201
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González-Grandío E, Poza-Carrión C, Sorzano COS, Cubas P. BRANCHED1 promotes axillary bud dormancy in response to shade in Arabidopsis. THE PLANT CELL 2013; 25:834-50. [PMID: 23524661 PMCID: PMC3634692 DOI: 10.1105/tpc.112.108480] [Citation(s) in RCA: 154] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Revised: 02/18/2013] [Accepted: 03/04/2013] [Indexed: 05/18/2023]
Abstract
Plants interpret a decrease in the red to far-red light ratio (R:FR) as a sign of impending shading by neighboring vegetation. This triggers a set of developmental responses known as shade avoidance syndrome. One of these responses is reduced branching through suppression of axillary bud outgrowth. The Arabidopsis thaliana gene BRANCHED1 (BRC1), expressed in axillary buds, is required for branch suppression in response to shade. Unlike wild-type plants, brc1 mutants develop several branches after a shade treatment. BRC1 transcription is positively regulated 4 h after exposure to low R:FR. Consistently, BRC1 is negatively regulated by phytochrome B. Transcriptional profiling of wild-type and brc1 buds of plants treated with simulated shade has revealed groups of genes whose mRNA levels are dependent on BRC1, among them a set of upregulated abscisic acid response genes and two networks of cell cycle- and ribosome-related downregulated genes. The downregulated genes have promoters enriched in TEOSINTE BRANCHED1, CYCLOIDEA, and PCF (TCP) binding sites, suggesting that they could be transcriptionally regulated by TCP factors. Some of these genes respond to BRC1 in seedlings and buds, supporting their close relationship with BRC1 activity. This response may allow the rapid adaptation of plants to fluctuations in the ratio of R:FR light.
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Affiliation(s)
- Eduardo González-Grandío
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - César Poza-Carrión
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Carlos Oscar S. Sorzano
- Departamento de Estructura de Macromoléculas, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
| | - Pilar Cubas
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología/Consejo Superior de Investigaciones Cientificas, Campus Universidad Autónoma de Madrid, 28049 Madrid, Spain
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202
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Gommers CMM, Visser EJW, St Onge KR, Voesenek LACJ, Pierik R. Shade tolerance: when growing tall is not an option. TRENDS IN PLANT SCIENCE 2013; 18:65-71. [PMID: 23084466 DOI: 10.1016/j.tplants.2012.09.008] [Citation(s) in RCA: 158] [Impact Index Per Article: 14.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/02/2012] [Revised: 09/04/2012] [Accepted: 09/21/2012] [Indexed: 05/18/2023]
Abstract
Two different plant strategies exist to deal with shade: shade avoidance and shade tolerance. All shade-exposed plants optimize photosynthesis to adapt to the decrease in light quality and quantity. When shaded, most species in open habitats express the shade-avoidance syndrome, a growth response to escape shade. Shade-tolerant species from forest understories cannot outgrow surrounding trees and adopt a tolerance response. Unlike shade avoidance, virtually nothing is known about regulation of shade tolerance. In this opinion article, we discuss potential modes of molecular regulation to adopt a shade-tolerance rather than a shade-avoidance strategy. We argue that molecular approaches using model and non-model species should help identify the molecular pathways that underpin shade tolerance, thus providing knowledge for further crop improvement.
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Affiliation(s)
- Charlotte M M Gommers
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH Utrecht, The Netherlands
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203
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Torres-Galea P, Hirtreiter B, Bolle C. Two GRAS proteins, SCARECROW-LIKE21 and PHYTOCHROME A SIGNAL TRANSDUCTION1, function cooperatively in phytochrome A signal transduction. PLANT PHYSIOLOGY 2013; 161:291-304. [PMID: 23109688 PMCID: PMC3532260 DOI: 10.1104/pp.112.206607] [Citation(s) in RCA: 60] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Photoreceptors, especially the far-red light-absorbing phytochrome A, play a crucial role in early seedling development, triggering the transition from etiolated to photomorphogenic growth. Here, we describe the biological functions of two GRAS proteins from Arabidopsis (Arabidopsis thaliana), SCARECROW-LIKE21 (SCL21) and PHYTOCHROME A SIGNAL TRANSDUCTION1 (PAT1), which are specifically involved in phytochrome A signal transduction. Loss-of-function mutants show an elongated hypocotyl under far-red light and are impaired in other far-red high-irradiance responses. The SCL21 transcript itself is down-regulated by far-red light in a phytochrome A- and PAT1-dependent manner. Our results demonstrate that both SCL21 and PAT1 are positive regulators of phytochrome A signal transduction for several high-irradiance responses. Genetic and biochemical evidence suggest a direct interaction of the two proteins.
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204
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Müller K, Weber W. Optogenetic tools for mammalian systems. MOLECULAR BIOSYSTEMS 2013; 9:596-608. [DOI: 10.1039/c3mb25590e] [Citation(s) in RCA: 76] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
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205
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Ranade SS, Abrahamsson S, Niemi J, García-Gil MR. <i>Pinus taeda</i> cDNA Microarray as a Tool for Candidate Gene Identification for Local Red/Far-Red Light Adaptive Response in <i>Pinus sylvestris</i>. ACTA ACUST UNITED AC 2013. [DOI: 10.4236/ajps.2013.43061] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
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206
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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: 61] [Impact Index Per Article: 5.5] [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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207
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Sassi M, Lu Y, Zhang Y, Wang J, Dhonukshe P, Blilou I, Dai M, Li J, Gong X, Jaillais Y, Yu X, Traas J, Ruberti I, Wang H, Scheres B, Vernoux T, Xu J. COP1 mediates the coordination of root and shoot growth by light through modulation of PIN1- and PIN2-dependent auxin transport in Arabidopsis. Development 2012; 139:3402-12. [PMID: 22912415 DOI: 10.1242/dev.078212] [Citation(s) in RCA: 113] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
When a plant germinates in the soil, elongation of stem-like organs is enhanced whereas leaf and root growth is inhibited. How these differential growth responses are orchestrated by light and integrated at the organismal level to shape the plant remains to be elucidated. Here, we show that light signals through the master photomorphogenesis repressor COP1 to coordinate root and shoot growth in Arabidopsis. In the shoot, COP1 regulates shoot-to-root auxin transport by controlling the transcription of the auxin efflux carrier gene PIN-FORMED1 (PIN1), thus appropriately tuning shoot-derived auxin levels in the root. This in turn directly influences root elongation and adapts auxin transport and cell proliferation in the root apical meristem by modulating PIN1 and PIN2 intracellular distribution in the root in a COP1-dependent fashion, thus permitting a rapid and precise tuning of root growth to the light environment. Our data identify auxin as a long-distance signal in developmental adaptation to light and illustrate how spatially separated control mechanisms can converge on the same signaling system to coordinate development at the whole plant level.
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Affiliation(s)
- Massimiliano Sassi
- CNRS, INRA, ENS Lyon, UCBL, Université de Lyon, Laboratoire de Reproduction et Développement des Plantes, 46 Allée d'Italie, 69364 Lyon Cedex 07, France
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208
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Bacchus W, Fussenegger M. The use of light for engineered control and reprogramming of cellular functions. Curr Opin Biotechnol 2012; 23:695-702. [DOI: 10.1016/j.copbio.2011.12.004] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2011] [Revised: 11/07/2011] [Accepted: 12/07/2011] [Indexed: 11/16/2022]
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209
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Ganesan M, Han YJ, Bae TW, Hwang OJ, Chandrasekhar T, Shin AY, Goh CH, Nishiguchi S, Song IJ, Lee HY, Kim JI, Song PS. Overexpression of phytochrome A and its hyperactive mutant improves shade tolerance and turf quality in creeping bentgrass and zoysiagrass. PLANTA 2012; 236:1135-1150. [PMID: 22644765 DOI: 10.1007/s00425-012-1662-6] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/22/2012] [Accepted: 05/03/2012] [Indexed: 06/01/2023]
Abstract
Phytochrome A (phyA) in higher plants is known to function as a far-red/shade light-sensing photoreceptor in suppressing shade avoidance responses (SARs) to shade stress. In this paper, the Avena PHYA gene was introduced into creeping bentgrass (Agrostis stolonifera L.) and zoysiagrass (Zoysia japonica Steud.) to improve turf quality by suppressing the SARs. In addition to wild-type PHYA, a hyperactive mutant gene (S599A-PHYA), in which a phosphorylation site involved in light-signal attenuation was removed, was also transformed into the turfgrasses. Phenotypic traits of the transgenic plants were compared to assess the suppression of SARs under a simulated shade condition and outdoor field conditions after three growth seasons. Under the shade condition, the S599A-PhyA transgenic creeping bentgrass plants showed shade avoidance-suppressing phenotypes with a 45 % shorter leaf lengths, 24 % shorter internode lengths, and twofold increases in chlorophyll concentrations when compared with control plants. Transgenic zoysiagrass plants overexpressing S599A-PHYA also showed shade-tolerant phenotypes under the shade condition with reductions in leaf length (15 %), internode length (30 %), leaf length/width ratio (19 %) and leaf area (22 %), as well as increases in chlorophyll contents (19 %) and runner lengths (30 %) compared to control plants. The phenotypes of transgenic zoysiagrass were also investigated in dense field habitats, and the transgenic turfgrass exhibited shade-tolerant phenotypes similar to those observed under laboratory shade conditions. Therefore, the present study suggests that the hyperactive phyA is effective for the development of shade-tolerant plants, and that the shade tolerance nature is sustained under field conditions.
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Affiliation(s)
- Markkandan Ganesan
- Faculty of Biotechnology and Subtropical Horticulture Research Institute, Jeju National University, Jeju 690-756, Korea
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210
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Christians MJ, Gingerich DJ, Hua Z, Lauer TD, Vierstra RD. The light-response BTB1 and BTB2 proteins assemble nuclear ubiquitin ligases that modify phytochrome B and D signaling in Arabidopsis. PLANT PHYSIOLOGY 2012; 160:118-34. [PMID: 22732244 PMCID: PMC3440189 DOI: 10.1104/pp.112.199109] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
Members of the Bric-a-Brac/Tramtrack/Broad Complex (BTB) family direct the selective ubiquitylation of proteins following their assembly into Cullin3-based ubiquitin ligases. Here, we describe a subfamily of nucleus-localized BTB proteins encoded by the LIGHT-RESPONSE BTB1 (LRB1) and LRB2 loci in Arabidopsis (Arabidopsis thaliana) that strongly influences photomorphogenesis. Whereas single lrb1 and lrb2 mutants are relatively normal phenotypically, double mutants are markedly hypersensitive to red light, but not to far-red or blue light, and are compromised in multiple photomorphogenic processes, including seed germination, cotyledon opening and expansion, chlorophyll accumulation, shade avoidance, and flowering time. This red light hypersensitivity can be overcome by eliminating phytochrome B (phyB) and phyD, indicating that LRB1/2 act downstream of these two photoreceptor isoforms. Levels of phyB/D proteins but not their messenger RNAs are abnormally high in light-grown lrb1 lrb2 plants, implying that their light-dependent turnover is substantially dampened. Whereas other red light-hypersensitive mutants accumulate phyA protein similar to or higher than the wild type in light, the lrb1 lrb2 mutants accumulate less, suggesting that LRB1/2 also positively regulate phyA levels in a phyB/D-dependent manner. Together, these data show that the BTB ubiquitin ligases assembled with LRB1/2 function redundantly as negative regulators of photomorphogenesis, possibly by influencing the turnover of phyB/D.
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211
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Hirose F, Inagaki N, Hanada A, Yamaguchi S, Kamiya Y, Miyao A, Hirochika H, Takano M. Cryptochrome and phytochrome cooperatively but independently reduce active gibberellin content in rice seedlings under light irradiation. PLANT & CELL PHYSIOLOGY 2012; 53:1570-82. [PMID: 22764280 PMCID: PMC3439870 DOI: 10.1093/pcp/pcs097] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
In contrast to a wealth of knowledge about the photoregulation of gibberellin metabolism in dicots, that in monocots remains largely unclear. In this study, we found that a blue light signal triggers reduction of active gibberellin content in rice seedlings with simultaneous repression of two gibberellin 20-oxidase genes (OsGA20ox2 and OsGA20ox4) and acute induction of four gibberellin 2-oxidase genes (OsGA2ox4-OsGA2ox7). For further examination of the regulation of these genes, we established a series of cryptochrome-deficient lines through reverse genetic screening from a Tos17 mutant population and construction of knockdown lines based on an RNA interference technique. By using these lines and phytochrome mutants, we elucidated that cryptochrome 1 (cry1), consisting of two species in rice plants (cry1a and cry1b), is indispensable for robust induction of the GA2ox genes. On the other hand, repression of the GA20ox genes is mediated by phytochromes. In addition, we found that the phytochromes also mediate the repression of a gibberellin 3-oxidase gene (OsGA3ox2) in the light. These results imply that, in rice seedlings, phytochromes mediate the repression of gibberellin biosynthesis capacity, while cry1 mediates the induction of gibberellin inactivation capacity. The cry1 action was demonstrated to be dominant in the reduction of active gibberellin content, but, in rice seedlings, the cumulative effects of these independent actions reduced active gibberellin content in the light. This pathway design in which different types of photoreceptors independently but cooperatively regulate active gibberellin content is unique from the viewpoint of dicot research. This redundancy should provide robustness to the response in rice plants.
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Affiliation(s)
- Fumiaki Hirose
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, 305-8602 Japan.
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212
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Kiss JZ, Millar KDL, Edelmann RE. Phototropism of Arabidopsis thaliana in microgravity and fractional gravity on the International Space Station. PLANTA 2012; 236:635-45. [PMID: 22481136 DOI: 10.1007/s00425-012-1633-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/07/2012] [Accepted: 03/22/2012] [Indexed: 05/21/2023]
Abstract
While there is a great deal of knowledge regarding plant growth and development in microgravity aboard orbiting spacecraft, there is little information available about these parameters in reduced or fractional gravity conditions (less than the nominal 1g on Earth). Thus, in these experiments using the European Modular Cultivation System on the International Space Station, we studied the interaction between phototropism and gravitropism in the WT and mutants of phytochrome A and B of Arabidopis thaliana. Fractional gravity and the 1 g control were provided by centrifuges in the spaceflight hardware, and unidirectional red and blue illumination followed a white light growth period in the time line of the space experiments. The existence of red-light-based positive phototropism in hypocotyls of seedlings that is mediated by phytochrome was confirmed in these microgravity experiments. Fractional gravity studies showed an attenuation of red-light-based phototropism in both roots and hypocotyls of seedlings occurring due to gravitational accelerations ranging from 0.l to 0.3 g. In contrast, blue-light negative phototropism in roots, which was enhanced in microgravity compared with the 1g control, showed a significant attenuation at 0.3 g. In addition, our studies suggest that the well-known red-light enhancement of blue-light-induced phototropism in hypocotyls is likely due to an indirect effect by the attenuation of gravitropism. However, red-light enhancement of root blue-light-based phototropism may occur via a more direct effect on the phototropism system itself, most likely through the phytochrome photoreceptors. To our knowledge, these experiments represent the first to examine the behavior of flowering plants in fractional or reduced gravity conditions.
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Affiliation(s)
- John Z Kiss
- Department of Botany, Miami University, Oxford, OH 45056, USA.
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213
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Castelain M, Le Hir R, Bellini C. The non-DNA-binding bHLH transcription factor PRE3/bHLH135/ATBS1/TMO7 is involved in the regulation of light signaling pathway in Arabidopsis. PHYSIOLOGIA PLANTARUM 2012; 145:450-60. [PMID: 22339648 DOI: 10.1111/j.1399-3054.2012.01600.x] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Plant basic Helix-loop-helix (bHLH) proteins are transcription factors that are involved in many developmental mechanisms, including light signaling and hormone homeostasis. Some of them are non-DNA-binding proteins and could act as dominant negative regulators of other bHLH proteins by forming heterodimers, in a similar way to animal inhibitor of DNA-binding proteins. It has been recently reported that several non-DNA-binding bHLHs are involved in light signaling (KDR/PRE6), gibberellic acid signaling (PRE1/BNQ1/bHLH136) or brassinosteroid signaling (ATBS1). Here we report that Arabidopsis lines overexpressing the PRE3/bHLH135/ATBS1/TMO7 gene are less responsive to red, far-red and blue light than wild-type which is likely to explain the light hyposensitive phenotype displayed when grown under white light conditions. Using quantitative polymerase chain reaction, we show that the expression of PRE3 and KDR/PRE6 genes is regulated by light and that light-related genes are deregulated in the PRE3-ox lines. We show that PRE3 is expressed in the shoot and root meristems and that PRE3-ox lines also have a defect in lateral root development. Our results not only suggest that PRE3 is involved in the regulation of light signaling, but also support the hypothesis that non-DNA-binding bHLH genes are promiscuous genes regulating a wide range of both overlapping and specific regulatory pathways.
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Affiliation(s)
- Mathieu Castelain
- Department of Forest Genetics and Plant Physiology, Umeå Plant Science Centre, Swedish University of Agricultural Sciences, 90187 Umeå, Sweden
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214
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Hopkins JA, Kiss JZ. Phototropism and gravitropism in transgenic lines of Arabidopsis altered in the phytochrome pathway. PHYSIOLOGIA PLANTARUM 2012; 145:461-73. [PMID: 22380624 DOI: 10.1111/j.1399-3054.2012.01607.x] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Phytochromes are a family of photoreceptor molecules, absorbing primarily in red and far-red, that are important in many aspects of plant development. These studies investigated the role of phytochromes in phototropism and gravitropism of seedlings of Arabidopsis thaliana. We used two transgenic lines, one which lacked phytochromes specifically in the roots (M0062/UASBVR) and the other lacked phytochromes in the shoots (CAB3::pBVR). These transgenic plants are deficient in the phytochrome chromophore in specific tissues due the expression of biliverdin IXa reductase (BVR), which binds to precursors of the chromophore. Experiments were performed in both light and dark conditions to determine whether roots directly perceive light signals or if the signal is perceived in the shoot and then transmitted to the root during tropistic curvature. Kinetics of tropisms and growth were assayed by standard methods or with a computer-based feedback system. We found that the perception of red light occurs directly in the root during phototropism in this organ and that signaling also may occur from root to shoot in gravitropism.
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Affiliation(s)
- Jane A Hopkins
- Department of Botany, Miami University, Oxford, OH 45056, USA
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215
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Deng Y, Yao J, Wang X, Guo H, Duan D. Transcriptome sequencing and comparative analysis of Saccharina japonica (Laminariales, Phaeophyceae) under blue light induction. PLoS One 2012; 7:e39704. [PMID: 22761876 PMCID: PMC3384632 DOI: 10.1371/journal.pone.0039704] [Citation(s) in RCA: 40] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2012] [Accepted: 05/24/2012] [Indexed: 12/12/2022] Open
Abstract
BACKGROUND Light has significant effect on the growth and development of Saccharina japonica, but there are limited reports on blue light mediated physiological responses and molecular mechanism. In this study, high-throughput paired-end RNA-sequencing (RNA-Seq) technology was applied to transcriptomes of S. japonica exposed to blue light and darkness, respectively. Comparative analysis of gene expression was designed to correlate the effect of blue light and physiological mechanisms on the molecular level. PRINCIPAL FINDINGS RNA-seq analysis yielded 70,497 non-redundant unigenes with an average length of 538 bp. 28,358 (40.2%) functional transcripts encoding regions were identified. Annotation through Swissprot, Nr, GO, KEGG, and COG databases showed 25,924 unigenes compared well (E-value <10(-5)) with known gene sequences, and 43 unigenes were putative BL photoreceptor. 10,440 unigenes were classified into Gene Ontology, and 8,476 unigenes were involved in 114 known pathways. Based on RPKM values, 11,660 (16.5%) differentially expressed unigenes were detected between blue light and dark exposed treatments, including 7,808 upregulated and 3,852 downregulated unigenes, suggesting S. japonica had undergone extensive transcriptome re-orchestration during BL exposure. The BL-specific responsive genes were indentified to function in processes of circadian rhythm, flavonoid biosynthesis, photoreactivation and photomorphogenesis. SIGNIFICANCE Transcriptome profiling of S. japonica provides clues to potential genes identification and future functional genomics study. The global survey of expression changes under blue light will enhance our understanding of molecular mechanisms underlying blue light induced responses in lower plants as well as facilitate future blue light photoreceptor identification and specific responsive pathways analysis.
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Affiliation(s)
- Yunyan Deng
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Jianting Yao
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Xiuliang Wang
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
| | - Hui Guo
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
- Graduate University of Chinese Academy of Sciences, Beijing, China
| | - Delin Duan
- Institute of Oceanology, Chinese Academy of Sciences, Qingdao, China
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216
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Lopez L, Carbone F, Bianco L, Giuliano G, Facella P, Perrotta G. Tomato plants overexpressing cryptochrome 2 reveal altered expression of energy and stress-related gene products in response to diurnal cues. PLANT, CELL & ENVIRONMENT 2012; 35:994-1012. [PMID: 22082487 DOI: 10.1111/j.1365-3040.2011.02467.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/02/2023]
Abstract
In order to sense and respond to the fluctuating light conditions, higher plants possess several families of photoreceptors, such as phytochromes (PHYs), cryptochromes (CRYs) and phototropins. CRYs are responsible for photomorphogenesis and play a role in circadian, developmental and adaptive growth regulation of plants. In tomato (Solanum lycopersicum), CRY2 controls vegetative development, flowering time, fruit antioxidant content as well as the diurnal transcription of several other photoreceptor genes. We applied large-scale molecular approaches to identify altered transcripts and proteins in tomato wild-type (WT) versus a CRY2 overexpressing transgenic genotype, under a diurnal rhythm. Our results showed that tomato CRY2 profoundly affects both gene and protein expression in response to daily light cycle. Particularly altered molecular pathways are related to biotic/abiotic stress, photosynthesis, including components of the light and dark reactions and of starch and sucrose biosynthesis, as well as to secondary metabolism, such as phenylpropanoid, phenolic and flavonoid/anthocyanin biosynthesis pathways. One of the most interesting results is the coordinated up-regulation, in the transgenic genotype, of a consistent number of transcripts and proteins involved in photorespiration and photosynthesis. It is conceivable that light modulates the energetic metabolism of tomato through a fine CRY2-mediated transcriptional control.
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Affiliation(s)
- Loredana Lopez
- ENEA, Trisaia Research Center, Rotondella (MT), Italy ENEA, Casaccia Research Center, Rome, Italy
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217
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Prasad BRV, Kumar SV, Nandi A, Chattopadhyay S. Functional interconnections of HY1 with MYC2 and HY5 in Arabidopsis seedling development. BMC PLANT BIOLOGY 2012; 12:37. [PMID: 22424472 PMCID: PMC3353174 DOI: 10.1186/1471-2229-12-37] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2011] [Accepted: 03/17/2012] [Indexed: 05/19/2023]
Abstract
Arabidopsis seedling development is controlled by many regulatory genes involved in multiple signaling pathways. The functional relationships of these genes working in multiple signaling cascades have started to be unraveled. Arabidopsis HY1/HO1 is a rate-limiting enzyme involved in biosynthesis of phytochrome chromophore. HY5 (a bZIP protein) promotes photomorphogenesis, however ZBF1/MYC2 (a bHLH protein) works as a negative regulator of photomorphogenic growth and light regulated gene expression. Further, MYC2 and HY1 have been shown to play important roles in jasmonic acid (JA) signaling pathways. Here, we show the genetic interactions of HY1 with two key transcription factor genes of light signaling, HY5 and MYC2, in Arabidopsis seedling development. Our studies reveal that although HY1 acts in an additive manner with HY5, it is epistatic to MYC2 in light-mediated seedling growth and gene expression. This study further demonstrates that HY1 additively or synergistically functions with HY5, however it works upstream to MYC2 in JA signaling pathways. Taken together, this study demonstrates the functional interrelations of HY1, MYC2 and HY5 in light and JA signaling pathways.
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Affiliation(s)
| | - Selva V Kumar
- National Institute of Plant Genome Research, New Delhi, India
| | - Ashis Nandi
- School of Life Sciences, Jawharlal Neheru University, New Delhi, India
| | - Sudip Chattopadhyay
- Department of Biotechnology, National Institute of Technology, Mahatma Gandhi Avenue, Durgapur 713209, West Bengal, India
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218
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Structural basis of ultraviolet-B perception by UVR8. Nature 2012; 484:214-9. [DOI: 10.1038/nature10931] [Citation(s) in RCA: 301] [Impact Index Per Article: 25.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2011] [Accepted: 02/10/2012] [Indexed: 12/26/2022]
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219
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Spillane KM, Dasgupta J, Mathies RA. Conformational homogeneity and excited-state isomerization dynamics of the bilin chromophore in phytochrome Cph1 from resonance Raman intensities. Biophys J 2012; 102:709-17. [PMID: 22325295 DOI: 10.1016/j.bpj.2011.11.4019] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2011] [Revised: 11/23/2011] [Accepted: 11/28/2011] [Indexed: 11/30/2022] Open
Abstract
The ground-state structure and excited-state isomerization dynamics of the P(r) and P(fr) forms of phytochrome Cph1 are investigated using resonance Raman intensity analysis. Electronic absorption and stimulated resonance Raman spectra of P(r) and P(fr) are presented; vibronic analysis of the Raman intensities and absorption spectra reveals that both conformers exist as a single, homogeneous population of molecules in the ground state. The homogeneous and inhomogeneous contributions to the overall electronic broadening are determined, and it is found that the broadening is largely homogeneous in nature, pointing to fast excited-state decay. Franck-Condon displacements derived from the Raman intensity analysis reveal the initial atomic motions in the excited state, including the highly displaced, nontotally symmetric torsional and C(15)-H HOOP modes that appear because of symmetry-reducing distortions about the C(14)-C(15) and C(15)=C(16) bonds. P(fr) is especially well primed for ultrafast isomerization and torsional Franck-Condon analysis predicts a <200 fs P(fr) → P(r) isomerization. This time is significantly faster than the observed 700 fs reaction time, indicating that the P(fr) S(1) surface has a D-ring rotational barrier caused by steric interactions with the protein.
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Affiliation(s)
- Katelyn M Spillane
- Department of Chemistry, University of California, Berkeley, California, USA
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220
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Kiyota S, Xie X, Takano M. Phytochromes A and C cooperatively regulate early and transient gene expression after red-light irradiation in rice seedlings. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2012; 51:10-17. [PMID: 22153234 DOI: 10.1016/j.plaphy.2011.10.002] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2011] [Accepted: 10/08/2011] [Indexed: 05/31/2023]
Abstract
Phytochromes are red/far-red photoreceptors encoded by a small gene family in higher plants. Differences in phenotype among mutants suggest distinct functions among phytochrome subfamilies. We attempted to find distinct functions among phytochromes by oligo-microarray analysis of single, double, and triple mutants in rice. In most cases, gene expression was redundantly regulated by phytochromes A and B after irradiation by a red light pulse in etiolated rice shoots. However, we found that several genes were specifically regulated by phytochromes A and C. Most of them were expressed immediately after the red light pulse in a transient manner. They are stress-related genes that may be involved in resistance to light stress when etiolated seedlings are exposed to light. These genes were not expressed in green leaves after the red light pulse, suggesting that they have a function specific to etiolated seedlings.
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Affiliation(s)
- Seiichiro Kiyota
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba 305-8602, Japan.
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221
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Liu J, Zhang F, Zhou J, Chen F, Wang B, Xie X. Phytochrome B control of total leaf area and stomatal density affects drought tolerance in rice. PLANT MOLECULAR BIOLOGY 2012; 78:289-300. [PMID: 22138855 DOI: 10.1007/s11103-011-9860-3] [Citation(s) in RCA: 73] [Impact Index Per Article: 6.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/24/2010] [Accepted: 11/21/2011] [Indexed: 05/18/2023]
Abstract
We report that phytochrome B (phyB) mutants exhibit improved drought tolerance compared to wild type (WT) rice (Oryza sativa L. cv. Nipponbare). To understand the underlying mechanism by which phyB regulates drought tolerance, we analyzed root growth and water loss from the leaves of phyB mutants. The root system showed no significant difference between the phyB mutants and WT, suggesting that improved drought tolerance has little relation to root growth. However, phyB mutants exhibited reduced total leaf area per plant, which was probably due to a reduction in the total number of cells per leaf caused by enhanced expression of Orysa;KRP1 and Orysa;KRP4 (encoding inhibitors of cyclin-dependent kinase complex activity) in the phyB mutants. In addition, the developed leaves of phyB mutants displayed larger epidermal cells than WT leaves, resulting in reduced stomatal density. phyB deficiency promoted the expression of both putative ERECTA family genes and EXPANSIN family genes involved in cell expansion in leaves, thus causing greater epidermal cell expansion in the phyB mutants. Reduced stomatal density resulted in reduced transpiration per unit leaf area in the phyB mutants. Considering all these findings, we propose that phyB deficiency causes both reduced total leaf area and reduced transpiration per unit leaf area, which explains the reduced water loss and improved drought tolerance of phyB mutants.
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Affiliation(s)
- Jing Liu
- College of Life Sciences, Shandong Normal University, 250014 Jinan, People's Republic of China
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222
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Facella P, Daddiego L, Giuliano G, Perrotta G. Gibberellin and auxin influence the diurnal transcription pattern of photoreceptor genes via CRY1a in tomato. PLoS One 2012; 7:e30121. [PMID: 22272283 PMCID: PMC3260215 DOI: 10.1371/journal.pone.0030121] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 12/13/2011] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Plant photoreceptors, phytochromes and cryptochromes, regulate many aspects of development and growth, such as seed germination, stem elongation, seedling de-etiolation, cotyledon opening, flower induction and circadian rhythms. There are several pieces of evidence of interaction between photoreceptors and phyto-hormones in all of these physiological processes, but little is known about molecular and genetic mechanisms underlying hormone-photoreceptor crosstalk. METHODOLOGY/PRINCIPAL FINDINGS In this work, we investigated the molecular effects of exogenous phyto-hormones to photoreceptor gene transcripts of tomato wt, as well as transgenic and mutant lines with altered cryptochromes, by monitoring day/night transcript oscillations. GA and auxin alter the diurnal expression level of different photoreceptor genes in tomato, especially in mutants that lack a working form of cryptochrome 1a: in those mutants the expression of some (IAA) or most (GA) photoreceptor genes is down regulated by these hormones. CONCLUSIONS/SIGNIFICANCE Our results highlight the presence of molecular relationships among cryptochrome 1a protein, hormones, and photoreceptors' gene expression in tomato, suggesting that manipulation of cryptochromes could represent a good strategy to understand in greater depth the role of phyto-hormones in the plant photoperceptive mechanism.
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Affiliation(s)
- Paolo Facella
- Italian National Agency for New Technologues, Energy and Sustainable Economic Development (ENA), Trisaia Research Center, Rotondella, Italy
| | - Loretta Daddiego
- Italian National Agency for New Technologues, Energy and Sustainable Economic Development (ENA), Trisaia Research Center, Rotondella, Italy
| | - Giovanni Giuliano
- Italian National Agency for New Technologues, Energy and Sustainable Economic Development (ENA), Casaccia Research Center, Rome, Italy
| | - Gaetano Perrotta
- Italian National Agency for New Technologues, Energy and Sustainable Economic Development (ENA), Trisaia Research Center, Rotondella, Italy
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223
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Zimmer M. What does it take to improve existing fluorescent proteins for in vivo imaging applications? Methods Mol Biol 2012; 872:235-241. [PMID: 22700415 DOI: 10.1007/978-1-61779-797-2_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/01/2023]
Abstract
Although fluorescent proteins are ubiquitously used as genetic tracers and imaging agents, there is significant room for improvement. This chapter discusses how new improved fluorescent proteins can be designed. It focuses on the design of far-red and infrared fluorescent proteins, since the currently-available red fluorescent proteins are not optimal for in vivo applications.
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Affiliation(s)
- Marc Zimmer
- Hale Laboratory, Connecticut College, New London, CT, USA.
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224
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Inomata K. Syntheses of Bilin Chromophores Toward the Investigation of Structure and Function of Phytochromes. HETEROCYCLES 2012. [DOI: 10.3987/rev-12-750] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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225
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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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226
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Sentandreu M, Martín G, González-Schain N, Leivar P, Soy J, Tepperman JM, Quail PH, Monte E. Functional profiling identifies genes involved in organ-specific branches of the PIF3 regulatory network in Arabidopsis. THE PLANT CELL 2011; 23:3974-91. [PMID: 22108407 PMCID: PMC3246323 DOI: 10.1105/tpc.111.088161] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/19/2011] [Revised: 09/07/2011] [Accepted: 11/03/2011] [Indexed: 05/20/2023]
Abstract
The phytochrome (phy)-interacting basic helix-loop-helix transcription factors (PIFs) constitutively sustain the etiolated state of dark-germinated seedlings by actively repressing deetiolation in darkness. This action is rapidly reversed upon light exposure by phy-induced proteolytic degradation of the PIFs. Here, we combined a microarray-based approach with a functional profiling strategy and identified four PIF3-regulated genes misexpressed in the dark (MIDAs) that are novel regulators of seedling deetiolation. We provide evidence that each one of these four MIDA genes regulates a specific facet of etiolation (hook maintenance, cotyledon appression, or hypocotyl elongation), indicating that there is branching in the signaling that PIF3 relays. Furthermore, combining inferred MIDA gene function from mutant analyses with their expression profiles in response to light-induced degradation of PIF3 provides evidence consistent with a model where the action of the PIF3/MIDA regulatory network enables an initial fast response to the light and subsequently prevents an overresponse to the initial light trigger, thus optimizing the seedling deetiolation process. Collectively, the data suggest that at least part of the phy/PIF system acts through these four MIDAs to initiate and optimize seedling deetiolation, and that this mechanism might allow the implementation of spatial (i.e., organ-specific) and temporal responses during the photomorphogenic program.
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Affiliation(s)
- Maria Sentandreu
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Guiomar Martín
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Nahuel González-Schain
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo Leivar
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Judit Soy
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - James M. Tepperman
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- United States Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720
- United States Department of Agriculture, Plant Gene Expression Center, Albany, California 94710
| | - Elena Monte
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics, Centro Superior de Investigaciones Científicas-Institut de Recerca i Tecnologia Agroalimentàries-Universitat Autònoma de Barcelona-Universitat de Barcelona, Campus Universitat Autonoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- Address correspondence to
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227
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Iwamoto M, Kiyota S, Hanada A, Yamaguchi S, Takano M. The multiple contributions of phytochromes to the control of internode elongation in rice. PLANT PHYSIOLOGY 2011; 157:1187-95. [PMID: 21911595 PMCID: PMC3252144 DOI: 10.1104/pp.111.184861] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/05/2011] [Accepted: 09/09/2011] [Indexed: 05/18/2023]
Abstract
Although phyAphyBphyC phytochrome-null mutants in rice (Oryza sativa) have morphological changes and exhibit internode elongation, even as seedlings, it is unknown how phytochromes contribute to the control of internode elongation. A gene for 1-aminocyclopropane-1-carboxylate oxidase (ACO1), which is an ethylene biosynthesis gene contributing to internode elongation, was up-regulated in phyAphyBphyC seedlings. ACO1 expression was controlled mainly by phyA and phyB, and a histochemical analysis showed that ACO1 expression was localized to the basal parts of leaf sheaths of phyAphyBphyC seedlings, similar to mature wild-type plants at the heading stage, when internode elongation was greatly promoted. In addition, the transcription levels of several ethylene- or gibberellin (GA)-related genes were changed in phyAphyBphyC mutants, and measurement of the plant hormone levels indicated low ethylene production and bioactive GA levels in the phyAphyBphyC mutants. We demonstrate that ethylene induced internode elongation and ACO1 expression in phyAphyBphyC seedlings but not in the wild type and that the presence of bioactive GAs was necessary for these effects. These findings indicate that phytochromes contribute to multiple steps in the control of internode elongation, such as the expression of the GA biosynthesis gene OsGA3ox2, ACO1 expression, and the onset of internode elongation.
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Affiliation(s)
- Masao Iwamoto
- Division of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
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228
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Ulijasz AT, Vierstra RD. Phytochrome structure and photochemistry: recent advances toward a complete molecular picture. CURRENT OPINION IN PLANT BIOLOGY 2011; 14:498-506. [PMID: 21733743 DOI: 10.1016/j.pbi.2011.06.002] [Citation(s) in RCA: 53] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2011] [Revised: 06/14/2011] [Accepted: 06/14/2011] [Indexed: 05/31/2023]
Abstract
Phytochromes are nature's primary photoreceptors dedicated to detecting the red and far-red regions of the visible light spectrum, a region also essential for photosynthesis and thus crucial to the survival of plants and other photosynthetic organisms. Given their roles in measuring competition and diurnal/seasonal light fluctuations, understanding how phytochromes work at the molecular level would greatly aid in engineering crop plants better suited to specific agricultural settings. Recently, scientists have determined the three-dimensional structures of prokaryotic phytochromes, which now provide clues as to how these modular photoreceptors might work at the atomic level. The models point toward a largely unifying mechanism whereby novel knot, hairpin, and dimeric interfaces transduce photoreversible bilin isomerization into protein conformational changes that alter signal output.
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Affiliation(s)
- Andrew T Ulijasz
- Department of Biological Sciences, 3209 North Maryland Avenue, University of Wisconsin-Milwaukee, Milwaukee, WI 53211, USA.
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229
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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: 234] [Impact Index Per Article: 18.0] [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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Holtan HE, Bandong S, Marion CM, Adam L, Tiwari S, Shen Y, Maloof JN, Maszle DR, Ohto MA, Preuss S, Meister R, Petracek M, Repetti PP, Reuber TL, Ratcliffe OJ, Khanna R. BBX32, an Arabidopsis B-Box protein, functions in light signaling by suppressing HY5-regulated gene expression and interacting with STH2/BBX21. PLANT PHYSIOLOGY 2011; 156:2109-23. [PMID: 21632973 PMCID: PMC3149924 DOI: 10.1104/pp.111.177139] [Citation(s) in RCA: 103] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2011] [Accepted: 05/30/2011] [Indexed: 05/18/2023]
Abstract
A B-box zinc finger protein, B-BOX32 (BBX32), was identified as playing a role in determining hypocotyl length during a large-scale functional genomics study in Arabidopsis (Arabidopsis thaliana). Further analysis revealed that seedlings overexpressing BBX32 display elongated hypocotyls in red, far-red, and blue light, along with reduced cotyledon expansion in red light. Through comparative analysis of mutant and overexpression line phenotypes, including global expression profiling and growth curve studies, we demonstrate that BBX32 acts antagonistically to ELONGATED HYPOCOTYL5 (HY5). We further show that BBX32 interacts with SALT TOLERANCE HOMOLOG2/BBX21, another B-box protein previously shown to interact with HY5. Based on these data, we propose that BBX32 functions downstream of multiple photoreceptors as a modulator of light responses. As such, BBX32 potentially has a native role in mediating gene repression to maintain dark adaptation.
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231
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Li Y, Swaminathan K, Hudson ME. Rapid, organ-specific transcriptional responses to light regulate photomorphogenic development in dicot seedlings. PLANT PHYSIOLOGY 2011; 156:2124-40. [PMID: 21653191 PMCID: PMC3149948 DOI: 10.1104/pp.111.179416] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/06/2011] [Accepted: 05/31/2011] [Indexed: 05/20/2023]
Abstract
The dicotyledon seedling undergoes organ-specific photomorphogenic development when exposed to light. The cotyledons open and expand, the apical hook opens, and the hypocotyl ceases to elongate. Using the large and easily dissected seedlings of soybean (Glycine max 'Williams 82'), we show that genes involved in photosynthesis and its regulation dominate transcripts specific to the cotyledon, even in etiolated seedlings. Genes for cell wall biosynthesis and metabolism are expressed at higher levels in the hypocotyl, while examination of genes expressed at higher levels in the hook region (including the shoot apical meristem) reveals genes involved in cell division and protein turnover. The early transcriptional events in these three organs in response to a 1-h treatment of far-red light are highly distinctive. Not only are different regulatory genes rapidly regulated by light in each organ, but the early-responsive genes in each organ contain a distinctive subset of known light-responsive cis-regulatory elements. We detected specific light-induced gene expression for the root phototropism gene RPT2 in the apical hook and also phenotypes in Arabidopsis (Arabidopsis thaliana) rpt2 mutants demonstrating that the gene is necessary for normal photomorphogenesis in the seedling apex. Significantly, expression of the RPT2 promoter fused to a β-glucuronidase reporter gene shows differential expression across the hook region. We conclude that organ-specific, light-responsive transcriptional networks are active early in photomorphogenesis in the aerial parts of dicotyledon seedlings.
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Affiliation(s)
| | | | - Matthew E. Hudson
- Department of Crop Sciences (Y.L., K.S., M.E.H.) and Energy Biosciences Institute and Institute for Genomic Biology (K.S., M.E.H.), University of Illinois at Urbana-Champaign, Urbana, Illinois 61801
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232
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Vierstra RD, Zhang J. Phytochrome signaling: solving the Gordian knot with microbial relatives. TRENDS IN PLANT SCIENCE 2011; 16:417-426. [PMID: 21719341 DOI: 10.1016/j.tplants.2011.05.011] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/23/2011] [Revised: 05/23/2011] [Accepted: 05/25/2011] [Indexed: 05/28/2023]
Abstract
Phytochromes encompass a diverse collection of biliproteins that regulate numerous photoresponses in plants and microorganisms. Whereas the plant versions have proven experimentally intractable for structural studies, the microbial forms have recently provided important insights into how these photoreceptors work at the atomic level. Here, we review the current understanding of these microbial phytochromes, which shows that they have a modular dimeric architecture that propagates light-driven rotation of the bilin to distal contacts between adjacent signal output domains. Surprising features underpinning this signaling include: a deeply buried chromophore; a knot and hairpin loop that stabilizes the photosensing domain; and an extended helical spine that translates conformational changes in the photosensing domain to the output domain. Conservation within the superfamily both in modular construction and sequence strongly suggests that higher plant phytochromes work similarly as light-regulated toggle switches.
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Affiliation(s)
- Richard D Vierstra
- Department of Genetics, 425-G Henry Mall, University of Wisconsin-Madison, Madison, WI 53706, USA.
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Yoo J, Shin DH, Cho MH, Kim TL, Bhoo SH, Hahn TR. An ankyrin repeat protein is involved in anthocyanin biosynthesis in Arabidopsis. PHYSIOLOGIA PLANTARUM 2011; 142:314-325. [PMID: 21395597 DOI: 10.1111/j.1399-3054.2011.01468.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/30/2023]
Abstract
The ankyrin domain is one of the most common protein motifs in eukaryotic proteins. Repeated ankyrin domains are ubiquitous and their mediation of protein-protein interactions is involved in a number of physiological and developmental responses such as the cell cycle, signal transduction and cell differentiation. A novel putative phytochrome-interacting ankyrin repeat protein 2 (PIA2) containing three repeated ankyrin domains was identified in Arabidopsis. An in vitro pull-down and phosphorylation assay revealed that PIA2 is phosphorylated and interacts directly with oat phytochrome A. The N-terminal domain of PIA2 was specifically phosphorylated, whereas interactions between the domains of PIA2 and phytochrome A had no Pr/Pfr preference. PIA2 was ubiquitously expressed in most tissues and was localized in both the nucleus and the cytoplasm independent of treatment with light of specific wavelengths. Anthocyanin accumulation in seedlings grown under far-red light, a typical phenotype of wild-type plants, was reduced in a loss-of-function mutant of PIA2 (pia2), whereas anthocyanin accumulation was increased in an overexpressing plant (PIA2-OX). The gene expression of UDP-flavonoid-3'-glucosyl-transferase (UF3GT), a major enzyme in the anthocyanin biosynthesis processes, was decreased in pia2 knockout plants suggesting that decreased anthocyanin was because of the decreased expression of UF3GT. Our results suggest that PIA2 plays a role in the anthocyanin biosynthesis during seedling development as a novel phytochrome-interacting protein.
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Affiliation(s)
- Jihye Yoo
- Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701, Korea
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234
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Xie XZ, Xue YJ, Zhou JJ, Zhang B, Chang H, Takano M. Phytochromes regulate SA and JA signaling pathways in rice and are required for developmentally controlled resistance to Magnaporthe grisea. MOLECULAR PLANT 2011; 4:688-96. [PMID: 21357645 DOI: 10.1093/mp/ssr005] [Citation(s) in RCA: 77] [Impact Index Per Article: 5.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/03/2023]
Abstract
Old leaves of wild-type rice plants (Oryza sativa L. cv. Nipponbare) are more resistant to blast fungus (Magnaporthe grisea) than new leaves. In contrast, both old and new leaves of the rice phytochrome triple mutant (phyAphyBphyC) are susceptible to blast fungus. We demonstrate that pathogenesis-related class 1 (PR1) proteins are rapidly and strongly induced during M. grisea infection and following exogenous jasmonate (JA) or salicylic acid (SA) exposure in the old leaves, but not in the new leaves of the wild-type. In contrast, the accumulation of PR1 proteins was significantly attenuated in old and new leaves of the phyAphyBphyC mutant. These results suggest that phytochromes are required for the induction of PR1 proteins in rice. Basal transcription levels of PR1a and PR1b were substantially higher in the wild-type as compared to the phyAphyBphyC mutant, suggesting that phytochromes also are required for basal expression of PR1 genes. Moreover, the transcript levels of genes known to function in SA- or JA-dependent defense pathways were regulated by leaf age and functional phytochromes. Taken together, our findings demonstrate that phytochromes are required in rice for age-related resistance to M. grisea and may indirectly increase PR1 gene expression by regulating SA- and JA-dependent defense pathways.
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Affiliation(s)
- Xian-Zhi Xie
- High-Tech Research Center, Shandong Academy of Agricultural Sciences, Jinan 250100, PR China.
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235
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Lian HL, He SB, Zhang YC, Zhu DM, Zhang JY, Jia KP, Sun SX, Li L, Yang HQ. Blue-light-dependent interaction of cryptochrome 1 with SPA1 defines a dynamic signaling mechanism. Genes Dev 2011; 25:1023-8. [PMID: 21511872 DOI: 10.1101/gad.2025111] [Citation(s) in RCA: 237] [Impact Index Per Article: 18.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Cryptochromes (CRYs) are blue-light photoreceptors that mediate various light responses in plants and animals. The signaling mechanism by which CRYs regulate light responses involves their physical interactions with COP1. Here, we report that CRY1 interacts physically with SPA1 in a blue-light-dependent manner. SPA acts genetically downstream from CRYs to regulate light-controlled development. Blue-light activation of CRY1 attenuates the association of COP1 with SPA1 in both yeast and plant cells. These results indicate that the blue-light-triggered CRY1-SPA1 interaction may negatively regulate COP1, at least in part, by promoting the dissociation of COP1 from SPA1. This interaction and consequent dissociation define a dynamic photosensory signaling mechanism.
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Affiliation(s)
- Hong-Li Lian
- Plant Science Institute, School of Agriculture and Biology, Shanghai Jiaotong University, Shanghai, China
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236
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Galstyan A, Cifuentes-Esquivel N, Bou-Torrent J, Martinez-Garcia JF. The shade avoidance syndrome in Arabidopsis: a fundamental role for atypical basic helix-loop-helix proteins as transcriptional cofactors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2011; 66:258-67. [PMID: 21205034 DOI: 10.1111/j.1365-313x.2011.04485.x] [Citation(s) in RCA: 66] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The shade avoidance syndrome (SAS) refers to a set of plant responses aimed at anticipating eventual shading by potential competitors. The SAS is initiated after perception of nearby vegetation as a reduction in the red to far-red ratio (R:FR) of the incoming light. Low R:FR light is perceived by the phytochromes, triggering dramatic changes in gene expression that, in seedlings, eventually result in an increased hypocotyl elongation to overgrow competitors. This response is inhibited by genes such as PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), PAR2 and LONG HYPOCOTYL IN FR 1 (HFR1), which are transcriptionally induced by low R:FR. Although PAR1/PAR2 and HFR1 proteins belong to different groups of basic helix-loop-helix (bHLH) transcriptional regulators, they all lack a typical basic domain required for binding to E-box and G-box motifs in the promoter of target genes. By overexpressing derivatives of PAR1 and HFR1 we show that these proteins are actually transcriptional cofactors that do not need to bind DNA to directly regulate transcription. We conclude that protein-protein interactions involving the HLH domain of PAR1 and HFR1 are a fundamental aspect of the mechanism by which these proteins regulate gene expression, most likely through interaction with true transcription factors that do bind to the target genes and eventually unleash the observed SAS responses.
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Affiliation(s)
- Anahit Galstyan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB, 08034-Barcelona, Spain
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237
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Peschke F, Kretsch T. Genome-wide analysis of light-dependent transcript accumulation patterns during early stages of Arabidopsis seedling deetiolation. PLANT PHYSIOLOGY 2011; 155:1353-66. [PMID: 21220763 PMCID: PMC3046591 DOI: 10.1104/pp.110.166801] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2010] [Accepted: 01/07/2011] [Indexed: 05/18/2023]
Abstract
Light is among the most important exogenous factors that regulate plant development. To sense light quality, intensity, direction, and duration, plants have evolved multiple photoreceptors that enable the detection of photons from the ultraviolet B (UV-B) to the far-red spectrum. To study the effect of different light qualities on early gene expression, dark-grown Arabidopsis (Arabidopsis thaliana) seedlings were either irradiated with continuous far-red, red, or blue light or received pulses of red, UV-A, or UV-A/B light. The expression profiles of seedlings harvested at 45 min and 4 h were determined on a full genome level and compared with the profiles of dark controls. Data were used to identify light-regulated genes and to group these genes according to their light responses. While most of the genes were regulated by more than one light quality, a considerable number of UV-B-specific gene expression responses were obtained. An extraordinarily high similarity in gene expression patterns was obtained for samples that perceived continuous irradiation with either far-red or blue light for 4 h. Mutant analyses hint that this coincidence is caused by a convergence of the signaling cascades that regulate gene expression downstream of cryptochrome blue light photoreceptors and phytochrome A. Whereas many early light-regulated genes exhibited uniform responses to all applied light treatments, highly divergent expression patterns developed at 4 h. These data clearly indicate that light signaling during early deetiolation undergoes a switch from a rapid, but unspecific, response mode to regulatory systems that measure the spectral composition and duration of incident light.
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238
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Abstract
This mini-symposium aims to provide an integrated perspective on recent developments in optogenetics. Research in this emerging field combines optical methods with targeted expression of genetically encoded, protein-based probes to achieve experimental manipulation and measurement of neural systems with superior temporal and spatial resolution. The essential components of the optogenetic toolbox consist of two kinds of molecular devices: actuators and reporters, which respectively enable light-mediated control or monitoring of molecular processes. The first generation of genetically encoded calcium reporters, fluorescent proteins, and neural activators has already had a great impact on neuroscience. Now, a second generation of voltage reporters, neural silencers, and functionally extended fluorescent proteins hold great promise for continuing this revolution. In this review, we will evaluate and highlight the limitations of presently available optogenic tools and discuss where these technologies and their applications are headed in the future.
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239
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Rodriguez-Romero J, Hedtke M, Kastner C, Müller S, Fischer R. Fungi, hidden in soil or up in the air: light makes a difference. Annu Rev Microbiol 2010; 64:585-610. [PMID: 20533875 DOI: 10.1146/annurev.micro.112408.134000] [Citation(s) in RCA: 166] [Impact Index Per Article: 11.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Light is one of the most important environmental factors for orientation of almost all organisms on Earth. Whereas light sensing is of crucial importance in plants to optimize light-dependent energy conservation, in nonphotosynthetic organisms, the synchronization of biological clocks to the length of a day is an important function. Filamentous fungi may use the light signal as an indicator for the exposure of hyphae to air and adapt their physiology to this situation or induce morphogenetic pathways. Although a yes/no decision appears to be sufficient for the light-sensing function in fungi, most species apply a number of different, wavelength-specific receptors. The core of all receptor types is a chromophore, a low-molecular-weight organic molecule, such as flavin, retinal, or linear tetrapyrrols for blue-, green-, or red-light sensing, respectively. Whereas the blue-light response in fungi is one of the best-studied light responses, all other light-sensing mechanisms are less well studied or largely unknown. The discovery of phytochrome in bacteria and fungi in recent years not only advanced the scientific field significantly, but also had great impact on our view of the evolution of phytochrome-like photoreceptors.
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Affiliation(s)
- Julio Rodriguez-Romero
- Karlsruhe Institute of Technology, Institute for Applied Biosciences, Department of Microbiology, D-76187 Karlsruhe, Germany
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240
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Kaminski S, Mroginski MA. Molecular Dynamics of Phycocyanobilin Binding Bacteriophytochromes: A Detailed Study of Structural and Dynamic Properties. J Phys Chem B 2010; 114:16677-86. [DOI: 10.1021/jp104903u] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Affiliation(s)
- Steve Kaminski
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
| | - Maria Andrea Mroginski
- Technische Universität Berlin, Institut für Chemie, Max-Volmer-Laboratorium, Sekr. PC 14, Strasse des 17. Juni 135, D-10623 Berlin, Germany
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241
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Salinas-Mondragon RE, Kajla JD, Perera IY, Brown CS, Sederoff HW. Role of inositol 1,4,5-triphosphate signalling in gravitropic and phototropic gene expression. PLANT, CELL & ENVIRONMENT 2010; 33:2041-55. [PMID: 20584147 DOI: 10.1111/j.1365-3040.2010.02204.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Plants sense light and gravity to orient their direction of growth. One common component in the early events of both phototropic and gravitropic signal transduction is activation of phospholipase C (PLC), which leads to an increase in inositol 1,4,5-triphosphate (InsP(3)) levels. The InsP(3) signal is terminated by hydrolysis of InsP(3) through inositolpolyphosphate-5-phosphatases (InsP 5-ptases). Arabidopsis plants expressing a heterologous InsP 5-ptase have low basal InsP(3) levels and exhibit reduced gravitropic and phototropic bending. Downstream effects of InsP(3)-mediated signalling are not understood. We used comparative transcript profiling to characterize gene expression changes in gravity- or light-stimulated Arabidopsis root apices that were manipulated in their InsP(3) metabolism either through inhibition of PLC activity or expression of InsP 5-ptase. We identified InsP(3)-dependent and InsP(3)-independent co-regulated gene sets in response to gravity or light stimulation. Inhibition of PLC activity in wild-type plants caused similar changes in transcript abundance in response to gravitropic and phototropic stimulation as in the transgenic lines. Therefore, we conclude that changes in gene expression in response to gravitropic and phototropic stimulation are mediated by two signal transduction pathways that vary in their dependence on changes in InsP(3).
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242
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Samma AA, Johnson CK, Song S, Alvarez S, Zimmer M. On the origin of fluorescence in bacteriophytochrome infrared fluorescent proteins. J Phys Chem B 2010; 114:15362-9. [PMID: 21047084 DOI: 10.1021/jp107119q] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Abstract
Tsien et al. (Science, 2009, 324, 804-807) recently reported the creation of the first infrared fluorescent protein (IFP). It was engineered from bacterial phytochrome by removing the PHY and histidine kinase-related domains, by optimizing the protein to prevent dimerization, and by limiting the biliverdins conformational freedom, especially around its D ring. We have used database analyses and molecular dynamics simulations with freely rotating chromophoric dihedrals in order to model the dihedral freedom available to the biliverdin D ring in the excited state and to show that the tetrapyrrole ligands in phytochromes are flexible and can adopt many conformations; however, their conformational space is limited/defined by the chemospatial characteristics of the protein cavity. Our simulations confirm that the reduced accessibility to conformations geared to an excited state proton transfer may be responsible for the fluorescence in IFP, just as has been suggested by Kennis et al. (Proc. Natl. Acad. Sci. U.S.A., 2010, 107, 9170-9175) for fluorescent bacteriophytochrome from Rhodopseudomonas palustris.
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Affiliation(s)
- Alex A Samma
- Chemistry Department, Connecticut College, New London, CT 06320, USA
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243
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Li J, Li G, Gao S, Martinez C, He G, Zhou Z, Huang X, Lee JH, Zhang H, Shen Y, Wang H, Deng XW. Arabidopsis transcription factor ELONGATED HYPOCOTYL5 plays a role in the feedback regulation of phytochrome A signaling. THE PLANT CELL 2010; 22:3634-49. [PMID: 21097709 PMCID: PMC3015127 DOI: 10.1105/tpc.110.075788] [Citation(s) in RCA: 131] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/13/2010] [Revised: 10/28/2010] [Accepted: 11/05/2010] [Indexed: 05/19/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor responsible for perceiving and mediating various responses to far-red light in Arabidopsis thaliana. FAR-RED ELONGATED HYPOCOTYL1 (FHY1) and its homolog FHY1-LIKE (FHL) are two small plant-specific proteins essential for light-regulated phyA nuclear accumulation and subsequent phyA signaling processes. FHY3 and its homolog FAR-RED IMPAIRED RESPONSE1 (FAR1) are two transposase-derived transcription factors that directly activate FHY1/FHL transcription and thus mediate subsequent phyA nuclear accumulation and responses. Here, we report that ELONGATED HYPOCOTYL5 (HY5), a well-characterized bZIP transcription factor involved in promoting photomorphogenesis, directly binds ACGT-containing elements a few base pairs away from the FHY3/FAR1 binding sites in the FHY1/FHL promoters. We demonstrate that HY5 physically interacts with FHY3/FAR1 through their respective DNA binding domains and negatively regulates FHY3/FAR1-activated FHY1/FHL expression under far-red light. Together, our data show that HY5 plays a role in negative feedback regulation of phyA signaling by attenuating FHY3/FAR1-activated FHY1/FHL expression, providing a mechanism for fine-tuning phyA signaling homeostasis.
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Affiliation(s)
- Jigang Li
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, 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
| | - Shumin Gao
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- College of Biological Sciences and Biotechnology, Beijing Forestry University, Beijing 100083, China
| | - Cristina Martinez
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Guangming He
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Zhenzhen Zhou
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Xi Huang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Jae-Hoon Lee
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Huiyong Zhang
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
| | - Yunping Shen
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- 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, National Laboratory of Protein Engineering and Plant Genetic Engineering, College of Life Sciences, Peking University, Beijing 100871, China
- Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Connecticut 06520-8104
- Address correspondence to
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244
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Spotlight on Aspergillus nidulans photosensory systems. Fungal Genet Biol 2010; 47:900-8. [DOI: 10.1016/j.fgb.2010.05.008] [Citation(s) in RCA: 127] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2010] [Revised: 05/09/2010] [Accepted: 05/19/2010] [Indexed: 12/14/2022]
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245
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Shin DH, Cho MH, Kim TL, Yoo J, Kim JI, Han YJ, Song PS, Jeon JS, Bhoo SH, Hahn TR. A small GTPase activator protein interacts with cytoplasmic phytochromes in regulating root development. J Biol Chem 2010; 285:32151-9. [PMID: 20551316 PMCID: PMC2952216 DOI: 10.1074/jbc.m110.133710] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2010] [Revised: 06/14/2010] [Indexed: 11/06/2022] Open
Abstract
Phytochromes enable plants to sense light information and regulate developmental responses. Phytochromes interact with partner proteins to transmit light signals to downstream components for plant development. PIRF1 (phytochrome-interacting ROP guanine-nucleotide exchange factor (RopGEF 1)) functions as a light-signaling switch regulating root development through the activation of ROPs (Rho-like GTPase of plant) in the cytoplasm. In vitro pulldown and yeast two-hybrid assays confirmed the interaction between PIRF1 and phytochromes. PIRF1 interacted with the N-terminal domain of phytochromes through its conserved PRONE (plant-specific ROP nucleotide exchanger) region. PIRF1 also interacted with ROPs and activated them in a phytochrome-dependent manner. The Pr form of phytochrome A enhanced the RopGEF activity of PIRF1, whereas the Pfr form inhibited it. A bimolecular fluorescence complementation analysis demonstrated that PIRF1 was localized in the cytoplasm and bound to the phytochromes in darkness but not in light. PIRF1 loss of function mutants (pirf1) of Arabidopsis thaliana showed a longer root phenotype in the dark. In addition, both PIRF1 overexpression mutants (PIRF1-OX) and phytochrome-null mutants (phyA-211 and phyB-9) showed retarded root elongation and irregular root hair formation, suggesting that PIRF1 is a negative regulator of phytochrome-mediated primary root development. We propose that phytochrome and ROP signaling are interconnected through PIRF1 in regulating the root growth and development in Arabidopsis.
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Affiliation(s)
- Dong Ho Shin
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Man-Ho Cho
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Tae-Lim Kim
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Jihye Yoo
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Jeong-Il Kim
- the Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, and
| | - Yun-Jeong Han
- the Department of Biotechnology and Kumho Life Science Laboratory, Chonnam National University, Gwangju 500-757, and
| | - Pill-Soon Song
- the Faculty of Biotechnology, Jeju National University, Jeju 690-756, Korea
| | - Jong-Seong Jeon
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Seong Hee Bhoo
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
| | - Tae-Ryong Hahn
- From the Graduate School of Biotechnology and Plant Metabolism Research Center, Kyung Hee University, Yongin 446-701
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246
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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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247
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Debrieux D, Fankhauser C. Light-induced degradation of phyA is promoted by transfer of the photoreceptor into the nucleus. PLANT MOLECULAR BIOLOGY 2010; 73:687-695. [PMID: 20473552 DOI: 10.1007/s11103-010-9649-9] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2009] [Accepted: 05/03/2010] [Indexed: 05/29/2023]
Abstract
Higher plants possess multiple members of the phytochrome family of red, far-red light sensors to modulate plant growth and development according to competition from neighbors. The phytochrome family is composed of the light-labile phyA and several light-stable members (phyB-phyE in Arabidopsis). phyA accumulates to high levels in etiolated seedlings and is essential for young seedling establishment under a dense canopy. In photosynthetically active seedlings high levels of phyA counteract the shade avoidance response. phyA levels are maintained low in light-grown plants by a combination of light-dependent repression of PHYA transcription and light-induced proteasome-mediated degradation of the activated photoreceptor. Light-activated phyA is transported from the cytoplasm where it resides in darkness to the nucleus where it is needed for most phytochrome-induced responses. Here we show that phyA is degraded by a proteasome-dependent mechanism both in the cytoplasm and the nucleus. However, phyA degradation is significantly slower in the cytoplasm than in the nucleus. In the nucleus phyA is degraded in a proteasome-dependent mechanism even in its inactive Pr (red light absorbing) form, preventing the accumulation of high levels of nuclear phyA in darkness. Thus, light-induced degradation of phyA is in part controlled by a light-regulated import into the nucleus where the turnover is faster. Although most phyA responses require nuclear phyA it might be useful to maintain phyA in the cytoplasm in its inactive form to allow accumulation of high levels of the light sensor in etiolated seedlings.
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Affiliation(s)
- Dimitry Debrieux
- Center for Integrative Genomics, Faculty of Biology and Medicine, University of Lausanne, Genopode Building, 1015 Lausanne, Switzerland
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248
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Riggsbee CW, Deiters A. Recent advances in the photochemical control of protein function. Trends Biotechnol 2010; 28:468-75. [PMID: 20667607 DOI: 10.1016/j.tibtech.2010.06.001] [Citation(s) in RCA: 105] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2010] [Revised: 05/21/2010] [Accepted: 06/01/2010] [Indexed: 12/20/2022]
Abstract
Biological processes are regulated with a high level of spatial and temporal resolution. To understand and manipulate these processes, scientists need to be able to regulate them with Nature's level of precision. In this context, light is a unique regulatory element because it can be precisely controlled in terms of location, timing and amplitude. Moreover, most biological laboratories have a wide range of light sources as standard equipment. This review article summarizes the most recent advances in light-mediated regulation of protein function and its application in a cellular context. Specifically, the photocaging of small-molecule modulators of protein function and of specific amino acid residues in proteins is discussed. In addition, examples of the photochemical control of protein function through the application of genetically engineered natural-light receptors are presented.
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Affiliation(s)
- Chad W Riggsbee
- Department of Chemistry, North Carolina State University, Raleigh, NC 27607, USA
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249
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Lindlöf A. Interplay between low-temperature pathways and light reduction. PLANT SIGNALING & BEHAVIOR 2010; 5:820-5. [PMID: 20484978 PMCID: PMC3115030 DOI: 10.4161/psb.5.7.11701] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/04/2010] [Accepted: 03/04/2010] [Indexed: 05/29/2023]
Abstract
Low temperature is one of the major factors that adversely affect crop yields by causing restraints on plant growth and productivity. However, most temperate plants have the ability to acclimate to cooler temperatures. Cold acclimation is a process which increases the freezing tolerance of an organism after exposure to low, non-freezing temperatures. The main trigger is a decrease in temperature levels, but light reduction has also been shown to have an important impact on acquired tolerance. Since the lowest temperatures are commonly reached during the night hours in winter time and is an annually recurring event, a favorable trait for plants is the possibility of sensing an imminent cold period. Consequently, extensive crosstalk between light- and temperature signaling pathways has been demonstrated and in this review interesting interaction points that have been previously reported in the literature are highlighted.
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Affiliation(s)
- Angelica Lindlöf
- Systems Biology Research Centre, School of Life Sciences, University of Skövde, Skövde, Sweden.
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Lee YS, Jeong DH, Lee DY, Yi J, Ryu CH, Kim SL, Jeong HJ, Choi SC, Jin P, Yang J, Cho LH, Choi H, An G. OsCOL4 is a constitutive flowering repressor upstream of Ehd1 and downstream of OsphyB. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2010; 63:18-30. [PMID: 20409004 DOI: 10.1111/j.1365-313x.2010.04226.x] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plants recognize environmental factors to determine flowering time. CONSTANS (CO) plays a central role in the photoperiod flowering pathway of Arabidopsis, and CO protein stability is modulated by photoreceptors. In rice, Hd1, an ortholog of CO, acts as a flowering promoter, and phytochromes repress Hd1 expression. Here, we investigated the functioning of OsCOL4, a member of the CONSTANS-like (COL) family in rice. OsCOL4 null mutants flowered early under short or long days. In contrast, OsCOL4 activation-tagging mutants (OsCOL4-D) flowered late in either environment. Transcripts of Ehd1, Hd3a, and RFT1 were increased in the oscol4 mutants, but reduced in the OsCOL4-D mutants. This finding indicates that OsCOL4 is a constitutive repressor functioning upstream of Ehd1. By comparison, levels of Hd1, OsID1, OsMADS50, OsMADS51, and OsMADS56 transcripts were not significantly changed in oscol4 or OsCOL4-D, suggesting that OsCOL4 functions independently from previously reported flowering pathways. In osphyB mutants, OsCOL4 expression was decreased and osphyB oscol4 double mutants flowered at the same time as the osphyB single mutants, indicating OsCOL4 functions downstream of OsphyB. We also present evidence for two independent pathways through which OsPhyB controls flowering time. These pathways are: (i) night break-sensitive, which does not need OsCOL4; and (ii) night break-insensitive, in which OsCOL4 functions between OsphyB and Ehd1.
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Affiliation(s)
- Yang-Seok Lee
- Department of Life Science, Pohang University of Science and Technology (POSTECH), Pohang 790-784, Korea
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