotes growth of cotyledons and leaves, as well as development and elongation of roots, whereas light inhibits elongation of hypocotyls. For distinct plant responses such as shade avoidance, far-red light or shifts in spectral light quality similarly have disparate impacts on distinct plant tissues, resulting in elongation of stems or petioles and a reduction in growth of leaf blades for many species. The physiological bases of such tissue- and organ-specific light responses were initially studied using localized irradiation of specific tissues and organs, or irradiation of dissected plant parts. These historical approaches were used to identify spatial-specific pools of photoreceptors responsible for regulating local, i.e., tissue- or organ-specific, or distal, i.e., interorgan, plant responses. The red/far-red responsive phytochromes have been the most widely studied among photoreceptors in this regard. Whereas, the spatial localization of photoreceptors regulating many tissue- or organ-specific light responses were identified, the underlying signaling networks responsible for mediating the observed responses have not been well defined. Recent approaches used to investigate the molecular bases of spatiotemporal light responses include selective irradiation of plants harboring mutations in specific photoreceptors, tissue-specific expression of photoreceptors, primarily in photoreceptor mutant backgrounds, or tissue-specific biochemical ablation of photoreceptor accumulation. Progressive integration of such approaches for regulating the availability of localized pools of phytochromes with the use of transcriptomic or proteomic analyses for assessing the genes or proteins which these spatially discrete pools of phytochrome regulate is yielding emergent insight into the molecular bases of spatiotemporal phytochrome signaling pathways responsible for regulating spatiotemporal light responses of which we have been aware of at the physiological level for decades. Here, I discuss historical and emerging approaches to elucidating spatiotemporal signaling mediated by phytochromes during photomorphogenesis.
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Affiliation(s)
- Beronda L. Montgomery
- Department of Energy — Plant Research Laboratory, Michigan State UniversityEast Lansing, MI, USA
- Department of Biochemistry and Molecular Biology, Michigan State UniversityEast Lansing, MI, USA
- *Correspondence: Beronda L. Montgomery,
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63
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Geilen K, Böhmer M. Dynamic subnuclear relocalisation of WRKY40 in response to Abscisic acid in Arabidopsis thaliana. Sci Rep 2015; 5:13369. [PMID: 26293691 PMCID: PMC4642543 DOI: 10.1038/srep13369] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2015] [Accepted: 07/23/2015] [Indexed: 11/20/2022] Open
Abstract
WRKY18, WRKY40 and WRKY60 are members of the WRKY transcription factor family and function as transcriptional regulators in ABA signal transduction in Arabidopsis thaliana. Here we show that WRKY18 and WRKY40, but not WRKY60, co-localise with PIF3, PIF4 and PHYB to Phytochrome B-containing nuclear bodies (PNBs). Localisation to the PNBs is phosphorylation-dependent and is inhibited by the general Ser/Thr-kinase inhibitor Staurosporine. Upon ABA treatment, WRKY40 relocalises from PNBs to the nucleoplasm in an OST1-dependent manner. This stimulus-induced relocalisation was not observed in response to other abiotic or biotic stimuli, including NaCl, MeJA or flg22 treatment. Bimolecular fluorescence complementation experiments indicate that while PIF3, PIF4 and PHYB physically interact in these bodies, PHYB, PIF3 and PIF4 do not interact with the two WRKY transcription factors, which may suggest a more general role for these bodies in regulation of transcriptional activity.
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Affiliation(s)
- Katja Geilen
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
| | - Maik Böhmer
- Institut für Biologie und Biotechnologie der Pflanzen, Westfälische Wilhelms-Universität, Münster, Germany
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64
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SUMOylation of phytochrome-B negatively regulates light-induced signaling in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2015; 112:11108-13. [PMID: 26283376 DOI: 10.1073/pnas.1415260112] [Citation(s) in RCA: 59] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The red/far red light absorbing photoreceptor phytochrome-B (phyB) cycles between the biologically inactive (Pr, λmax, 660 nm) and active (Pfr; λmax, 730 nm) forms and functions as a light quality and quantity controlled switch to regulate photomorphogenesis in Arabidopsis. At the molecular level, phyB interacts in a conformation-dependent fashion with a battery of downstream regulatory proteins, including PHYTOCHROME INTERACTING FACTOR transcription factors, and by modulating their activity/abundance, it alters expression patterns of genes underlying photomorphogenesis. Here we report that the small ubiquitin-like modifier (SUMO) is conjugated (SUMOylation) to the C terminus of phyB; the accumulation of SUMOylated phyB is enhanced by red light and displays a diurnal pattern in plants grown under light/dark cycles. Our data demonstrate that (i) transgenic plants expressing the mutant phyB(Lys996Arg)-YFP photoreceptor are hypersensitive to red light, (ii) light-induced SUMOylation of the mutant phyB is drastically decreased compared with phyB-YFP, and (iii) SUMOylation of phyB inhibits binding of PHYTOCHROME INTERACTING FACTOR 5 to phyB Pfr. In addition, we show that OVERLY TOLERANT TO SALT 1 (OTS1) de-SUMOylates phyB in vitro, it interacts with phyB in vivo, and the ots1/ots2 mutant is hyposensitive to red light. Taken together, we conclude that SUMOylation of phyB negatively regulates light signaling and it is mediated, at least partly, by the action of OTS SUMO proteases.
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65
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Klose C, Venezia F, Hussong A, Kircher S, Schäfer E, Fleck C. Systematic analysis of how phytochrome B dimerization determines its specificity. NATURE PLANTS 2015; 1:15090. [PMID: 27250256 DOI: 10.1038/nplants.2015.90] [Citation(s) in RCA: 66] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/01/2015] [Indexed: 05/12/2023]
Abstract
Phytochromes are red/far-red-light detecting photoreceptors that regulate plant growth and development. They photo-interconvert between an inactive Pr (red-light absorbing) and a physiologically active Pfr (far-red-light absorbing) form, acting as light-controlled molecular switches. Although the two major plant phytochromes A (phyA) and B (phyB) share similar absorption properties, they exhibit dramatic differences in their action spectra. Since both phytochromes antagonistically regulate seedling development under vegetative shade, it is essential for plants to clearly distinguish between phyA and phyB action. This discrimination is not comprehensible solely by the molecular properties of the phytochromes, but is evidently due to the dynamics of the phytochrome system. Using an integrated experimental and mathematical modelling approach we show that phytochrome dimerization is an essential element for phyB function. Our findings reveal that light-independent Pfr to Pr relaxation (dark reversion) and association/dissociation to nuclear bodies (NBs) severely depend on the conformational state of the phyB dimer. We conclude that only Pfr-Pfr homodimers of phyB can be responsible for triggering physiological responses, leading to a suppression of phyB function in the far-red range of the light spectrum.
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Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Filippo Venezia
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, Freiburg 79104, Germany
| | - Andrea Hussong
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Stefan Kircher
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, Freiburg 79104, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen UR, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
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66
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Enders TA, Oh S, Yang Z, Montgomery BL, Strader LC. Genome Sequencing of Arabidopsis abp1-5 Reveals Second-Site Mutations That May Affect Phenotypes. THE PLANT CELL 2015; 27:1820-6. [PMID: 26106149 PMCID: PMC4531353 DOI: 10.1105/tpc.15.00214] [Citation(s) in RCA: 36] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/12/2015] [Revised: 05/18/2015] [Accepted: 06/04/2015] [Indexed: 05/19/2023]
Abstract
Auxin regulates numerous aspects of plant growth and development. For many years, investigating roles for AUXIN BINDING PROTEIN1 (ABP1) in auxin response was impeded by the reported embryo lethality of mutants defective in ABP1. However, identification of a viable Arabidopsis thaliana TILLING mutant defective in the ABP1 auxin binding pocket (abp1-5) allowed inroads into understanding ABP1 function. During our own studies with abp1-5, we observed growth phenotypes segregating independently of the ABP1 lesion, leading us to sequence the genome of the abp1-5 line described previously. We found that the abp1-5 line we sequenced contains over 8000 single nucleotide polymorphisms in addition to the ABP1 mutation and that at least some of these mutations may originate from the Arabidopsis Wassilewskija accession. Furthermore, a phyB null allele in the abp1-5 background is likely causative for the long hypocotyl phenotype previously attributed to disrupted ABP1 function. Our findings complicate the interpretation of abp1-5 phenotypes for which no complementation test was conducted. Our findings on abp1-5 also provide a cautionary tale illustrating the need to use multiple alleles or complementation lines when attributing roles to a gene product.
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Affiliation(s)
- Tara A Enders
- Department of Biology, Washington University, St. Louis, Missouri 63130
| | - Sookyung Oh
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824
| | - Zhenbiao Yang
- Center for Plant Cell Biology, Department of Botany and Plant Sciences, University of California, Riverside, California 92521
| | - Beronda L Montgomery
- Department of Energy Plant Research Laboratory, Michigan State University, East Lansing, Michigan 48824 Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan 48824
| | - Lucia C Strader
- Department of Biology, Washington University, St. Louis, Missouri 63130
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67
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Qiu Y, Li M, Pasoreck EK, Long L, Shi Y, Galvão RM, Chou CL, Wang H, Sun AY, Zhang YC, Jiang A, Chen M. HEMERA Couples the Proteolysis and Transcriptional Activity of PHYTOCHROME INTERACTING FACTORs in Arabidopsis Photomorphogenesis. THE PLANT CELL 2015; 27:1409-27. [PMID: 25944101 PMCID: PMC4456642 DOI: 10.1105/tpc.114.136093] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/30/2014] [Revised: 03/25/2015] [Accepted: 04/10/2015] [Indexed: 05/20/2023]
Abstract
Phytochromes (phys) are red and far-red photoreceptors that control plant development and growth by promoting the proteolysis of a family of antagonistically acting basic helix-loop-helix transcription factors, the PHYTOCHROME-INTERACTING FACTORs (PIFs). We have previously shown that the degradation of PIF1 and PIF3 requires HEMERA (HMR). However, the biochemical function of HMR and the mechanism by which it mediates PIF degradation remain unclear. Here, we provide genetic evidence that HMR acts upstream of PIFs in regulating hypocotyl growth. Surprisingly, genome-wide analysis of HMR- and PIF-dependent genes reveals that HMR is also required for the transactivation of a subset of PIF direct-target genes. We show that HMR interacts with all PIFs. The HMR-PIF interaction is mediated mainly by HMR's N-terminal half and PIFs' conserved active-phytochrome B binding motif. In addition, HMR possesses an acidic nine-amino-acid transcriptional activation domain (9aaTAD) and a loss-of-function mutation in this 9aaTAD impairs the expression of PIF target genes and the destruction of PIF1 and PIF3. Together, these in vivo results support a regulatory mechanism for PIFs in which HMR is a transcriptional coactivator binding directly to PIFs and the 9aaTAD of HMR couples the degradation of PIF1 and PIF3 with the transactivation of PIF target genes.
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Affiliation(s)
- Yongjian Qiu
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Meina Li
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Elise K Pasoreck
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Lingyun Long
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Yiting Shi
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Rafaelo M Galvão
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Conrad L Chou
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - He Wang
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Amanda Y Sun
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Yiyin C Zhang
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Anna Jiang
- Department of Biology, Duke University, Durham, North Carolina 27708
| | - Meng Chen
- Department of Biology, Duke University, Durham, North Carolina 27708
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68
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Klose C, Viczián A, Kircher S, Schäfer E, Nagy F. Molecular mechanisms for mediating light-dependent nucleo/cytoplasmic partitioning of phytochrome photoreceptors. THE NEW PHYTOLOGIST 2015; 206:965-71. [PMID: 26042244 PMCID: PMC4406131 DOI: 10.1111/nph.13207] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2014] [Accepted: 11/05/2014] [Indexed: 05/19/2023]
Abstract
The photoreceptors phytochromes monitor the red/far-red part of the spectrum, exist in the biologically active Pfr (far-red absorbing) or inactive Pr (red absorbing) forms, and function as red/far-red light-regulated molecular switches to modulate plant development and growth. Phytochromes are synthesized in the cytoplasm, and light induces translocation of the Pfr conformer into the nucleus. Nuclear import of phytochromes is a highly regulated process and is fine-tuned by the quality and quantity of light. It appears that phytochrome A (phyA) and phytochrome B (phyB) do not possess active endogenous nuclear import signals (NLSs), thus light-induced translocation of these photoreceptors into the nucleus requires direct protein–protein interactions with their NLS-containing signaling partners. Sub-cellular partitioning of the various phytochrome species is mediated by different molecular machineries. Translocation of phyA into the nucleus is promoted by FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL), but the identity of nuclear transport facilitators mediating the import of phyB-E into the nucleus remains elusive. Phytochromes localized in the nucleus are associated with specific protein complexes, termed photobodies. The size and distribution of these structures are regulated by the intensity and duration of irradiation, and circumstantial evidence indicates that they are involved in fine-tuning phytochrome signaling.
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Affiliation(s)
- Cornelia Klose
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - András Viczián
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
| | - Stefan Kircher
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Eberhard Schäfer
- Institute of Botany, University of FreiburgSchänzlestrasse 1, D-79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research CentreTemesvári krt. 62, H-6726, Szeged, Hungary
- School of Biological Sciences, Institute of Molecular Plant Science, University of EdinburghEdinburgh, EH9 3JH, UK
- Author for correspondence: Ferenc Nagy Tel: +36 62599718
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69
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Wang H, Wang H. Phytochrome signaling: time to tighten up the loose ends. MOLECULAR PLANT 2015; 8:540-51. [PMID: 25670340 DOI: 10.1016/j.molp.2014.11.021] [Citation(s) in RCA: 78] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/29/2014] [Revised: 11/12/2014] [Accepted: 11/14/2014] [Indexed: 05/18/2023]
Abstract
Phytochromes are red and far-red light photoreceptors that play fundamental roles in controlling many aspects of plant growth and development in response to light. The past two decades have witnessed the mechanistic elucidation of the action mode of phytochromes, including their regulation by external and endogenous factors and how they exert their function as transcriptional regulators. More importantly, recent advances have substantially deepened our understanding on the integration of the phytochrome-mediated signal into other cellular and developmental processes, such as elongation of hypocotyls, shoot branching, circadian clock, and flowering time, which often involves complex intercellular and interorgan signaling. Based on these advances, this review illustrates a blueprint of our current understanding of phytochrome signaling and its crosstalk with other signaling pathways, and also points out still open questions that need to be addressed in the future.
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Affiliation(s)
- Hai Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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70
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Arabidopsis DET1 degrades HFR1 but stabilizes PIF1 to precisely regulate seed germination. Proc Natl Acad Sci U S A 2015; 112:3817-22. [PMID: 25775589 DOI: 10.1073/pnas.1502405112] [Citation(s) in RCA: 54] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Seed is an essential propagation organ and a critical strategy adopted by terrestrial flowering plants to colonize the land. The ability of seeds to accurately respond to light is vital for plant survival. However, the underlying mechanism is largely unknown. In this study, we reveal a circuit of triple feed-forward loops adopted by Arabidopsis seeds to exclusively repress germination in dark conditions and precisely initiate germination under diverse light conditions. We identify that de-etiolated 1 (DET1), an evolutionarily conserved protein, is a central repressor of light-induced seed germination. Genetic analysis demonstrates that DET1 functions upstream of long hypocotyl in far-red 1 (HFR1) and phytochrome interacting factor 1 (PIF1), the key positive and negative transcription regulators in seed germination. We further find that DET1 and constitutive photomorphogenic 10 (COP10) target HFR1 for protein degradation by assembling a COP10-DET1-damaged DNA binding protein 1-cullin4 E3 ligase complex. Moreover, DET1 and COP10 directly interact with and promote the protein stability of PIF1. Computational modeling reveals that phytochrome B (phyB)-DET1-HFR1-PIF1 and phyB-DET1-Protease-PIF1 are new signaling pathways, independent of the previously identified phyB-PIF1 pathway, respectively mediating the rapid and time-lapse responses to light irradiation. The model-simulated results are highly consistent with their experimental validations, suggesting that our mathematical model captures the essence of Arabidopsis seed germination networks. Taken together, this study provides a comprehensive molecular framework for light-regulated seed germination, improving our understanding of how plants respond to changeable environments.
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71
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Trupkin SA, Legris M, Buchovsky AS, Tolava Rivero MB, Casal JJ. Phytochrome B Nuclear Bodies Respond to the Low Red to Far-Red Ratio and to the Reduced Irradiance of Canopy Shade in Arabidopsis. PLANT PHYSIOLOGY 2014; 165:1698-1708. [PMID: 24948827 PMCID: PMC4119049 DOI: 10.1104/pp.114.242438] [Citation(s) in RCA: 52] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/07/2014] [Accepted: 06/13/2014] [Indexed: 05/13/2023]
Abstract
The current consensus is that plant responses to canopy shade involve the perception of low red to far-red ratios (R:FRs) by phytochrome B (phyB), which leads to the direct activation of auxin synthesis genes by PHYTOCHROME INTERACTING FACTORs (PIFs). In addition to its effect on R:FRs, shade also reduces irradiance, but whether shade-induced drops in irradiance affect phyB activity has not been demonstrated. To address this issue, we investigated whether irradiance and R:FRs have similar effects on the nuclear distribution of phyB in petiole cells of light-grown plants. Under high-irradiance white light, phyB formed large nuclear bodies. Lowering irradiance without changing R:FRs or lowering R:FRs by adding far-red light led to the appearance of small nuclear bodies containing phyB. Large nuclear bodies remained but with some concomitant reduction in diameter. The appearance of small nuclear bodies was rapid, stable, and reversible upon the return to high irradiance and high R:FRs. High levels of red light but not of blue light were enough to restrain the formation of small phyB nuclear bodies. Irradiance was effective within the range found in natural canopies and even under relatively low R:FRs. The promotion of leaf hyponasty by lowering irradiance was impaired in phyB and pif mutants, as previously reported for the response to R:FRs. The expression of auxin-related genes showed a similar hierarchy of response to low R:FRs and low irradiance. We propose that phyB is able to perceive not only the low R:FRs, but also the low irradiance of shade.
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Affiliation(s)
- Santiago Ariel Trupkin
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina (S.A.T., A.S.B., M.B.T.R., J.J.C.); andFundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina (M.L., J.J.C.)
| | - Martina Legris
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina (S.A.T., A.S.B., M.B.T.R., J.J.C.); andFundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina (M.L., J.J.C.)
| | - Ana Sabrina Buchovsky
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina (S.A.T., A.S.B., M.B.T.R., J.J.C.); andFundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina (M.L., J.J.C.)
| | - María Belén Tolava Rivero
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina (S.A.T., A.S.B., M.B.T.R., J.J.C.); andFundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina (M.L., J.J.C.)
| | - Jorge José Casal
- Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura, Facultad de Agronomía, Universidad de Buenos Aires, and Consejo Nacional de Investigaciones Científicas y Técnicas, 1417 Buenos Aires, Argentina (S.A.T., A.S.B., M.B.T.R., J.J.C.); andFundación Instituto Leloir, Instituto de Investigaciones Bioquímicas de Buenos Aires-Consejo Nacional de Investigaciones Científicas y Técnicas, C1405BWE Buenos Aires, Argentina (M.L., J.J.C.)
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72
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Van Buskirk EK, Reddy AK, Nagatani A, Chen M. Photobody Localization of Phytochrome B Is Tightly Correlated with Prolonged and Light-Dependent Inhibition of Hypocotyl Elongation in the Dark. PLANT PHYSIOLOGY 2014; 165:595-607. [PMID: 24769533 PMCID: PMC4044834 DOI: 10.1104/pp.114.236661] [Citation(s) in RCA: 65] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/04/2014] [Accepted: 04/25/2014] [Indexed: 05/20/2023]
Abstract
Photobody localization of Arabidopsis (Arabidopsis thaliana) phytochrome B (phyB) fused to green fluorescent protein (PBG) correlates closely with the photoinhibition of hypocotyl elongation. However, the amino-terminal half of phyB fused to green fluorescent protein (NGB) is hypersensitive to light despite its inability to localize to photobodies. Therefore, the significance of photobodies in regulating hypocotyl growth remains debatable. Accumulating evidence indicates that under diurnal conditions, photoactivated phyB persists into darkness to inhibit hypocotyl elongation. Here, we examine whether photobodies are involved in inhibiting hypocotyl growth in darkness by comparing the PBG and NGB lines after the red light-to-dark transition. Surprisingly, after the transition from 10 μmol m-2 s-1 red light to darkness, PBG inhibits hypocotyl elongation three times longer than NGB. The disassembly of photobodies in PBG hypocotyl nuclei correlates tightly with the accumulation of the growth-promoting transcription factor PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Destabilizing photobodies by either decreasing the light intensity or adding monochromatic far-red light treatment before the light-to-dark transition leads to faster PIF3 accumulation and a dramatic reduction in the capacity for hypocotyl growth inhibition in PBG. In contrast, NGB is defective in PIF3 degradation, and its hypocotyl growth in the dark is nearly unresponsive to changes in light conditions. Together, our results support the model that photobodies are required for the prolonged, light-dependent inhibition of hypocotyl elongation in the dark by repressing PIF3 accumulation and by stabilizing the far-red light-absorbing form of phyB. Our study suggests that photobody localization patterns of phyB could serve as instructive cues that control light-dependent photomorphogenetic responses in the dark.
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Affiliation(s)
- Elise K Van Buskirk
- Department of Biology, Duke University, Durham, North Carolina 27708 (E.K.V.B., A.K.R., M.C.); andDepartment of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (A.N.)
| | - Amit K Reddy
- Department of Biology, Duke University, Durham, North Carolina 27708 (E.K.V.B., A.K.R., M.C.); andDepartment of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (A.N.)
| | - Akira Nagatani
- Department of Biology, Duke University, Durham, North Carolina 27708 (E.K.V.B., A.K.R., M.C.); andDepartment of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (A.N.)
| | - Meng Chen
- Department of Biology, Duke University, Durham, North Carolina 27708 (E.K.V.B., A.K.R., M.C.); andDepartment of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan (A.N.)
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73
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Liu Y, Liu Q, Yan Q, Shi L, Fang Y. Nucleolus-tethering system (NoTS) reveals that assembly of photobodies follows a self-organization model. Mol Biol Cell 2014; 25:1366-73. [PMID: 24554768 PMCID: PMC3983000 DOI: 10.1091/mbc.e13-09-0527] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2013] [Revised: 01/27/2014] [Accepted: 02/13/2014] [Indexed: 01/08/2023] Open
Abstract
Protein-protein interactions play essential roles in regulating many biological processes. At the cellular level, many proteins form nuclear foci known as nuclear bodies in which many components interact with each other. Photobodies are nuclear bodies containing proteins for light-signaling pathways in plants. What initiates the formation of photobodies is poorly understood. Here we develop a nucleolar marker protein nucleolin2 (Nuc2)-based method called the nucleolus-tethering system (NoTS) by artificially tethering a protein of interest to the nucleolus to analyze the initiation of photobodies. A candidate initiator is evaluated by visualizing whether a protein fused with Nuc2 forms body-like structures at the periphery of the nucleolus, and other components are recruited to the de novo-formed bodies. The interaction between two proteins can also be revealed through relocation and recruitment of interacting proteins to the nucleolus. Using the NoTS, we test the interactions among components in photobodies. In addition, we demonstrate that components of photobodies such as CONSTITUTIVELY PHOTOMORPHOGENIC 1, photoreceptors, and transcription factors tethered to the nucleolus have the capacity to form body-like structures at the periphery of the nucleolus, which contain other components of photobodies, suggesting a self-organization model for the biogenesis of photobodies.
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Affiliation(s)
- Yin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qi Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Qingqing Yan
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Leilei Shi
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Yuda Fang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
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74
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Guo T, Fang Y. Functional organization and dynamics of the cell nucleus. FRONTIERS IN PLANT SCIENCE 2014; 5:378. [PMID: 25161658 PMCID: PMC4130368 DOI: 10.3389/fpls.2014.00378] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/16/2014] [Accepted: 07/16/2014] [Indexed: 05/16/2023]
Abstract
The eukaryotic cell nucleus enclosed within the nuclear envelope harbors organized chromatin territories and various nuclear bodies as sub-nuclear compartments. This higher-order nuclear organization provides a unique environment to regulate the genome during replication, transcription, maintenance, and other processes. In this review, we focus on the plant four-dimensional nuclear organization, its dynamics and function in response to signals during development or stress.
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Affiliation(s)
| | - Yuda Fang
- *Correspondence: Yuda Fang, National key Laboratory of Plant Molecular Genetics, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China e-mail:
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75
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Liu P, Sharrock RA. Directed dimerization: an in vivo expression system for functional studies of type II phytochromes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:915-926. [PMID: 23738620 DOI: 10.1111/tpj.12255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 06/02/2023]
Abstract
Type II phytochromes (phy) in Arabidopsis form homodimers and heterodimers, resulting in a diverse collection of light-stable red/far-red (R/FR) sensing photoreceptors. We describe an in vivo protein engineering system and its use in characterizing the activities of these molecules. Using a phyB null mutant background, singly and doubly transgenic plants were generated that express fusion proteins containing the phyB-phyE N-terminal photosensory regions (NB-NE PSRs), a nuclear localization sequence, and small yeast protein domains that mediate either homodimerization or heterodimerization. Activity of NB/NB homodimers but not monomeric NB subunits in control of seedling and adult plant responses to R light is demonstrated. Heterodimers of the NB sequence with the chromophoreless NB(C357S) sequence, which mimic phyB Pfr/Pr photo-heterodimers, mediate R sensitivity in leaves and petioles but not hypocotyls. Homodimerization of the NC, ND and NE sequences and directed heterodimerization of these photosensory regions with the NB region reveal form-specific R-induced activities for different type II phy dimers. The experimental approach developed here of directed assembly of defined protein dimer combinations in vivo may be applicable to other systems.
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Affiliation(s)
- Peng Liu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
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76
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Nito K, Wong CCL, Yates JR, Chory J. Tyrosine phosphorylation regulates the activity of phytochrome photoreceptors. Cell Rep 2013; 3:1970-9. [PMID: 23746445 DOI: 10.1016/j.celrep.2013.05.006] [Citation(s) in RCA: 61] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Revised: 05/03/2013] [Accepted: 05/06/2013] [Indexed: 10/26/2022] Open
Abstract
Phytochromes are red/far-red light receptors that function in photomorphogenesis of plants. Photoisomerization of phytochrome by red light leads to its translocation to the nucleus, where it regulates gene expression. We examined whether phytochrome is phosphorylated in response to light, and we report that phytochrome B (phyB)'s N terminus contains a region with a number of phosphoserines, threonines, and tyrosines. The light-dependent phosphorylation of tyrosine 104 (Y104) appears to play a negative role in phyB's activity, because a phosphomimic mutant, phyBY104E, is unable to complement any phyB-related phenotype, is defective in binding to its signaling partner PIF3, and fails to form stable nuclear bodies even though it retains normal photochemistry in vitro. In contrast, plants stably expressing a nonphosphorylatable mutant, phyBY104F, are hypersensitive to light. The proper response to changes in the light environment is crucial for plant survival, and our study brings tyrosine phosphorylation to the forefront of light-signaling mechanisms.
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Affiliation(s)
- Kazumasa Nito
- Plant Biology Laboratory, Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, CA 92037, USA
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77
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Zhang J, Stankey RJ, Vierstra RD. Structure-guided engineering of plant phytochrome B with altered photochemistry and light signaling. PLANT PHYSIOLOGY 2013; 161:1445-57. [PMID: 23321421 PMCID: PMC3585608 DOI: 10.1104/pp.112.208892] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/10/2013] [Indexed: 05/22/2023]
Abstract
Phytochromes (phys) encompass a diverse collection of biliproteins that enable cellular light perception by photoconverting between a red-light-absorbing ground state (Pr) and a far-red light-absorbing active state (Pfr). Based on the central role of plant phys in controlling numerous agriculturally important processes, their rational redesign offers great promise toward accelerating crop improvement. Employing as templates the available three-dimensional models of the photosensory module within bacterial phys, we report here our initial attempt to apply structure-guided mutagenesis to phy engineering using Arabidopsis (Arabidopsis thaliana) phyB, the dominant isoform in light-grown plants, as the example. A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns, some of which also impacted phenotypic outputs. Of particular interest are the Y361F substitution, which created Arabidopsis plants with greatly enhanced light sensitivity, mutants variably altered in Pfr-to-Pr thermal reversion and nuclear aggregation, and the D307A substitution, which failed to photoconvert from Pr to Pfr and display light-induced nuclear aggregation but retained some biological activity and accelerated turnover in red light. Taken together, this collection provides variants potentially useful to agriculture as well as new tools to better understand the molecular mechanisms underpinning phy signaling.
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78
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Medzihradszky M, Bindics J, Ádám É, Viczián A, Klement É, Lorrain S, Gyula P, Mérai Z, Fankhauser C, Medzihradszky KF, Kunkel T, Schäfer E, Nagy F. Phosphorylation of phytochrome B inhibits light-induced signaling via accelerated dark reversion in Arabidopsis. THE PLANT CELL 2013; 25:535-44. [PMID: 23378619 PMCID: PMC3608776 DOI: 10.1105/tpc.112.106898] [Citation(s) in RCA: 90] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2012] [Revised: 12/21/2012] [Accepted: 01/13/2013] [Indexed: 05/20/2023]
Abstract
The photoreceptor phytochrome B (phyB) interconverts between the biologically active Pfr (λmax = 730 nm) and inactive Pr (λmax = 660 nm) forms in a red/far-red-dependent fashion and regulates, as molecular switch, many aspects of light-dependent development in Arabidopsis thaliana. phyB signaling is launched by the biologically active Pfr conformer and mediated by specific protein-protein interactions between phyB Pfr and its downstream regulatory partners, whereas conversion of Pfr to Pr terminates signaling. Here, we provide evidence that phyB is phosphorylated in planta at Ser-86 located in the N-terminal domain of the photoreceptor. Analysis of phyB-9 transgenic plants expressing phospho-mimic and nonphosphorylatable phyB-yellow fluorescent protein (YFP) fusions demonstrated that phosphorylation of Ser-86 negatively regulates all physiological responses tested. The Ser86Asp and Ser86Ala substitutions do not affect stability, photoconversion, and spectral properties of the photoreceptor, but light-independent relaxation of the phyB(Ser86Asp) Pfr into Pr, also termed dark reversion, is strongly enhanced both in vivo and in vitro. Faster dark reversion attenuates red light-induced nuclear import and interaction of phyB(Ser86Asp)-YFP Pfr with the negative regulator PHYTOCHROME INTERACTING FACTOR3 compared with phyB-green fluorescent protein. These data suggest that accelerated inactivation of the photoreceptor phyB via phosphorylation of Ser-86 represents a new paradigm for modulating phytochrome-controlled signaling.
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Affiliation(s)
| | - János Bindics
- Faculty of Biology, University of Freiburg, D-79104, Freiburg Germany
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
| | - Éva Klement
- Proteomics Laboratory, Biological Research Centre, H-6726 Szeged, Hungary
| | - Séverine Lorrain
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | - Péter Gyula
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
| | - Zsuzsanna Mérai
- Faculty of Biology, University of Freiburg, D-79104, Freiburg Germany
| | - Christian Fankhauser
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, CH-1015 Lausanne, Switzerland
| | | | - Tim Kunkel
- Faculty of Biology, University of Freiburg, D-79104, Freiburg Germany
| | - Eberhard Schäfer
- Faculty of Biology, University of Freiburg, D-79104, Freiburg Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, H-6726 Szeged, Hungary
- School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JR, United Kingdom
- Address correspondence to
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79
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Zheng X, Wu S, Zhai H, Zhou P, Song M, Su L, Xi Y, Li Z, Cai Y, Meng F, Yang L, Wang H, Yang J. Arabidopsis phytochrome B promotes SPA1 nuclear accumulation to repress photomorphogenesis under far-red light. THE PLANT CELL 2013; 25:115-33. [PMID: 23371951 PMCID: PMC3584529 DOI: 10.1105/tpc.112.107086] [Citation(s) in RCA: 68] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 12/10/2012] [Accepted: 12/19/2012] [Indexed: 05/19/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor mediating deetiolation under far-red (FR) light, whereas phyB predominantly regulates light responses in red light. SUPPRESSOR OF PHYA-105 (SPA1) forms an E3 ubiquitin ligase complex with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), which is responsible for the degradation of various photomorphogenesis-promoting factors, resulting in desensitization to light signaling. However, the role of phyB in FR light signaling and the regulatory pathway from light-activated phytochromes to the COP1-SPA1 complex are largely unknown. Here, we confirm that PHYB overexpression causes an etiolation response with reduced ELONGATED HYPOCOTYL5 (HY5) accumulation under FR light. Notably, phyB exerts its nuclear activities and promotes seedling etiolation in both the presence and absence of phyA in response to FR light. PhyB acts upstream of SPA1 and is functionally dependent on it in FR light signaling. PhyB interacts and forms a protein complex with SPA1, enhancing its nuclear accumulation under FR light. During the dark-to-FR transition, phyB is rapidly imported into the nucleus and facilitates nuclear SPA1 accumulation. These findings support the notion that phyB plays a role in repressing FR light signaling. Activity modulation of the COP1-SPA E3 complex by light-activated phytochromes is an effective and pivotal regulatory step in light signaling.
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Affiliation(s)
- Xu Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Suowei Wu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huqu Zhai
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Peng Zhou
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Meifang Song
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Liang Su
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yulin Xi
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Graduate School, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Zhiyong Li
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Yingfan Cai
- College of Bio-information, Chongqing University of Posts and Telecommunication, Chongqing 400065, China
| | - Fanhua Meng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Haiyang Wang
- College of Life Sciences, Capital Normal University, Beijing 100048, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520
| | - Jianping Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
- Address correspondence to
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80
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Galvão RM, Li M, Kothadia SM, Haskel JD, Decker PV, Van Buskirk EK, Chen M. Photoactivated phytochromes interact with HEMERA and promote its accumulation to establish photomorphogenesis in Arabidopsis. Genes Dev 2012; 26:1851-63. [PMID: 22895253 DOI: 10.1101/gad.193219.112] [Citation(s) in RCA: 69] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023]
Abstract
Plant development is profoundly regulated by ambient light cues through the red/far-red photoreceptors, the phytochromes. Early phytochrome signaling events include the translocation of phytochromes from the cytoplasm to subnuclear domains called photobodies and the degradation of antagonistically acting phytochrome-interacting factors (PIFs). We recently identified a key phytochrome signaling component, HEMERA (HMR), that is essential for both phytochrome B (phyB) localization to photobodies and PIF degradation. However, the signaling mechanism linking phytochromes and HMR is unknown. Here we show that phytochromes directly interact with HMR to promote HMR protein accumulation in the light. HMR binds more strongly to the active form of phytochromes. This interaction is mediated by the photosensory domains of phytochromes and two phytochrome-interacting regions in HMR. Missense mutations in either HMR or phyB that alter the phytochrome/HMR interaction can also change HMR levels and photomorphogenetic responses. HMR accumulation in a constitutively active phyB mutant (YHB) is required for YHB-dependent PIF3 degradation in the dark. Our genetic and biochemical studies strongly support a novel phytochrome signaling mechanism in which photoactivated phytochromes directly interact with HMR and promote HMR accumulation, which in turn mediates the formation of photobodies and the degradation of PIFs to establish photomorphogenesis.
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Affiliation(s)
- Rafaelo M Galvão
- Department of Biology, Duke University, Durham, North Carolina 27708, USA
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81
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Kircher S, Bauer D, Schäfer E, Nagy F. Intramolecular uncoupling of chromophore photoconversion from structural signaling determinants drive mutant phytochrome B photoreceptor to far-red light perception. PLANT SIGNALING & BEHAVIOR 2012; 7:904-906. [PMID: 22836504 PMCID: PMC3474681 DOI: 10.4161/psb.20714] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
The phytochrome (phy) photoreceptor family regulates almost all aspects of plant development in a broad range of light environments including seed germination, onset of the photomorphogenic program in seedling stage, the shade avoidance syndrome in competing plant communities, flowering induction and senescence of adult plants. During evolution two clearly distinct classes of phy-s emerged covering these very different physiological tasks. ( 1) PhyA is rapidly degraded in its activated state. PhyA functions in controlling seed germination at very low light intensities (very low fluence response, VLFR) and seedling establishment under photosynthetic shade conditions (high irradiance response, HIR) where the far-red portion of the transmitted light to understorey habitats is substantially enhanced. Arabidopsis phyB together with phyC, D and E belongs to the relatively stable sensor class in comparison to the light labile phyA. PhyB functions at all stages of development including seed germination and seedling establishment, mediates classical red/far-red reversible low fluence responses (LFR) as well as red light high irradiance responses, and it is considered to be the dominating phytochrome sensor of its class.
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Affiliation(s)
- Stefan Kircher
- Institute of Biology II; Faculty of Biology, University of Freiburg, Germany.
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82
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Oka Y, Ono Y, Toledo-Ortiz G, Kokaji K, Matsui M, Mochizuki N, Nagatani A. Arabidopsis phytochrome a is modularly structured to integrate the multiple features that are required for a highly sensitized phytochrome. THE PLANT CELL 2012; 24:2949-62. [PMID: 22843485 PMCID: PMC3426125 DOI: 10.1105/tpc.111.094201] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytochrome is a red (R)/far-red (FR) light-sensing photoreceptor that regulates various aspects of plant development. Among the members of the phytochrome family, phytochrome A (phyA) exclusively mediates atypical phytochrome responses, such as the FR high irradiance response (FR-HIR), which is elicited under prolonged FR. A proteasome-based degradation pathway rapidly eliminates active Pfr (the FR-absorbing form of phyA) under R. To elucidate the structural basis for the phyA-specific properties, we systematically constructed 16 chimeric phytochromes in which each of four parts of the phytochrome molecule, namely, the N-terminal extension plus the Per/Arnt/Sim domain (N-PAS), the cGMP phosphodiesterase/adenyl cyclase/FhlA domain (GAF), the phytochrome domain (PHY), and the entire C-terminal half, was occupied by either the phyA or phytochrome B sequence. These phytochromes were expressed in transgenic Arabidopsis thaliana to examine their physiological activities. Consequently, the phyA N-PAS sequence was shown to be necessary and sufficient to promote nuclear accumulation under FR, whereas the phyA sequence in PHY was additionally required to exhibit FR-HIR. Furthermore, the phyA sequence in PHY alone substantially increased the light sensitivity to R. In addition, the GAF phyA sequence was important for rapid Pfr degradation. In summary, distinct structural modules, each of which confers different properties to phyA, are assembled on the phyA molecule.
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Affiliation(s)
- Yoshito Oka
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
- Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Tsurumiku, Yokohama, Kanagawa 2300-0045, Japan
| | - Yuya Ono
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Gabriela Toledo-Ortiz
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Keio Kokaji
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Minami Matsui
- Plant Functional Genomics Research Group, Plant Science Center, RIKEN Yokohama Institute, Tsurumiku, Yokohama, Kanagawa 2300-0045, Japan
| | - Nobuyoshi Mochizuki
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
| | - Akira Nagatani
- Laboratory of Plant Physiology, Graduate School of Science, Kyoto University, Kitashirakawa-Oiwake-Cho, Sakyo-Ku, Kyoto 606-8502, Japan
- Address correspondence to
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83
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Valdés AE, Rizzardi K, Johannesson H, Para A, Sundås-Larsson A, Landberg K. Arabidopsis thaliana TERMINAL FLOWER2 is involved in light-controlled signalling during seedling photomorphogenesis. PLANT, CELL & ENVIRONMENT 2012; 35:1013-25. [PMID: 22145973 DOI: 10.1111/j.1365-3040.2011.02468.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
Plants respond to changes in the environment by altering their growth pattern. Light is one of the most important environmental cues and affects plants throughout the life cycle. It is perceived by photoreceptors such as phytochromes that absorb light of red and far-red wavelengths and control, for example, seedling de-etiolation, chlorophyll biosynthesis and shade avoidance response. We report that the terminal flower2 (tfl2) mutant, carrying a mutation in the Arabidopsis thaliana HETEROCHROMATIN PROTEIN1 homolog, functions in negative regulation of phytochrome dependent light signalling. tfl2 shows defects in both hypocotyl elongation and shade avoidance response. Double mutant analysis indicates that mutants of the red/far-red light absorbing phytochrome family of plant photoreceptors, phyA and phyB, are epistatic to tfl2 in far-red and red light, respectively. An overlap between genes regulated by light and by auxin has earlier been reported and, in tfl2 plants light-dependent auxin-regulated genes are misexpressed. Further, we show that TFL2 binds to IAA5 and IAA19 suggesting that TFL2 might be involved in regulation of phytochrome-mediated light responses through auxin action.
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Affiliation(s)
- Ana Elisa Valdés
- Department of Physiological Botany, Evolutionary Biology Centre, Uppsala University, Norbyvägen 18d, SE-75236 Uppsala, Sweden
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84
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Van Buskirk EK, Decker PV, Chen M. Photobodies in light signaling. PLANT PHYSIOLOGY 2012; 158:52-60. [PMID: 21951469 PMCID: PMC3252093 DOI: 10.1104/pp.111.186411] [Citation(s) in RCA: 124] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2011] [Accepted: 09/22/2011] [Indexed: 05/17/2023]
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85
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Oka Y, Kong SG, Matsushita T. A non-covalently attached chromophore can mediate phytochrome B signaling in Arabidopsis. PLANT & CELL PHYSIOLOGY 2011; 52:2088-102. [PMID: 22006939 DOI: 10.1093/pcp/pcr139] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytochrome B (phyB) is the major informational photoreceptor in light-grown plants. The phyB polypeptide is folded into two domains, the N-terminal domain and the C-terminal domain. The N-terminal domain covalently binds to the chromophore via a particular cysteine residue, which allows the holoprotein to absorb light and undergo a photoreversible conformational change. The N-terminal domain of phyB interacts with transcription factors, such as PIF3 (PHYTOCHROME-INTERACTING FACTOR 3), to transduce the light signal to downstream components. Since substitution of the chromophore attachment site, Cys357, with alanine (C357A) abolishes the biological activity of Arabidopsis phyB, the covalent attachment with the chromophore is widely assumed to be necessary for phyB signal transduction. In this study, we show that Arabidopsis phyB is capable of transducing signals with a non-covalently retained chromophore. Substituting the Tyr276 residue of phyB with histidine (Y276H) is known to confer constitutive phyB signaling. PhyB containing both Y276H and C357A substitutions exhibited light-independent biological activity in transgenic Arabidopsis plants in a chromophore-dependent manner. Spectrophotometric analysis showed that the N-terminal domain of phyB containing just the C357A substitution could retain the chromophore non-covalently. The N-terminal domain containing both the Y276H and C357A substitutions interacted with PIF3 in a light-independent but chromophore-dependent fashion in yeast two-hybrid assays. From these results, we conclude that the constitutive phyB signaling conferred by Y276H requires the chromophore, but that the chromophore does not need to be covalently bonded to phyB.
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Affiliation(s)
- Yoshito Oka
- RIKEN Plant Science Center, Yokohama, 230-0045 Japan
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86
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Altered dark- and photoconversion of phytochrome B mediate extreme light sensitivity and loss of photoreversibility of the phyB-401 mutant. PLoS One 2011; 6:e27250. [PMID: 22073299 PMCID: PMC3207837 DOI: 10.1371/journal.pone.0027250] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2010] [Accepted: 10/12/2011] [Indexed: 11/19/2022] Open
Abstract
The phyB-401 mutant is 10(3) fold more sensitive to red light than its wild-type analogue and shows loss of photoreversibility of hypocotyl growth inhibition. The phyB-401 photoreceptor displays normal spectral properties and shows almost no dark reversion when expressed in yeast cells. To gain insight into the molecular mechanism underlying this complex phenotype, we generated transgenic lines expressing the mutant and wild-type phyB in phyB-9 background. Analysis of these transgenic lines demonstrated that the mutant photoreceptor displays a reduced rate of dark-reversion but normal P(fr) to P(r) photoconversion in vivo and shows an altered pattern of association/dissociation with nuclear bodies compared to wild-type phyB. In addition we show (i) an enhanced responsiveness to far-red light for hypocotyl growth inhibition and CAB2 expression and (ii) that far-red light mediated photoreversibility of red light induced responses, including inhibition of hypocotyl growth, formation of nuclear bodies and induction of CAB2 expression is reduced in these transgenic lines. We hypothesize that the incomplete photoreversibility of signalling is due to the fact that far-red light induced photoconversion of the chromophore is at least partially uncoupled from the P(fr) to P(r) conformation change of the protein. It follows that the phyB-401 photoreceptor retains a P(fr)-like structure (P(r) (*)) for a few hours after the far-red light treatment. The greatly reduced rate of dark reversion and the formation of a biologically active P(r) (*) conformer satisfactorily explain the complex phenotype of the phyB-401 mutant and suggest that amino acid residues surrounding the position 564 G play an important role in fine-tuning phyB signalling.
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Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011; 9:e0148. [PMID: 22303272 PMCID: PMC3268501 DOI: 10.1199/tab.0148] [Citation(s) in RCA: 241] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Gang Li
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Haiyang Wang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-biotechnology, State Key Laboratory of Protein and Plant Gene Research, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut, 06520-8104
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88
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Chen M, Chory J. Phytochrome signaling mechanisms and the control of plant development. Trends Cell Biol 2011; 21:664-71. [PMID: 21852137 DOI: 10.1016/j.tcb.2011.07.002] [Citation(s) in RCA: 268] [Impact Index Per Article: 20.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2011] [Revised: 07/01/2011] [Accepted: 07/05/2011] [Indexed: 11/18/2022]
Abstract
As they emerge from the ground, seedlings adopt a photosynthetic lifestyle, which is accompanied by dramatic changes in morphology and global alterations in gene expression that optimizes the plant body plan for light capture. Phytochromes are red and far-red photoreceptors that play a major role during photomorphogenesis, a complex developmental program that seedlings initiate when they first encounter light. The earliest phytochrome signaling events after excitation by red light include their rapid translocation from the cytoplasm to subnuclear bodies (photobodies) that contain other proteins involved in photomorphogenesis, including a number of transcription factors and E3 ligases. In the light, phytochromes and negatively acting transcriptional regulators that interact directly with phytochromes are destabilized, whereas positively acting transcriptional regulators are stabilized. Here, we discuss recent advances in our knowledge of the mechanisms linking phytochrome photoactivation in the cytoplasm and transcriptional regulation in the nucleus.
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Affiliation(s)
- Meng Chen
- Department of Biology, Duke University, Durham, NC 27708, USA.
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89
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Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011. [PMID: 22303272 DOI: 10.1199/2ftab.0148e0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
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90
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Nagatani A. Phytochrome: structural basis for its functions. CURRENT OPINION IN PLANT BIOLOGY 2010; 13:565-70. [PMID: 20801708 DOI: 10.1016/j.pbi.2010.07.002] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2010] [Accepted: 07/30/2010] [Indexed: 05/20/2023]
Abstract
Phytochrome mediates various physiological as well as developmental responses to light stimuli in plants. Phytochrome is a soluble chromoprotein consisting of the N-terminal photosensory and C-terminal dimerization moieties. Close homologues of plant phytochromes are widely found in prokaryotes. Recently, the crystal structures of the core photosensory module of bacterial phytochromes are resolved. Intriguingly, three sub-domains (PAS, GAF and PHY) in the module are connected by unusual structures named 'light-sensing knot' and 'tongue', which are in tight contact with the chromophore. These findings enable us to review previous data on the structure-function relationships in phytochrome. Consequently, functional importance of these peculiar structures is further highlighted. Thus, the three-dimensional structure provides a framework for understanding how phytochrome processes the light signals.
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Affiliation(s)
- Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Sakyo-ku, Kyoto 606-8502, Japan.
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91
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Toledo-Ortiz G, Kiryu Y, Kobayashi J, Oka Y, Kim Y, Nam HG, Mochizuki N, Nagatani A. Subcellular sites of the signal transduction and degradation of phytochrome A. PLANT & CELL PHYSIOLOGY 2010; 51:1648-1660. [PMID: 20739301 DOI: 10.1093/pcp/pcq121] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Phytochrome regulates various physiological and developmental processes throughout the life cycle of plants. Among the members of the phytochrome family, phytochrome A (phyA) exclusively mediates the far-red light high irradiance response (FR-HIR), which is elicited by continuous far-red light. In FR-HIR, nuclear accumulation of phyA, which precedes physiological responses, is proposed to be required for the response. In contrast to FR, red light induces rapid degradation of phyA to suppress undesirable long-term photomorphogenic responses of phyA. In the present study, we compared biological activities between phyA derivatives to which either a nuclear localization (NLS) or export (NES) signal sequence was attached. Those derivatives were expressed under the control of the PHYA promoter in the Arabidopsis phyA mutant. Detailed microscopic observation revealed that the phyA-green fluorescent protein (GFP) without a signal sequence is localized exclusively in the cytoplasm in darkness. Rapid nuclear entry was observed after exposure to both red and far-red light. Interestingly, both phyA-GFP-NLS and phyA-GFP-NES were rapidly degraded under continuous red light. Furthermore, a proteasome inhibitor delayed degradation equally under these two conditions. Therefore, similar mechanisms for phyA degradation may exist in the cytoplasm and nucleus. As expected from previous reports, phyA-GFP-NLS, but not phyA-GFP-NES, mediated different aspects of FR-HIR, such as inhibition of hypocotyl elongation and rapid induction of gene expression, confirming that phyA nuclear localization is required for FR-HIR. In addition, a detailed time course analysis of phyA-GFP and phyA-GFP-NLS responses revealed that they were almost indistinguishable, raising the question of the physiological relevance of phyA cytoplasmic retention in darkness.
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Affiliation(s)
- Gabriela Toledo-Ortiz
- Department of Botany, Graduate School of Science, Kyoto University, Kyoto, 606-8502 Japan
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92
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Rösler J, Jaedicke K, Zeidler M. Cytoplasmic phytochrome action. PLANT & CELL PHYSIOLOGY 2010; 51:1248-1254. [PMID: 20576692 DOI: 10.1093/pcp/pcq091] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/29/2023]
Abstract
Phytochrome photoperception is a common mechanism for the detection of red and far-red light in bacteria, cyanobacteria, fungi and plants. However, the responses following phytochrome activation appear to be quite diverse between species. Lower plants, such as mosses, show phytochrome-mediated directional responses, namely phototropism and polarotropism. These cannot be explained by nuclear gene regulation and are thought to be triggered by phytochromes in the cytoplasm or at the plasma membrane. In higher plants, similar directional responses are mediated via phototropin, a blue light receptor, with phytochromes mainly controlling morphogenetic responses through gene regulation. However, cytoplasmic phytochrome responses exist in higher plants too, which appear to be intertwined with directional blue light perception. By summarizing the respective findings, a possible conservation of cytoplasmic phytochrome function in higher and lower plants is addressed here.
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Affiliation(s)
- Jutta Rösler
- Department of Plant Physiology, Justus-Liebig-University Giessen, Giessen, Germany
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93
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Arabidopsis HEMERA/pTAC12 initiates photomorphogenesis by phytochromes. Cell 2010; 141:1230-40. [PMID: 20603003 DOI: 10.1016/j.cell.2010.05.007] [Citation(s) in RCA: 187] [Impact Index Per Article: 13.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2009] [Revised: 01/21/2010] [Accepted: 04/23/2010] [Indexed: 10/19/2022]
Abstract
Light plays a profound role in plant development, yet how photoreceptor excitation directs phenotypic plasticity remains elusive. One of the earliest effects of light is the regulated translocation of the red/far-red photoreceptors, phytochromes, from the cytoplasm to subnuclear foci called phytochrome nuclear bodies. The function of these nuclear bodies is unknown. We report the identification of hemera, a seedling lethal mutant of Arabidopsis with altered phytochrome nuclear body patterns. hemera mutants are impaired in all phytochrome responses examined, including proteolysis of phytochrome A and phytochrome-interacting transcription factors. HEMERA was identified previously as pTAC12, a component of a plastid complex associated with transcription. Here, we show that HEMERA has a function in the nucleus, where it acts specifically in phytochrome signaling, is predicted to be structurally similar to the multiubiquitin-binding protein, RAD23, and can partially rescue yeast rad23mutants. Together, these results implicate phytochrome nuclear bodies as sites of proteolysis.
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94
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Jang IC, Henriques R, Seo HS, Nagatani A, Chua NH. Arabidopsis PHYTOCHROME INTERACTING FACTOR proteins promote phytochrome B polyubiquitination by COP1 E3 ligase in the nucleus. THE PLANT CELL 2010; 22:2370-83. [PMID: 20605855 PMCID: PMC2929111 DOI: 10.1105/tpc.109.072520] [Citation(s) in RCA: 184] [Impact Index Per Article: 13.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/29/2009] [Revised: 05/07/2010] [Accepted: 06/23/2010] [Indexed: 05/18/2023]
Abstract
Many plant photoresponses from germination to shade avoidance are mediated by phytochrome B (phyB). In darkness, phyB exists as the inactive Pr in the cytosol but upon red (R) light treatment, the active Pfr translocates into nuclei to initiate signaling. Degradation of phyB Pfr likely regulates signal termination, but the mechanism is not understood. Here, we show that phyB is stable in darkness, but in R, a fraction of phyB translocates into nuclei and becomes degraded by 26S proteasomes. Nuclear phyB degradation is mediated by COP1 E3 ligase, which preferentially interacts with the PhyB N-terminal region (PhyB-N). PhyB-N polyubiquitination by CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1) in vitro can be enhanced by different PHYTOCHROME INTERACTING FACTOR (PIF) proteins that promote COP1/PhyB interaction. Consistent with these results, nuclear phyB accumulates to higher levels in pif single and double mutants and in cop1-4. Our results identify COP1 as an E3 ligase for phyB and other stable phytochromes and uncover the mechanism by which PIFs negatively regulate phyB levels.
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Affiliation(s)
- In-Cheol Jang
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10065
| | - Rossana Henriques
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10065
| | - Hak Soo Seo
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10065
| | - Akira Nagatani
- Department of Botany, Graduate School of Science, Kyoto University, Kitashirakawa, Kyoto 606-8502, Japan
| | - Nam-Hai Chua
- Laboratory of Plant Molecular Biology, The Rockefeller University, New York, New York 10065
- Address correspondence to
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95
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Abdurakhmonov IY, Buriev ZT, Logan-Young CJ, Abdukarimov A, Pepper AE. Duplication, divergence and persistence in the Phytochrome photoreceptor gene family of cottons (Gossypium spp.). BMC PLANT BIOLOGY 2010; 10:119. [PMID: 20565911 PMCID: PMC3095280 DOI: 10.1186/1471-2229-10-119] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/05/2009] [Accepted: 06/20/2010] [Indexed: 02/08/2023]
Abstract
BACKGROUND Phytochromes are a family of red/far-red photoreceptors that regulate a number of important developmental traits in cotton (Gossypium spp.), including plant architecture, fiber development, and photoperiodic flowering. Little is known about the composition and evolution of the phytochrome gene family in diploid (G. herbaceum, G. raimondii) or allotetraploid (G. hirsutum, G. barbadense) cotton species. The objective of this study was to obtain a preliminary inventory and molecular-evolutionary characterization of the phytochrome gene family in cotton. RESULTS We used comparative sequence resources to design low-degeneracy PCR primers that amplify genomic sequence tags (GSTs) for members of the PHYA, PHYB/D, PHYC and PHYE gene sub-families from A- and D-genome diploid and AD-genome allotetraploid Gossypium species. We identified two paralogous PHYA genes (designated PHYA1 and PHYA2) in diploid cottons, the result of a Malvaceae-specific PHYA gene duplication that occurred approximately 14 million years ago (MYA), before the divergence of the A- and D-genome ancestors. We identified a single gene copy of PHYB, PHYC, and PHYE in diploid cottons. The allotetraploid genomes have largely retained the complete gene complements inherited from both of the diploid genome ancestors, with at least four PHYA genes and two genes encoding PHYB, PHYC and PHYE in the AD-genomes. We did not identify a PHYD gene in any cotton genomes examined. CONCLUSIONS Detailed sequence analysis suggests that phytochrome genes retained after duplication by segmental duplication and allopolyploidy appear to be evolving independently under a birth-and-death-process with strong purifying selection. Our study provides a preliminary phytochrome gene inventory that is necessary and sufficient for further characterization of the biological functions of each of the cotton phytochrome genes, and for the development of 'candidate gene' markers that are potentially useful for cotton improvement via modern marker-assisted selection strategies.
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Affiliation(s)
- Ibrokhim Y Abdurakhmonov
- Center of Genomic Technologies, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent, 111226 Uzbekistan
| | - Zabardast T Buriev
- Center of Genomic Technologies, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent, 111226 Uzbekistan
| | | | - Abdusattor Abdukarimov
- Center of Genomic Technologies, Academy of Sciences of Uzbekistan. Yuqori Yuz, Qibray region Tashkent, 111226 Uzbekistan
| | - Alan E Pepper
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
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96
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Rausenberger J, Hussong A, Kircher S, Kirchenbauer D, Timmer J, Nagy F, Schäfer E, Fleck C. An integrative model for phytochrome B mediated photomorphogenesis: from protein dynamics to physiology. PLoS One 2010; 5:e10721. [PMID: 20502669 PMCID: PMC2873432 DOI: 10.1371/journal.pone.0010721] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/22/2010] [Indexed: 12/05/2022] Open
Abstract
Background Plants have evolved various sophisticated mechanisms to respond and adapt to changes of abiotic factors in their natural environment. Light is one of the most important abiotic environmental factors and it regulates plant growth and development throughout their entire life cycle. To monitor the intensity and spectral composition of the ambient light environment, plants have evolved multiple photoreceptors, including the red/far-red light-sensing phytochromes. Methodology/Principal Findings We have developed an integrative mathematical model that describes how phytochrome B (phyB), an essential receptor in Arabidopsis thaliana, controls growth. Our model is based on a multiscale approach and connects the mesoscopic intracellular phyB protein dynamics to the macroscopic growth phenotype. To establish reliable and relevant parameters for the model phyB regulated growth we measured: accumulation and degradation, dark reversion kinetics and the dynamic behavior of different nuclear phyB pools using in vivo spectroscopy, western blotting and Fluorescence Recovery After Photobleaching (FRAP) technique, respectively. Conclusions/Significance The newly developed model predicts that the phyB-containing nuclear bodies (NBs) (i) serve as storage sites for phyB and (ii) control prolonged dark reversion kinetics as well as partial reversibility of phyB Pfr in extended darkness. The predictive power of this mathematical model is further validated by the fact that we are able to formalize a basic photobiological observation, namely that in light-grown seedlings hypocotyl length depends on the total amount of phyB. In addition, we demonstrate that our theoretical predictions are in excellent agreement with quantitative data concerning phyB levels and the corresponding hypocotyl lengths. Hence, we conclude that the integrative model suggested in this study captures the main features of phyB-mediated photomorphogenesis in Arabidopsis.
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Affiliation(s)
- Julia Rausenberger
- Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andrea Hussong
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Stefan Kircher
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | | | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Ferenc Nagy
- Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, Freiburg, Germany
- * E-mail: (ES); (CF)
| | - Christian Fleck
- Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
- * E-mail: (ES); (CF)
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97
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Gabriele S, Rizza A, Martone J, Circelli P, Costantino P, Vittorioso P. The Dof protein DAG1 mediates PIL5 activity on seed germination by negatively regulating GA biosynthetic gene AtGA3ox1. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 61:312-23. [PMID: 19874540 DOI: 10.1111/j.1365-313x.2009.04055.x] [Citation(s) in RCA: 93] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
We have previously shown that inactivation of the gene encoding the Arabidopsis thaliana transcription factor DOF AFFECTING GERMINATION 1 (DAG1) renders seed germination more sensitive to both phytochrome B (phyB) and gibberellins (GA). dag1 mutant seeds require less red (R) light fluence and a lower GA concentration than WT to germinate. Here, we show that inactivation of the gene PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) results in down-regulation of DAG1. Inactivation of PIL5 in the dag1 mutant background further increased the germination potential of dag1 mutant seeds, supporting the suggestion that DAG1 is under the positive control of PIL5. Germination of dag1phyB seeds showed a reduced requirement of gibberellins as compared with phyB mutant seeds, both in the presence and in the absence of GA biosynthesis. Furthermore, the GA biosynthetic gene AtGA3ox1 is upregulated in dag1 seeds as compared with the WT, and DAG1 actually binds to the AtGA3ox1 promoter, as shown by chromatin immunoprecipitation experiments. Expression analysis at different time points confirms that AtGA3ox1 is directly regulated by DAG1, while suggesting that DAG1 is not a direct regulatory target of PIL5. Our data indicate that in the phyB pathway leading to seed germination, DAG1 negatively regulates GA biosynthesis and suggest that DAG1 acts downstream of PIL5. In addition, the analysis of hypocotyls of dag1 and phyB mutant plantlets, of plantlets overexpressing phyB in the dag1 mutant, as well as of dag1phyB double mutant suggests that DAG1 may act as a negative regulatory element downstream of phyB also in hypocotyl elongation.
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Affiliation(s)
- Stefano Gabriele
- Istituto Pasteur Fondazione Cenci Bolognetti, Dipartimento di Genetica e Biologia Molecolare, Università La Sapienza, Piazzale Aldo Moro 5, 00185 Rome, Italy
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98
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Mathews S. Evolutionary studies illuminate the structural-functional model of plant phytochromes. THE PLANT CELL 2010; 22:4-16. [PMID: 20118225 PMCID: PMC2828699 DOI: 10.1105/tpc.109.072280] [Citation(s) in RCA: 79] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/16/2009] [Revised: 01/12/2010] [Accepted: 01/13/2010] [Indexed: 05/18/2023]
Abstract
A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.
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Affiliation(s)
- Sarah Mathews
- Arnold Arboretum of Harvard University, Cambridge, Massachusetts 02138, USA.
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99
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Müller R, Fernández AP, Hiltbrunner A, Schäfer E, Kretsch T. The histidine kinase-related domain of Arabidopsis phytochrome a controls the spectral sensitivity and the subcellular distribution of the photoreceptor. PLANT PHYSIOLOGY 2009; 150:1297-309. [PMID: 19403732 PMCID: PMC2705050 DOI: 10.1104/pp.109.135988] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/28/2009] [Accepted: 04/26/2009] [Indexed: 05/19/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor for sensing extremely low amounts of light and for mediating various far-red light-induced responses in higher plants. Translocation from the cytosol to the nucleus is an essential step in phyA signal transduction. EID1 (for EMPFINDLICHER IM DUNKELROTEN LICHT1) is an F-box protein that functions as a negative regulator in far-red light signaling downstream of the phyA in Arabidopsis (Arabidopsis thaliana). To identify factors involved in EID1-dependent light signal transduction, pools of ethylmethylsulfonate-treated eid1-3 seeds were screened for seedlings that suppress the hypersensitive phenotype of the mutant. The phenotype of the suppressor mutant presented here is caused by a missense mutation in the PHYA gene that leads to an amino acid transition in its histidine kinase-related domain. The novel phyA-402 allele alters the spectral sensitivity and the persistence of far-red light-induced high-irradiance responses. The strong eid1-3 suppressor phenotype of phyA-402 contrasts with the moderate phenotype observed when phyA-402 is introgressed into the wild-type background, which indicates that the mutation mainly alters functions in an EID1-dependent signaling cascade. The mutation specifically inhibits nuclear accumulation of the photoreceptor molecule upon red light irradiation, even though it still interacts with FHY1 (for far-red long hypocotyl 1) and FHL (for FHY1-like protein), two factors that are essential for nuclear accumulation of phyA. Degradation of the mutated phyA is unaltered even under light conditions that inhibit its nuclear accumulation, indicating that phyA degradation may occur mostly in the cytoplasm.
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Affiliation(s)
- Rebecca Müller
- Albert-Ludwigs-Universität Freiburg, Institut für Biologie 2/Botanik, 79104 Freiburg, Germany
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100
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Kikis EA, Oka Y, Hudson ME, Nagatani A, Quail PH. Residues clustered in the light-sensing knot of phytochrome B are necessary for conformer-specific binding to signaling partner PIF3. PLoS Genet 2009; 5:e1000352. [PMID: 19165330 PMCID: PMC2621353 DOI: 10.1371/journal.pgen.1000352] [Citation(s) in RCA: 55] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2008] [Accepted: 12/22/2008] [Indexed: 11/18/2022] Open
Abstract
The bHLH transcription factor, PHYTOCHROME INTERACTING FACTOR 3 (PIF3), interacts specifically with the photoactivated, Pfr, form of Arabidopsis phytochrome B (phyB). This interaction induces PIF3 phosphorylation and degradation in vivo and modulates phyB-mediated seedling deetiolation in response to red light. To identify missense mutations in the phyB N-terminal domain that disrupt this interaction, we developed a yeast reverse-hybrid screen. Fifteen individual mutations identified in this screen, or in previous genetic screens for Arabidopsis mutants showing reduced sensitivity to red light, were shown to also disrupt light-induced binding of phyB to PIF3 in in vitro co-immunoprecipitation assays. These phyB missense mutants fall into two general classes: Class I (eleven mutants) containing those defective in light signal perception, due to aberrant chromophore attachment or photoconversion, and Class II (four mutants) containing those normal in signal perception, but defective in the capacity to transduce this signal to PIF3. By generating a homology model for the three-dimensional structure of the Arabidopsis phyB chromophore-binding region, based on the crystal structure of Deinococcus radiodurans phytochrome, we predict that three of the four Class II mutated phyB residues are solvent exposed in a cleft between the presumptive PAS and GAF domains. This deduction suggests that these residues could be directly required for the physical interaction of phyB with PIF3. Because these three residues are also necessary for phyB-imposed inhibition of hypocotyl elongation in response to red light, they are functionally necessary for signal transfer from photoactivated phyB, not only to PIF3 and other related bHLH transcription factors tested here, but also to other downstream signaling components involved in regulating seedling deetiolation. Plants monitor their environment for informational light signals that are used to direct adaptive morphogenic responses. The phytochrome (phy) family of photoreceptors are central to this process. Upon photoperception, phy molecules rapidly translocate to the nucleus where they interact with basic helix-loop-helix transcription factors, termed PIFs (phy-Interacting Factors), and induce gene-expression changes that control morphogenic responses. The molecular determinants in the phy protein responsible for direct intermolecular signal transfer from the activated photoreceptor to transduction partners are undefined. Using random mutagenesis of Arabidopsis phyB, coupled with a reverse-hybrid protein-interaction screen, we identified missense mutations in the N-terminal domain that abrogate the binding of the photoreceptor molecule to PIF3. A subset of these mutated phyB molecules retain the capacity for light-signal perception but are defective in the capacity to transduce that signal to PIF3 and other related PIFs. The mutated residues in these molecules are predicted to cluster at the surface of the protein in a structure termed the “light-sensing knot.” These residues are necessary for phyB-regulated growth in the living plant, establishing that the protein region identified appears to function as a component of the molecular interface responsible for direct signal transfer to transduction partners in the cell.
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Affiliation(s)
- Elise A. Kikis
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
| | - Yoshito Oka
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
| | - Matthew E. Hudson
- Department of Crop Sciences, University of Illinois, Urbana, Illinois, United States of America
| | - Akira Nagatani
- Department of Biology, Graduate School of Science, Kyoto University, Kyoto, Japan
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California Berkeley, Berkeley, California, United States of America
- USDA/ARS – Plant Gene Expression Center, Albany, California, United States of America
- * E-mail:
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