1
|
Peng KC, Siao W, Hsieh HL. FAR-RED INSENSITIVE 219 and phytochrome B corepress shade avoidance via modulating nuclear speckle formation. PLANT PHYSIOLOGY 2023; 192:1449-1465. [PMID: 36869668 PMCID: PMC10231371 DOI: 10.1093/plphys/kiad103] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2022] [Revised: 11/22/2022] [Accepted: 11/22/2022] [Indexed: 06/01/2023]
Abstract
Plants can sense the shade from neighboring plants by detecting a reduction of the red:far-red light (R:FR) ratio. Phytochrome B (phyB) is the primary photoreceptor that perceives shade light and regulates jasmonic acid (JA) signaling. However, the molecular mechanisms underlying phyB and JA signaling integration in shade responses remain largely unknown. Here, we show the interaction of phyB and FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT1 (JAR1) in a functional demand manner in Arabidopsis (Arabidopsis thaliana) seedling development. Genetic evidence and interaction studies indicated that phyB and FIN219 synergistically and negatively regulate shade-induced hypocotyl elongation. Moreover, phyB interacted with various isoforms of FIN219 under high and low R:FR light. Methyl jasmonate (MeJA) treatment, FIN219 mutation, and PHYBOE digalactosyldiacylglycerol synthase1-1 (dgd1-1) plants, which show increased levels of JA, altered the patterns of phyB-associated nuclear speckles under the same conditions. Surprisingly, PHYBOE dgd1-1 showed a shorter hypocotyl phenotype than its parental mutants under shade conditions. Microarray assays using PHYBOE and PHYBOE fin219-2 indicated that PHYB overexpression substantially affects defense response-related genes under shade light and coregulates expression of auxin-responsive genes with FIN219. Thus, our findings reveal that phyB substantially crosstalks with JA signaling through FIN219 to modulate seedling development under shade light.
Collapse
Affiliation(s)
- Kai-Chun Peng
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
| | - Wei Siao
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Department of Plant Biotechnology and Bioinformatics, Ghent University, 9052 Ghent, Belgium
- Center for Plant Systems Biology, VIB, 9052 Ghent, Belgium
| | - Hsu-Liang Hsieh
- Institute of Plant Biology, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Department of Life Science, College of Life Science, National Taiwan University, Taipei 106, Taiwan
- Master Program in Global Agriculture Technology and Genomic Science, National Taiwan University, Taipei 106, Taiwan
| |
Collapse
|
2
|
Singh S, Vergish S, Jain N, Sharma AK, Khurana P, Khurana JP. OsCRY2 and OsFBO10 co-regulate photomorphogenesis and photoperiodic flowering in indica rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2023; 330:111631. [PMID: 36773757 DOI: 10.1016/j.plantsci.2023.111631] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Revised: 02/02/2023] [Accepted: 02/04/2023] [Indexed: 06/18/2023]
Abstract
Cryptochromes (CRYs) are a class of photoreceptors that perceive blue/ultraviolet-A light of the visible spectrum to mediate a vast number of physiological responses in bacteria, fungi, animals and plants. In the present study, we have characterized OsCRY2 in a photoperiod sensitive indica variety, Basmati 370, by generating and analyzing overexpression (OE) and knock-down (KD) transgenic lines. The OsCRY2OE lines displayed dwarfism as shown in their reduced plant height and leaf length, attributed largely by an overall reduction in their cell size. The OsCRY2OE lines flowered significantly earlier and showed shorter and broader seeds with an overall reduced seed weight. The OsCRY2KD lines showed contrasting phenotypes, such as increased plant height and delayed flowering, however, decreased seed size and weight were also observed in the KD lines, along with reduced spikelet fertility and high seed shattering rate in mature panicles. Novel interactions were confirmed between OsCRY2 and members of ZEITLUPE family of blue/ultraviolet-A light photoreceptors, encoded by OsFBO8, OsFBO9 and OsFBO10 which are orthologous to ZEITLUPE (ZTL), LOV KELCH PROTEIN2 (LKP2) and FLAVIN BINDING, KELCH REPEAT F-BOX1 (FKF1), respectively, of Arabidopsis thaliana. Since FKF1 is known to play a role in regulating photoperiodic flowering, OsFBO10 was chosen for further studies. OsCRY2 and OsFBO10 interacted in the nucleus and cytoplasm of the cell and cross-regulated the expression of each other. They were also found to regulate the expression of several genes involved in photoperiodic flowering in rice. Both OsCRY2 and OsFBO10 played a positive role in photomorphogenic responses in different light conditions. The physical interaction of OsCRY2 with OsFBO10, their involvement in common physiological and developmental pathways and their cross-regulation of each other suggest that the two photoreceptors may regulate common developmental pathways in plants, either jointly or redundantly.
Collapse
Affiliation(s)
- Shipra Singh
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Satyam Vergish
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Nitin Jain
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Arun Kumar Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| | - Paramjit Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India.
| | - Jitendra P Khurana
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi, South Campus, New Delhi 110021, India
| |
Collapse
|
3
|
Li Z, Sheerin DJ, von Roepenack-Lahaye E, Stahl M, Hiltbrunner A. The phytochrome interacting proteins ERF55 and ERF58 repress light-induced seed germination in Arabidopsis thaliana. Nat Commun 2022; 13:1656. [PMID: 35351902 PMCID: PMC8964797 DOI: 10.1038/s41467-022-29315-3] [Citation(s) in RCA: 14] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2021] [Accepted: 03/07/2022] [Indexed: 11/20/2022] Open
Abstract
Seed germination is a critical step in the life cycle of plants controlled by the phytohormones abscisic acid (ABA) and gibberellin (GA), and by phytochromes, an important class of photoreceptors in plants. Here we show that light-dependent germination is enhanced in mutants deficient in the AP2/ERF transcription factors ERF55 and ERF58. Light-activated phytochromes repress ERF55/ERF58 expression and directly bind ERF55/ERF58 to displace them from the promoter of PIF1 and SOM, genes encoding transcriptional regulators that prevent the completion of germination. The same mechanism controls the expression of genes that encode ABA or GA metabolic enzymes to decrease levels of ABA and possibly increase levels of GA. Interestingly, ERF55 and ERF58 are themselves under transcriptional control of ABA and GA, suggesting that they are part of a self-reinforcing signalling loop which controls the completion of germination. Overall, we identified a role of ERF55/ERF58 in phytochrome-mediated regulation of germination completion.
Collapse
Affiliation(s)
- Zenglin Li
- grid.5963.9Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - David J. Sheerin
- grid.5963.9Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany
| | - Edda von Roepenack-Lahaye
- grid.10392.390000 0001 2190 1447Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Mark Stahl
- grid.10392.390000 0001 2190 1447Centre for Plant Molecular Biology, University of Tübingen, Tübingen, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, Germany. .,Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, Germany.
| |
Collapse
|
4
|
Ahn G, Jung IJ, Cha JY, Jeong SY, Shin GI, Ji MG, Kim MG, Lee SY, Kim WY. Phytochrome B Positively Regulates Red Light-Mediated ER Stress Response in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2022; 13:846294. [PMID: 35283886 PMCID: PMC8905361 DOI: 10.3389/fpls.2022.846294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Accepted: 02/02/2022] [Indexed: 06/14/2023]
Abstract
Light plays a crucial role in plant growth and development, and light signaling is integrated with various stress responses to adapt to different environmental changes. During this process, excessive protein synthesis overwhelms the protein-folding ability of the endoplasmic reticulum (ER), causing ER stress. Although crosstalk between light signaling and ER stress response has been reported in plants, the molecular mechanisms underlying this crosstalk are poorly understood. Here, we demonstrate that the photoreceptor phytochrome B (phyB) induces the expression of ER luminal protein chaperones as well as that of unfolded protein response (UPR) genes. The phyB-5 mutant was less sensitive to tunicamycin (TM)-induced ER stress than were the wild-type plants, whereas phyB-overexpressing plants displayed a more sensitive phenotype under white light conditions. ER stress response genes (BiP2 and BiP3), UPR-related bZIP transcription factors (bZIP17, bZIP28, and bZIP60), and programmed cell death (PCD)-associated genes (OXI1, NRP1, and MC8) were upregulated in phyB-overexpressing plants, but not in phyB-5, under ER stress conditions. The ER stress-sensitive phenotype of phyB-5 under red light conditions was eliminated with a reduction in photo-equilibrium by far-red light and darkness. The N-terminal domain of phyB is essential for signal transduction of the ER stress response in the nucleus, which is similar to light signaling. Taken together, our results suggest that phyB integrates light signaling with the UPR to relieve ER stress and maintain proper plant growth.
Collapse
Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - In Jung Jung
- National Institute of Wildlife Disease Control and Prevention (NIWDC), Ministry of Environment, Gwangju, South Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Myung Geun Ji
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| | - Min Gab Kim
- College of Pharmacy and Research Institute of Pharmaceutical Science, Gyeongsang National University, Jinju, South Korea
| | - Sang Yeol Lee
- Division of Applied Life Science (BK21 Four), Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, South Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21 Four), Institute of Agricultural and Life Science, Research Institute of Life Science, Gyeongsang National University, Jinju, South Korea
| |
Collapse
|
5
|
Schenk T, Trimborn L, Chen S, Schenkel C, Hoecker U. Light-induced degradation of SPA2 via its N-terminal kinase domain is required for photomorphogenesis. PLANT PHYSIOLOGY 2021; 187:276-288. [PMID: 33822236 PMCID: PMC8418447 DOI: 10.1093/plphys/kiab156] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/11/2020] [Accepted: 03/19/2021] [Indexed: 06/12/2023]
Abstract
Arabidopsis (Arabidopsis thaliana) CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1) and members of the SUPPRESSOR OF PHYTOCHROMEA-105 (SPA) protein family form an E3 ubiquitin ligase that suppresses light signaling in darkness by polyubiquitinating positive regulators of the light response. COP1/SPA is inactivated by light to allow photomorphogenesis to proceed. Mechanisms of inactivation include light-induced degradation of SPA1 and, in particular, SPA2, corresponding to a particularly efficient inactivation of COP1/SPA2 by light. Here, we show that SPA3 and SPA4 proteins are stable in the light, indicating that light-induced destabilization is specific to SPA1 and SPA2, possibly related to the predominant function of SPA1 and SPA2 in dark-grown etiolating seedlings. SPA2 degradation involves cullin and the COP10-DEETIOLATED-DAMAGED-DNA BINDING PROTEIN (DDB1) CDD complex, besides COP1. Consistent with this finding, light-induced SPA2 degradation required the DDB1-interacting Trp-Asp (WD)-repeat domain of SPA2. Deletion of the N-terminus of SPA2 containing the kinase domain led to strong stabilization of SPA2 in darkness and fully abolished light-induced degradation of SPA2. This prevented seedling de-etiolation even in very strong far-red and blue light and reduced de-etiolation in red light, indicating destabilization of SPA2 through its N-terminal domain is essential for light response. SPA2 is exclusively destabilized by phytochrome A in far-red and blue light. However, deletion of the N-terminal domain of SPA2 did not abolish SPA2-phytochrome A interaction in yeast nor in vivo. Our domain mapping suggests there are two SPA2-phytochrome A interacting domains, the N-terminal domain and the WD-repeat domain. Conferring a light-induced SPA2-phyA interaction only via the WD-repeat domain may thus not lead to COP1/SPA2 inactivation.
Collapse
Affiliation(s)
- Tobias Schenk
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, Cologne 50674, Germany
| | - Laura Trimborn
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, Cologne 50674, Germany
| | - Song Chen
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, Cologne 50674, Germany
| | - Christian Schenkel
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, Cologne 50674, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Str. 47b, Cologne 50674, Germany
| |
Collapse
|
6
|
Kahle N, Sheerin DJ, Fischbach P, Koch LA, Schwenk P, Lambert D, Rodriguez R, Kerner K, Hoecker U, Zurbriggen MD, Hiltbrunner A. COLD REGULATED 27 and 28 are targets of CONSTITUTIVELY PHOTOMORPHOGENIC 1 and negatively affect phytochrome B signalling. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1038-1053. [PMID: 32890447 DOI: 10.1111/tpj.14979] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2020] [Revised: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 05/23/2023]
Abstract
Phytochromes are red/far-red light receptors in plants involved in the regulation of growth and development. Phytochromes can sense the light environment and contribute to measuring day length; thereby, they allow plants to respond and adapt to changes in the ambient environment. Two well-characterized signalling pathways act downstream of phytochromes and link light perception to the regulation of gene expression. The CONSTITUTIVELY PHOTOMORPHOGENIC 1/SUPPRESSOR OF PHYA-105 (COP1/SPA) E3 ubiquitin ligase complex and the PHYTOCHROME INTERACTING FACTORs (PIFs) are key components of these pathways and repress light responses in the dark. In light-grown seedlings, phytochromes inhibit COP1/SPA and PIF activity and thereby promote light signalling. In a yeast-two-hybrid screen for proteins binding to light-activated phytochromes, we identified COLD-REGULATED GENE 27 (COR27). COR27 and its homologue COR28 bind to phyA and phyB, the two primary phytochromes in seed plants. COR27 and COR28 have been described previously with regard to a function in the regulation of freezing tolerance, flowering and the circadian clock. Here, we show that COR27 and COR28 repress early seedling development in blue, far-red and in particular red light. COR27 and COR28 contain a conserved Val-Pro (VP)-peptide motif, which mediates binding to the COP1/SPA complex. COR27 and COR28 are targeted for degradation by COP1/SPA and mutant versions with a VP to AA amino acid substitution in the VP-peptide motif are stabilized. Overall, our data suggest that COR27 and COR28 accumulate in light but act as negative regulators of light signalling during early seedling development, thereby preventing an exaggerated response to light.
Collapse
Affiliation(s)
- Nikolai Kahle
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - David J Sheerin
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Patrick Fischbach
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Leonie-Alexa Koch
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Philipp Schwenk
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Spemann Graduate School of Biology and Medicine (SGBM), University of Freiburg, Freiburg, 79104, Germany
| | - Dorothee Lambert
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Ryan Rodriguez
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
| | - Konstantin Kerner
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Ute Hoecker
- Institute for Plant Sciences, University of Cologne, Cologne, 50674, Germany
| | - Matias D Zurbriggen
- Institute of Synthetic Biology and CEPLAS, Heinrich Heine University Düsseldorf, Düsseldorf, 40225, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, Freiburg, 79104, Germany
- Signalling Research Centres BIOSS and CIBSS, University of Freiburg, Freiburg, 79104, Germany
| |
Collapse
|
7
|
Xu D, Marino G, Klingl A, Enderle B, Monte E, Kurth J, Hiltbrunner A, Leister D, Kleine T. Extrachloroplastic PP7L Functions in Chloroplast Development and Abiotic Stress Tolerance. PLANT PHYSIOLOGY 2019; 180:323-341. [PMID: 30760637 PMCID: PMC6501107 DOI: 10.1104/pp.19.00070] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2019] [Accepted: 02/05/2019] [Indexed: 05/18/2023]
Abstract
Chloroplast biogenesis is indispensable for proper plant development and environmental acclimation. In a screen for mutants affected in photosynthesis, we identified the protein phosphatase7-like (pp7l) mutant, which displayed delayed chloroplast development in cotyledons and young leaves. PP7L, PP7, and PP7-long constitute a subfamily of phosphoprotein phosphatases. PP7 is thought to transduce a blue-light signal perceived by crys and phy a that induces expression of SIGMA FACTOR5 (SIG5). We observed that, like PP7, PP7L was predominantly localized to the nucleus in Arabidopsis (Arabidopsis thaliana), and the pp7l phenotype was similar to that of the sig6 mutant. However, SIG6 expression was unaltered in pp7l mutants. Instead, loss of PP7L compromised translation and ribosomal RNA (rRNA) maturation in chloroplasts, pointing to a distinct mechanism influencing chloroplast development. Promoters of genes deregulated in pp7l-1 were enriched in PHYTOCHROME-INTERACTING FACTOR (PIF)-binding motifs and the transcriptome of pp7l-1 resembled those of pif and CONSTITUTIVE PHOTOMORPHOGENESIS1 (COP1) signalosome complex (csn) mutants. However, pif and csn mutants, as well as cop1, cryptochromes (cry)1 cry2, and phytochromes (phy)A phyB mutants, do not share the pp7l photosynthesis phenotype. PhyB protein levels were elevated in pp7l mutants, but phyB overexpression plants did not resemble pp7l These results indicate that PP7L operates through a different pathway and that the control of greening and photosystem biogenesis can be separated. The lack of PP7L increased susceptibility to salt and high-light stress, whereas PP7L overexpression conferred resistance to high-light stress. Strikingly, PP7L was specifically recruited to Brassicales for the regulation of chloroplast development. This study adds another player involved in chloroplast biogenesis.
Collapse
Affiliation(s)
- Duorong Xu
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Giada Marino
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas Klingl
- Plant Development, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Beatrix Enderle
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
| | - Elena Monte
- Plant Development and Signal Transduction Program, Center for Research in Agricultural Genomics Consejo Superior de Investigaciones Científicas-Institute of Agrifood Research and Technology-Universidad Autonoma de Barcelona-Universidad de Barcelona, 08193 Barcelona, Spain
| | - Joachim Kurth
- Plant Development, Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Andreas Hiltbrunner
- Institute of Biology II, Faculty of Biology, University of Freiburg, 79104, Freiburg, Germany
- Centre for Biological Signalling Studies (BIOSS), University of Freiburg, 79104 Freiburg, Germany
| | - Dario Leister
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| | - Tatjana Kleine
- Plant Molecular Biology (Botany), Department Biology I, Ludwig-Maximilians-Universität München, 82152 Planegg-Martinsried, Germany
| |
Collapse
|
8
|
Lim J, Park JH, Jung S, Hwang D, Nam HG, Hong S. Antagonistic Roles of PhyA and PhyB in Far-Red Light-Dependent Leaf Senescence in Arabidopsis thaliana. PLANT & CELL PHYSIOLOGY 2018; 59:1753-1764. [PMID: 30099525 DOI: 10.1093/pcp/pcy153] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/04/2018] [Accepted: 07/29/2018] [Indexed: 05/22/2023]
Abstract
Leaf senescence is regulated by diverse developmental and environmental factors to maximize plant fitness. The red to far-red light ratio (R:FR) detected by plant phytochromes is reduced under vegetation shade, thus initiating leaf senescence. However, the role of phytochromes in promoting leaf senescence under FR-enriched conditions is not fully understood. In this study, we investigated the role of phyA and phyB in regulating leaf senescence under FR in Arabidopsis thaliana (Arabidopsis). FR enrichment and intermittent FR pulses promoted the senescence of Arabidopsis leaves. Additionally, phyA and phyB mutants showed enhanced and repressed senescence phenotypes in FR, respectively, indicating that phyA and phyB antagonistically regulate FR-dependent leaf senescence. Transcriptomic analysis using phyA and phyB mutants in FR identified differentially expressed genes (DEGs) involved in leaf senescence-related processes, such as responses to light, phytohormones, temperature, photosynthesis and defense, showing opposite expression patterns in phyA and phyB mutants. These contrasting expression profiles of DEGs support the antagonism between phyA and phyB in FR-dependent leaf senescence. Among the genes showing antagonistic regulation, we confirmed that the expression of WRKY6, which encodes a senescence-associated transcription factor, was negatively and positively regulated by phyA and phyB, respectively. The wrky6 mutant showed a repressed senescence phenotype compared with the wild type in FR, indicating that WRKY6 plays a positive role in FR-dependent leaf senescence. Our results imply that antagonism between phyA and phyB is involved in fine-tuning leaf senescence under varying FR conditions in Arabidopsis.
Collapse
Affiliation(s)
- Junhyun Lim
- Division of Integrative Biosciences & Biotechnology, POSTECH, Pohang, Gyeongbuk, Republic of Korea
| | - Ji-Hwan Park
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
| | - Sukjoon Jung
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Daehee Hwang
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Hong Gil Nam
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| | - Sunghyun Hong
- Center for Plant Aging Research, Institute for Basic Science (IBS), Daegu, Republic of Korea
- Department of New Biology, DGIST, Daegu, Republic of Korea
| |
Collapse
|
9
|
PCH1 and PCHL promote photomorphogenesis in plants by controlling phytochrome B dark reversion. Nat Commun 2017; 8:2221. [PMID: 29263319 PMCID: PMC5738371 DOI: 10.1038/s41467-017-02311-8] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2017] [Accepted: 11/18/2017] [Indexed: 11/08/2022] Open
Abstract
Phytochrome B (phyB) is the primary red light photoreceptor in plants, and regulates both growth and development. The relative levels of phyB in the active state are determined by the light conditions, such as direct sunlight or shade, but are also affected by light-independent dark reversion. Dark reversion is a temperature-dependent thermal relaxation process, by which phyB reverts from the active to the inactive state. Here, we show that the homologous phyB-binding proteins PCH1 and PCHL suppress phyB dark reversion, resulting in plants with dramatically enhanced light sensitivity. Moreover, far-red and blue light upregulate the expression of PCH1 and PCHL in a phyB independent manner, thereby increasing the response to red light perceived by phyB. PCH1 and PCHL therefore provide a node for the molecular integration of different light qualities by regulation of phyB dark reversion, allowing plants to adapt growth and development to the ambient environment.
Collapse
|
10
|
Viczián A, Klose C, Ádám É, Nagy F. New insights of red light-induced development. PLANT, CELL & ENVIRONMENT 2017; 40:2457-2468. [PMID: 27943362 DOI: 10.1111/pce.12880] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/14/2016] [Revised: 12/04/2016] [Accepted: 12/05/2016] [Indexed: 05/14/2023]
Abstract
The red/far-red light absorbing photoreceptors phytochromes regulate development and growth and thus play an essential role in optimizing adaptation of the sessile plants to the ever-changing environment. Our understanding of how absorption of a red/far-red photon by phytochromes initiates/modifies diverse physiological responses has been steadily improving. Research performed in the last 5 years has been especially productive and led to significant conceptual changes about the mode of action of these photoreceptors. In this review, we focus on the phytochrome B photoreceptor, the major phytochrome species active in light-grown plants. We discuss how its light-independent inactivation (termed dark/thermal reversion), post-translational modification, including ubiquitination, phosphorylation and sumoylation, as well as heterodimerization with other phytochrome species modify red light-controlled physiological responses. Finally, we discuss how photobiological properties of phytochrome B enable this photoreceptor to function also as a thermosensor.
Collapse
Affiliation(s)
- András Viczián
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Cornelia Klose
- Institute of Biology2/Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Hungarian Academy of Sciences, Temesvári krt. 62, H-6726, Szeged, Hungary
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| |
Collapse
|
11
|
Biological activity and dimerization state of modified phytochrome A proteins. PLoS One 2017; 12:e0186468. [PMID: 29049346 PMCID: PMC5648194 DOI: 10.1371/journal.pone.0186468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2017] [Accepted: 10/02/2017] [Indexed: 11/29/2022] Open
Abstract
To assess potential physical interactions of type I phyA with the type II phyB-phyE phytochromes in vivo, transgenes expressing fusion gene forms of phyA were introduced into the Arabidopsis phyA mutant background. When a single c-Myc (myc) epitope is added to either the N- or C-terminus of phyA, the constructs completely complement phyA mutant phenotypes. However, addition of larger tags, such as six consecutive myc epitopes or the yellow fluorescent protein sequence, result in fusion proteins that show reduced activity. All the tagged phyA proteins migrate as dimers on native gels and co-immunoprecipitation reveals no binding interaction of phyA to any of the type II phys in the dark or under continuous far-red light. Dimers of the phyA 1–615 amino acid N-terminal photosensory domain (NphyA), generated in vivo with a yeast GAL4 dimerization domain and attached to a constitutive nuclear localization sequence, are expressed at a low level and, although they cause a cop phenotype in darkness and mediate a very low fluence response to pulses of FR, have no activity under continuous FR. It is concluded that type I phyA in its Pr form is present in plants predominantly or exclusively as a homodimer and does not stably interact with type II phys in a dimer-to-dimer manner. In addition, its activity in mediating response to continuous FR is sensitive to modification of its N- or C-terminus.
Collapse
|
12
|
Sánchez-Lamas M, Lorenzo CD, Cerdán PD. Bottom-up Assembly of the Phytochrome Network. PLoS Genet 2016; 12:e1006413. [PMID: 27820825 PMCID: PMC5098793 DOI: 10.1371/journal.pgen.1006413] [Citation(s) in RCA: 28] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2015] [Accepted: 10/10/2016] [Indexed: 11/19/2022] Open
Abstract
Plants have developed sophisticated systems to monitor and rapidly acclimate to environmental fluctuations. Light is an essential source of environmental information throughout the plant's life cycle. The model plant Arabidopsis thaliana possesses five phytochromes (phyA-phyE) with important roles in germination, seedling establishment, shade avoidance, and flowering. However, our understanding of the phytochrome signaling network is incomplete, and little is known about the individual roles of phytochromes and how they function cooperatively to mediate light responses. Here, we used a bottom-up approach to study the phytochrome network. We added each of the five phytochromes to a phytochrome-less background to study their individual roles and then added the phytochromes by pairs to study their interactions. By analyzing the 16 resulting genotypes, we revealed unique roles for each phytochrome and identified novel phytochrome interactions that regulate germination and the onset of flowering. Furthermore, we found that ambient temperature has both phytochrome-dependent and -independent effects, suggesting that multiple pathways integrate temperature and light signaling. Surprisingly, none of the phytochromes alone conferred a photoperiodic response. Although phyE and phyB were the strongest repressors of flowering, both phyB and phyC were needed to confer a flowering response to photoperiod. Thus, a specific combination of phytochromes is required to detect changes in photoperiod, whereas single phytochromes are sufficient to respond to light quality, indicating how phytochromes signal different light cues.
Collapse
Affiliation(s)
| | | | - Pablo D. Cerdán
- Fundación Instituto Leloir, IIBBA-CONICET, Buenos Aires, Argentina
- Facultad de Ciencias Exactas y Naturales, Universidad de Buenos Aires, Buenos Aires, Argentina
| |
Collapse
|
13
|
Lee YS, Yi J, An G. OsPhyA modulates rice flowering time mainly through OsGI under short days and Ghd7 under long days in the absence of phytochrome B. PLANT MOLECULAR BIOLOGY 2016; 91:413-427. [PMID: 27039184 DOI: 10.1007/s11103-016-0474-7] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2015] [Accepted: 03/27/2016] [Indexed: 06/05/2023]
Abstract
Phytochromes recognize light signals and control diverse developmental processes. In rice, all three phytochrome genes-OsphyA, OsphyB, and OsphyC-are involved in regulating flowering time. We investigated the role of OsPhyA by comparing the osphyA osphyB double mutant to an osphyB single mutant. Plants of the double mutant flowered later than the single under short days (SD) but bolted earlier under long days (LD). Under SD, this delayed-flowering phenotype was primarily due to the decreased expression of Oryza sativa GIGANTEA (OsGI), which controls three flowering activators: Heading date 1 (Hd1), OsMADS51, and Oryza sativa Indeterminate 1 (OsId1). Under LD, although the expression of several repressors, e.g., Hd1, Oryza sativa CONSTANS-like 4 (OsCOL4), and AP2 genes, was affected in the double mutant, that of Grain number, plant height and heading date 7 (Ghd7) was the most significantly reduced. These results indicated that OsPhyA influences flowering time mainly by affecting the expression of OsGI under SD and Ghd7 under LD when phytochrome B is absent. We also demonstrated that far-red light delays flowering time via both OsPhyA and OsPhyB.
Collapse
Affiliation(s)
- Yang-Seok Lee
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea
| | - Jakyung Yi
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea
| | - Gynheung An
- Crop Biotech Institute, Kyung Hee University, Yongin, 446-701, Korea.
- Department of Genetic Engineering, Kyung Hee University, Yongin, 446-701, Korea.
| |
Collapse
|
14
|
Klose C, Venezia F, Hussong A, Kircher S, Schäfer E, Fleck C. Systematic analysis of how phytochrome B dimerization determines its specificity. NATURE PLANTS 2015; 1:15090. [PMID: 27250256 DOI: 10.1038/nplants.2015.90] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2014] [Accepted: 06/01/2015] [Indexed: 05/12/2023]
Abstract
Phytochromes are red/far-red-light detecting photoreceptors that regulate plant growth and development. They photo-interconvert between an inactive Pr (red-light absorbing) and a physiologically active Pfr (far-red-light absorbing) form, acting as light-controlled molecular switches. Although the two major plant phytochromes A (phyA) and B (phyB) share similar absorption properties, they exhibit dramatic differences in their action spectra. Since both phytochromes antagonistically regulate seedling development under vegetative shade, it is essential for plants to clearly distinguish between phyA and phyB action. This discrimination is not comprehensible solely by the molecular properties of the phytochromes, but is evidently due to the dynamics of the phytochrome system. Using an integrated experimental and mathematical modelling approach we show that phytochrome dimerization is an essential element for phyB function. Our findings reveal that light-independent Pfr to Pr relaxation (dark reversion) and association/dissociation to nuclear bodies (NBs) severely depend on the conformational state of the phyB dimer. We conclude that only Pfr-Pfr homodimers of phyB can be responsible for triggering physiological responses, leading to a suppression of phyB function in the far-red range of the light spectrum.
Collapse
Affiliation(s)
- Cornelia Klose
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Filippo Venezia
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- Centre for Biological Systems Analysis, University of Freiburg, Habsburgerstr. 49, Freiburg 79104, Germany
| | - Andrea Hussong
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Stefan Kircher
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, Schänzlestrasse 1, Freiburg 79104, Germany
- BIOSS Centre for Biological Signalling Studies, University of Freiburg, Schänzlestr. 18, Freiburg 79104, Germany
| | - Christian Fleck
- Laboratory for Systems and Synthetic Biology, Wageningen UR, Dreijenplein 10, Wageningen 6703 HB, The Netherlands
| |
Collapse
|
15
|
Zhu L, Bu Q, Xu X, Paik I, Huang X, Hoecker U, Deng XW, Huq E. CUL4 forms an E3 ligase with COP1 and SPA to promote light-induced degradation of PIF1. Nat Commun 2015; 6:7245. [PMID: 26037329 DOI: 10.1038/ncomms8245] [Citation(s) in RCA: 84] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2015] [Accepted: 04/22/2015] [Indexed: 02/01/2023] Open
Abstract
Plants undergo contrasting developmental programs in dark and light. Photomorphogenesis, a light-adapted programme is repressed in the dark by the synergistic actions of CUL4(COP1-SPA) E3 ubiquitin ligase and a subset of basic helix-loop-helix transcription factors called phytochrome interacting factors (PIFs). To promote photomorphogenesis, light activates the phytochrome family of sensory photoreceptors, which inhibits these repressors by poorly understood mechanisms. Here, we show that the CUL4(COP1-SPA) E3 ubiquitin ligase is necessary for the light-induced degradation of PIF1 in Arabidopsis. The light-induced ubiquitylation and subsequent degradation of PIF1 is reduced in the cop1, spaQ and cul4 backgrounds. COP1, SPA1 and CUL4 preferentially form complexes with the phosphorylated forms of PIF1 in response to light. The cop1 and spaQ seeds display strong hyposensitive response to far-red light-mediated seed germination and light-regulated gene expression. These data show a mechanism by which an E3 ligase attenuates its activity by degrading its cofactor in response to light.
Collapse
Affiliation(s)
- Ling Zhu
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Qingyun Bu
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xiaosa Xu
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Inyup Paik
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| | - Xi Huang
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Zülpicher Strasse 47b, 50674 Cologne, Germany
| | - Xing Wang Deng
- Peking-Yale Joint Center for Plant Molecular Genetics and Agro-Biotechnology, State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas 78712, USA
| |
Collapse
|
16
|
Song MF, Zhang S, Hou P, Shang HZ, Gu HK, Li JJ, Xiao Y, Guo L, Su L, Gao JW, Yang JP. Ectopic expression of a phytochrome B gene from Chinese cabbage (Brassica rapa L. ssp. pekinensis) in Arabidopsis thaliana promotes seedling de-etiolation, dwarfing in mature plants, and delayed flowering. PLANT MOLECULAR BIOLOGY 2015; 87:633-43. [PMID: 25724426 DOI: 10.1007/s11103-015-0302-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2013] [Accepted: 02/18/2015] [Indexed: 05/22/2023]
Abstract
Phytochrome B (phyB) is an essential red light receptor that predominantly mediates seedling de-etiolation, shade-avoidance response, and flowering time. In this study, we isolate a full-length cDNA of PHYB, designated BrPHYB, from Chinese cabbage (Brassica rapa L. ssp. pekinensis), and we find that BrphyB protein has high amino acid sequence similarity and the closest evolutionary relationship to Arabidopsis thaliana phyB (i.e., AtphyB). Quantitative reverse transcription (RT)-PCR results indicate that the BrPHYB gene is ubiquitously expressed in different tissues under all light conditions. Constitutive expression of the BrPHYB gene in A. thaliana significantly enhances seedling de-etiolation under red- and white-light conditions, and causes dwarf stature in mature plants. Unexpectedly, overexpression of BrPHYB in transgenic A. thaliana resulted in reduced expression of gibberellins biosynthesis genes and delayed flowering under short-day conditions, whereas AtPHYB overexpression caused enhanced expression of FLOWERING LOCUS T and earlier flowering. Our results suggest that BrphyB might play an important role in regulating the development of Chinese cabbage. BrphyB and AtphyB have conserved functions during de-etiolation and vegetative plant growth and divergent functions in the regulation of flowering time.
Collapse
Affiliation(s)
- Mei-Fang Song
- Beijing Radiation Center, Beijing, 100875, People's Republic of China
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
17
|
Xie X, Kagawa T, Takano M. The phytochrome B/phytochrome C heterodimer is necessary for phytochrome C-mediated responses in rice seedlings. PLoS One 2014; 9:e97264. [PMID: 24853557 PMCID: PMC4031084 DOI: 10.1371/journal.pone.0097264] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2013] [Accepted: 04/16/2014] [Indexed: 01/19/2023] Open
Abstract
Background PhyC levels have been observed to be markedly lower in phyB mutants than in Arabidopsis or rice wild type etiolated seedlings, but the mechanism of this phenomenon has not been fully elucidated. Results In the present study, we investigated the mechanism by which phyB affects the protein concentration and photo-sensing abilities of phyC and demonstrated that rice phyC exists predominantly as phyB/phyC heterodimers in etiolated seedlings. PHYC-GFP protein was detected when expressed in phyA phyC mutants, but not in phyA phyB mutants, suggesting that phyC requires phyB for its photo-sensing abilities. Interestingly, when a mutant PHYB gene that has no chromophore binding site, PHYB(C364A), was introduced into phyB mutants, the phyC level was restored. Moreover, when PHYB(C364A) was introduced into phyA phyB mutants, the seedlings exhibited de-etiolation under both far-red light (FR) and red light (R) conditions, while the phyA phyB mutants were blind to both FR and R. These results are the first direct evidence that phyC is responsible for regulating seedling de-etiolation under both FR and R. These findings also suggest that phyB is indispensable for the expression and function of phyC, which depends on the formation of phyB/phyC heterodimers. Significance The present report clearly demonstrates the similarities and differences in the properties of phyC between Arabidopsis and rice and will advance our understanding of phytochrome functions in monocots and dicots.
Collapse
Affiliation(s)
- Xianzhi Xie
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- Shandong Rice Research Institute, Shandong Academy of Agricultural Sciences, Jinan, Shandong, China
| | - Takatoshi Kagawa
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
| | - Makoto Takano
- Photobiology and Photosynthesis Research Unit, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan
- * E-mail:
| |
Collapse
|
18
|
Abdurakhmonov IY, Buriev ZT, Saha S, Jenkins JN, Abdukarimov A, Pepper AE. Phytochrome RNAi enhances major fibre quality and agronomic traits of the cotton Gossypium hirsutum L. Nat Commun 2014; 5:3062. [PMID: 24430163 DOI: 10.1038/ncomms4062] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2013] [Accepted: 12/04/2013] [Indexed: 02/08/2023] Open
Abstract
Simultaneous improvement of fibre quality, early-flowering, early-maturity and productivity in Upland cotton (G. hirsutum) is a challenging task for conventional breeding. The influence of red/far-red light ratio on the fibre length prompted us to examine the phenotypic effects of RNA interference (RNAi) of the cotton PHYA1 gene. Here we show a suppression of up to ~70% for the PHYA1 transcript, and compensatory overexpression of up to ~20-fold in the remaining phytochromes in somatically regenerated PHYA1 RNAi cotton plants. Two independent transformants of three generations exhibited vigorous root and vegetative growth, early-flowering, significantly improved upper half mean fibre length and an improvement in other major fibre characteristics. Small decreases in lint traits were observed but seed cotton yield was increased an average 10-17% compared with controls. RNAi-associated phenotypes were heritable and transferable via sexual hybridization. These results should aid in the development of early-maturing and productive Upland cultivars with superior fibre quality.
Collapse
Affiliation(s)
- Ibrokhim Y Abdurakhmonov
- 1] Centre of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Ministry of Agriculture & Water Resources of Uzbekistan, and 'Uzpakhtasanoat' Association, University street-2, Kibray region, Tashkent 111215, Uzbekistan [2]
| | - Zabardast T Buriev
- 1] Centre of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Ministry of Agriculture & Water Resources of Uzbekistan, and 'Uzpakhtasanoat' Association, University street-2, Kibray region, Tashkent 111215, Uzbekistan [2]
| | - Sukumar Saha
- USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture, P. O. Box 5367, 812 Highway 12E, Mississippi State, Mississippi 39762, USA
| | - Johnie N Jenkins
- USDA-ARS, Crop Science Research Laboratory, Genetics and Precision Agriculture, P. O. Box 5367, 812 Highway 12E, Mississippi State, Mississippi 39762, USA
| | - Abdusattor Abdukarimov
- 1] Centre of Genomics and Bioinformatics, Academy of Sciences of Uzbekistan, Ministry of Agriculture & Water Resources of Uzbekistan, and 'Uzpakhtasanoat' Association, University street-2, Kibray region, Tashkent 111215, Uzbekistan [2]
| | - Alan E Pepper
- Department of Biology, Texas A&M University, College Station, Texas 77843, USA
| |
Collapse
|
19
|
Detection of phytochrome-like genes from Rhazya stricta (Apocynaceae) using de novo genome assembly. C R Biol 2013; 336:521-9. [PMID: 24296076 DOI: 10.1016/j.crvi.2013.10.009] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/22/2013] [Revised: 10/09/2013] [Accepted: 10/10/2013] [Indexed: 11/21/2022]
Abstract
Phytochrome-like genes in the wild plant species Rhazya stricta Decne were characterized using a de novo genome assembly of next generation sequence data. Rhazya stricta contains more than 100 alkaloids with multiple pharmacological properties, and leaf extracts have been used to cure chronic rheumatism, to treat tumors, and in the treatment of several other diseases. Phytochromes are known to be involved in the light-regulated biosynthesis of some alkaloids. Phytochromes are soluble chromoproteins that function in the absorption of red and far-red light and the transduction of intracellular signals during light-regulated plant development. De novo assembly of the nuclear genome of R. stricta recovered 45,641 contigs greater than 1000bp long, which were used in constructing a local database. Five sequences belonging to Arabidopsis thaliana phytochrome gene family (i.e., AtphyABCDE) were used to identify R. stricta contigs with phytochrome-like sequences using BLAST. This led to the identification of three contigs with phytochrome-like sequences covering AtphyA-, AtphyC- and AtphyE-like full-length genes. Annotation of the three sequences showed that each contig consists of one phytochrome-like gene with three exons and two introns. BLASTn and BLASTp results indicated that RsphyA mRNA and protein sequences had homologues in Wrightia coccinea and and Solanum tuberosum, respectively. RsphyC-like mRNA and protein sequence were homologous to Vitis vinifera and Vitis riparia. RsphyE-like mRNA coding and protein sequences were homologous to Ipomoea nil. Multiple-sequence alignment of phytochrome proteins indicated a homology with 30 sequences from 23 different species of flowering plants. Phylogenetic analysis confirmed that each R. stricta phytochrome gene is related to the same phytochrome gene of other flowering plants. It is proposed that the absence of phyB gene in R. stricta is due to RsphyA gene taking over the role of phyB.
Collapse
|
20
|
Ádám É, Kircher S, Liu P, Mérai Z, González-Schain N, Hörner M, Viczián A, Monte E, Sharrock RA, Schäfer E, Nagy F. Comparative functional analysis of full-length and N-terminal fragments of phytochrome C, D and E in red light-induced signaling. THE NEW PHYTOLOGIST 2013; 200:86-96. [PMID: 23772959 DOI: 10.1111/nph.12364] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2013] [Accepted: 05/12/2013] [Indexed: 06/02/2023]
Abstract
Phytochromes (phy) C, D and E are involved in the regulation of red/far-red light-induced photomorphogenesis of Arabidopsis thaliana, but only limited data are available on the mode of action and biological function of these lesser studied phytochrome species. We fused N-terminal fragments or full-length PHYC, D and E to YELLOW FLUORESCENT PROTEIN (YFP), and analyzed the function, stability and intracellular distribution of these fusion proteins in planta. The activity of the constitutively nuclear-localized homodimers of N-terminal fragments was comparable with that of full-length PHYC, D, E-YFP, and resulted in the regulation of various red light-induced photomorphogenic responses in the studied genetic backgrounds. PHYE-YFP was active in the absence of phyB and phyD, and PHYE-YFP controlled responses, as well as accumulation, of the fusion protein in the nuclei, was saturated at low fluence rates of red light and did not require functional FAR-RED ELONGATED HYPOCOTYL1 (FHY-1) and FHY-1-like proteins. Our data suggest that PHYC-YFP, PHYD-YFP and PHYE-YFP fusion proteins, as well as their truncated N-terminal derivatives, are biologically active in the modulation of red light-regulated photomorphogenesis. We propose that PHYE-YFP can function as a homodimer and that low-fluence red light-induced translocation of phyE and phyA into the nuclei is mediated by different molecular mechanisms.
Collapse
Affiliation(s)
- Éva Ádám
- Institute of Plant Biology, Biological Research Centre, Temesvári krt.62., H-6726, Szeged, Hungary
| | - Stefan Kircher
- Institute of Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Peng Liu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Zsuzsanna Mérai
- Institute of Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
| | - Nahuel González-Schain
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Univ. Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Maximilian Hörner
- BIOSS Center for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, D-79104, Freiburg, Germany
| | - András Viczián
- Institute of Plant Biology, Biological Research Centre, Temesvári krt.62., H-6726, Szeged, Hungary
| | - Elena Monte
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus Univ. Autònoma de Barcelona, Bellaterra, 08193, Barcelona, Spain
| | - Robert A Sharrock
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT, 59717, USA
| | - Eberhard Schäfer
- Institute of Botany, University of Freiburg, Schänzlestrasse 1, D-79104, Freiburg, Germany
- BIOSS Center for Biological Signalling Studies, University of Freiburg, Schänzlestrasse 18, D-79104, Freiburg, Germany
| | - Ferenc Nagy
- Institute of Plant Biology, Biological Research Centre, Temesvári krt.62., H-6726, Szeged, Hungary
- Institute of Molecular Plant Science, School of Biological Sciences, University of Edinburgh, Edinburgh, EH9 3JH, UK
| |
Collapse
|
21
|
Liu P, Sharrock RA. Directed dimerization: an in vivo expression system for functional studies of type II phytochromes. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:915-926. [PMID: 23738620 DOI: 10.1111/tpj.12255] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/26/2013] [Revised: 05/16/2013] [Accepted: 05/29/2013] [Indexed: 06/02/2023]
Abstract
Type II phytochromes (phy) in Arabidopsis form homodimers and heterodimers, resulting in a diverse collection of light-stable red/far-red (R/FR) sensing photoreceptors. We describe an in vivo protein engineering system and its use in characterizing the activities of these molecules. Using a phyB null mutant background, singly and doubly transgenic plants were generated that express fusion proteins containing the phyB-phyE N-terminal photosensory regions (NB-NE PSRs), a nuclear localization sequence, and small yeast protein domains that mediate either homodimerization or heterodimerization. Activity of NB/NB homodimers but not monomeric NB subunits in control of seedling and adult plant responses to R light is demonstrated. Heterodimers of the NB sequence with the chromophoreless NB(C357S) sequence, which mimic phyB Pfr/Pr photo-heterodimers, mediate R sensitivity in leaves and petioles but not hypocotyls. Homodimerization of the NC, ND and NE sequences and directed heterodimerization of these photosensory regions with the NB region reveal form-specific R-induced activities for different type II phy dimers. The experimental approach developed here of directed assembly of defined protein dimer combinations in vivo may be applicable to other systems.
Collapse
Affiliation(s)
- Peng Liu
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, MT 59717, USA
| | | |
Collapse
|
22
|
Control of a four-color sensing photoreceptor by a two-color sensing photoreceptor reveals complex light regulation in cyanobacteria. Proc Natl Acad Sci U S A 2013; 110:12834-9. [PMID: 23858449 DOI: 10.1073/pnas.1303371110] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/13/2023] Open
Abstract
Photoreceptors are biologically important for sensing changes in the color and intensity of ambient light and, for photosynthetic organisms, processing this light information to optimize food production through photosynthesis. Cyanobacteria are an evolutionarily and ecologically important prokaryotic group of oxygenic photosynthesizers that contain cyanobacteriochrome (CBCR) photoreceptors, whose family members sense nearly the entire visible spectrum of light colors. Some cyanobacteria contain 12 to 15 different CBCRs, and many family members contain multiple light-sensing domains. However, the complex interactions that must be occurring within and between these photoreceptors remain unexplored. Here we describe the regulation and photobiology of a unique CBCR called IflA (influenced by far-red light), demonstrating that a second CBCR called RcaE strongly regulates IflA abundance and that IflA uses two distinct photosensory domains to respond to four different light colors: blue, green, red, and far-red. The absorption of red or far-red light by one domain affects the conformation of the other domain, and the rate of relaxation of one of these domains is influenced by the conformation of the other. Deletion of iflA results in delayed growth at low cell density, suggesting that IflA accelerates growth under this condition, apparently by sensing the ratio of red to far-red light in the environment. The types of complex photobiological interactions described here, both between unrelated CBCR family members and within photosensory domains of a single CBCR, may be advantageous for species using these photoreceptors in aquatic environments, where light color ratios are influenced by many biotic and abiotic factors.
Collapse
|
23
|
Zhang J, Stankey RJ, Vierstra RD. Structure-guided engineering of plant phytochrome B with altered photochemistry and light signaling. PLANT PHYSIOLOGY 2013; 161:1445-57. [PMID: 23321421 PMCID: PMC3585608 DOI: 10.1104/pp.112.208892] [Citation(s) in RCA: 36] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/10/2012] [Accepted: 01/10/2013] [Indexed: 05/22/2023]
Abstract
Phytochromes (phys) encompass a diverse collection of biliproteins that enable cellular light perception by photoconverting between a red-light-absorbing ground state (Pr) and a far-red light-absorbing active state (Pfr). Based on the central role of plant phys in controlling numerous agriculturally important processes, their rational redesign offers great promise toward accelerating crop improvement. Employing as templates the available three-dimensional models of the photosensory module within bacterial phys, we report here our initial attempt to apply structure-guided mutagenesis to phy engineering using Arabidopsis (Arabidopsis thaliana) phyB, the dominant isoform in light-grown plants, as the example. A collection of phyB mutants was generated affecting the bilin-binding pocket that altered photochemistry, thermal stability, and/or nuclear localization patterns, some of which also impacted phenotypic outputs. Of particular interest are the Y361F substitution, which created Arabidopsis plants with greatly enhanced light sensitivity, mutants variably altered in Pfr-to-Pr thermal reversion and nuclear aggregation, and the D307A substitution, which failed to photoconvert from Pr to Pfr and display light-induced nuclear aggregation but retained some biological activity and accelerated turnover in red light. Taken together, this collection provides variants potentially useful to agriculture as well as new tools to better understand the molecular mechanisms underpinning phy signaling.
Collapse
|
24
|
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.
Collapse
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
| |
Collapse
|
25
|
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.
Collapse
|
26
|
Soy J, Leivar P, González-Schain N, Sentandreu M, Prat S, Quail PH, Monte E. Phytochrome-imposed oscillations in PIF3 protein abundance regulate hypocotyl growth under diurnal light/dark conditions in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2012; 71:390-401. [PMID: 22409654 PMCID: PMC3465574 DOI: 10.1111/j.1365-313x.2012.04992.x] [Citation(s) in RCA: 49] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/19/2023]
Abstract
Arabidopsis seedlings display rhythmic growth when grown under diurnal conditions, with maximal elongation rates occurring at the end of the night under short-day photoperiods. Current evidence indicates that this behavior involves the action of the growth-promoting bHLH factors PHYTOCHROME-INTERACTING FACTOR 4 (PIF4) and PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) at the end of the night, through a coincidence mechanism that combines their transcriptional regulation by the circadian clock with control of protein accumulation by light. To assess the possible role of PIF3 in this process, we have analyzed hypocotyl responses and marker gene expression in pif single- and higher-order mutants. The data show that PIF3 plays a prominent role as a promoter of seedling growth under diurnal light/dark conditions, in conjunction with PIF4 and PIF5. In addition, we provide evidence that PIF3 functions in this process through its intrinsic transcriptional regulatory activity, at least in part by directly targeting growth-related genes, and independently of its ability to regulate phytochrome B (phyB) levels. Furthermore, in sharp contrast to PIF4 and PIF5, our data show that the PIF3 gene is not subject to transcriptional regulation by the clock, but that PIF3 protein abundance oscillates under diurnal conditions as a result of a progressive decline in PIF3 protein degradation mediated by photoactivated phyB, and consequent accumulation of the bHLH factor during the dark period. Collectively, the data suggest that phyB-mediated, post-translational regulation allows PIF3 accumulation to peak just before dawn, at which time it accelerates hypocotyl growth, together with PIF4 and PIF5, by directly regulating the induction of growth-related genes.
Collapse
Affiliation(s)
- Judit Soy
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Pablo Leivar
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Nahuel González-Schain
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Maria Sentandreu
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
| | - Salomé Prat
- Departamento de Genética Molecular de Plantas, Centro Nacional de Biotecnología CSIC, Campus Universidad Autónoma de Madrid, Cantoblanco, 28049 Madrid, Spain
| | - Peter H. Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
- United States Department of Agriculture, Plant Gene Expression Center, Albany, CA 94710, USA
| | - Elena Monte
- Departament de Genètica Molecular, Center for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universidad Autònoma de Barcelona, Bellaterra, 08193 Barcelona, Spain
- For correspondence ()
| |
Collapse
|
27
|
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.
Collapse
|
28
|
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.
Collapse
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
| |
Collapse
|
29
|
Li J, Li G, Wang H, Wang Deng X. Phytochrome signaling mechanisms. THE ARABIDOPSIS BOOK 2011. [PMID: 22303272 DOI: 10.1199/2ftab.0148e0148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Phytochromes are red (R)/far-red (FR) light photoreceptors that play fundamental roles in photoperception of the light environment and the subsequent adaptation of plant growth and development. There are five distinct phytochromes in Arabidopsis thaliana, designated phytochrome A (phyA) to phyE. phyA is light-labile and is the primary photoreceptor responsible for mediating photomorphogenic responses in FR light, whereas phyB-phyE are light stable, and phyB is the predominant phytochrome regulating de-etiolation responses in R light. Phytochromes are synthesized in the cytosol in their inactive Pr form. Upon light irradiation, phytochromes are converted to the biologically active Pfr form, and translocate into the nucleus. phyB can enter the nucleus by itself in response to R light, whereas phyA nuclear import depends on two small plant-specific proteins FAR-RED ELONGATED HYPOCOTYL 1 (FHY1) and FHY1-LIKE (FHL). Phytochromes may function as light-regulated serine/threonine kinases, and can phosphorylate several substrates, including themselves in vitro. Phytochromes are phosphoproteins, and can be dephosphorylated by a few protein phosphatases. Photoactivated phytochromes rapidly change the expression of light-responsive genes by repressing the activity of CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), an E3 ubiquitin ligase targeting several photomorphogenesis-promoting transcription factors for degradation, and by inducing rapid phosphorylation and degradation of Phytochrome-Interacting Factors (PIFs), a group of bHLH transcription factors repressing photomorphogenesis. Phytochromes are targeted by COP1 for degradation via the ubiquitin/26S proteasome pathway.
Collapse
|
30
|
Chao D, Lin H. The tricks plants use to reach appropriate light. SCIENCE CHINA-LIFE SCIENCES 2010; 53:916-26. [PMID: 20821290 DOI: 10.1007/s11427-010-4047-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/12/2010] [Accepted: 02/25/2010] [Indexed: 11/30/2022]
Abstract
The perception of ambient light signals that produce a relevant response to ensure exposure to appropriate levels of light energy is vital for plants. In response to this, intricate molecular mechanisms to mediate light signaling have evolved in plants. Among the responses induced by light, seedling extension is a determining event for plant survival in darkness, especially in the initial stage of plant growth. Here we review previous studies and recent progress towards an understanding of light signaling that regulates seedling elongation. We focus on the three regions of the sunlight spectrum that primarily control seedling elongation, namely red/far-red light, blue/UV-A light and UV-B light, and summarize the four signaling pathways that correspond to the three effective spectra.
Collapse
Affiliation(s)
- DaiYin Chao
- Department of Horticulture and Landscape Architecture, Purdue University, West Lafayette, Indiana 47907, USA.
| | | |
Collapse
|
31
|
Rausenberger J, Hussong A, Kircher S, Kirchenbauer D, Timmer J, Nagy F, Schäfer E, Fleck C. An integrative model for phytochrome B mediated photomorphogenesis: from protein dynamics to physiology. PLoS One 2010; 5:e10721. [PMID: 20502669 PMCID: PMC2873432 DOI: 10.1371/journal.pone.0010721] [Citation(s) in RCA: 70] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2009] [Accepted: 04/22/2010] [Indexed: 12/05/2022] Open
Abstract
Background Plants have evolved various sophisticated mechanisms to respond and adapt to changes of abiotic factors in their natural environment. Light is one of the most important abiotic environmental factors and it regulates plant growth and development throughout their entire life cycle. To monitor the intensity and spectral composition of the ambient light environment, plants have evolved multiple photoreceptors, including the red/far-red light-sensing phytochromes. Methodology/Principal Findings We have developed an integrative mathematical model that describes how phytochrome B (phyB), an essential receptor in Arabidopsis thaliana, controls growth. Our model is based on a multiscale approach and connects the mesoscopic intracellular phyB protein dynamics to the macroscopic growth phenotype. To establish reliable and relevant parameters for the model phyB regulated growth we measured: accumulation and degradation, dark reversion kinetics and the dynamic behavior of different nuclear phyB pools using in vivo spectroscopy, western blotting and Fluorescence Recovery After Photobleaching (FRAP) technique, respectively. Conclusions/Significance The newly developed model predicts that the phyB-containing nuclear bodies (NBs) (i) serve as storage sites for phyB and (ii) control prolonged dark reversion kinetics as well as partial reversibility of phyB Pfr in extended darkness. The predictive power of this mathematical model is further validated by the fact that we are able to formalize a basic photobiological observation, namely that in light-grown seedlings hypocotyl length depends on the total amount of phyB. In addition, we demonstrate that our theoretical predictions are in excellent agreement with quantitative data concerning phyB levels and the corresponding hypocotyl lengths. Hence, we conclude that the integrative model suggested in this study captures the main features of phyB-mediated photomorphogenesis in Arabidopsis.
Collapse
Affiliation(s)
- Julia Rausenberger
- Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Andrea Hussong
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | - Stefan Kircher
- Institute of Biology II, University of Freiburg, Freiburg, Germany
| | | | - Jens Timmer
- Institute of Physics, University of Freiburg, Freiburg, Germany
- Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
| | - Ferenc Nagy
- Freiburg Institute for Advanced Studies, University of Freiburg, Freiburg, Germany
- Institute of Plant Biology, Biological Research Center, Szeged, Hungary
- School of Biological Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Eberhard Schäfer
- Institute of Biology II, University of Freiburg, Freiburg, Germany
- * E-mail: (ES); (CF)
| | - Christian Fleck
- Centre for Biological Systems Analysis, University of Freiburg, Freiburg, Germany
- Institute of Physics, University of Freiburg, Freiburg, Germany
- * E-mail: (ES); (CF)
| |
Collapse
|
32
|
Takano M, Inagaki N, Xie X, Kiyota S, Baba-Kasai A, Tanabata T, Shinomura T. Phytochromes are the sole photoreceptors for perceiving red/far-red light in rice. Proc Natl Acad Sci U S A 2009; 106:14705-10. [PMID: 19706555 PMCID: PMC2732857 DOI: 10.1073/pnas.0907378106] [Citation(s) in RCA: 86] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2008] [Indexed: 11/18/2022] Open
Abstract
Phytochromes are believed to be solely responsible for red and far-red light perception, but this has never been definitively tested. To directly address this hypothesis, a phytochrome triple mutant (phyAphyBphyC) was generated in rice (Oryza sativa L. cv. Nipponbare) and its responses to red and far-red light were monitored. Since rice only has three phytochrome genes (PHYA, PHYB and PHYC), this mutant is completely lacking any phytochrome. Rice seedlings grown in the dark develop long coleoptiles while undergoing regular circumnutation. The phytochrome triple mutants also show this characteristic skotomorphogenesis, even under continuous red or far-red light. The morphology of the triple mutant seedlings grown under red or far-red light appears completely the same as etiolated seedlings, and they show no expression of the light-induced genes. This is direct evidence demonstrating that phytochromes are the sole photoreceptors for perceiving red and far-red light, at least during rice seedling establishment. Furthermore, the shape of the triple mutant plants was dramatically altered. Most remarkably, triple mutants extend their internodes even during the vegetative growth stage, which is a time during which wild-type rice plants never elongate their internodes. The triple mutants also flowered very early under long day conditions and set very few seeds due to incomplete male sterility. These data indicate that phytochromes play an important role in maximizing photosynthetic abilities during the vegetative growth stage in rice.
Collapse
Affiliation(s)
- Makoto Takano
- Department of Plant Sciences, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305-8602, Japan.
| | | | | | | | | | | | | |
Collapse
|
33
|
Riemann M, Bouyer D, Hisada A, Müller A, Yatou O, Weiler EW, Takano M, Furuya M, Nick P. Phytochrome A requires jasmonate for photodestruction. PLANTA 2009; 229:1035-45. [PMID: 19184094 DOI: 10.1007/s00425-009-0891-9] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/07/2008] [Accepted: 01/07/2009] [Indexed: 05/23/2023]
Abstract
The plant photoreceptor phytochrome is organised in a small gene family with phytochrome A (phyA) being unique, because it is specifically degraded upon activation by light. This so called photodestruction is thought to be important for dynamic aspects of sensing such as measuring day length or shading by competitors. Signal-triggered proteolytic degradation has emerged as central element of signal crosstalk in plants during recent years, but many of the molecular players are still unknown. We therefore analyzed a jasmonate (JA)-deficient rice mutant, hebiba, that in several aspects resembles a mutant affected in photomorphogenesis. In this mutant, the photodestruction of phyA is delayed as shown by in vivo spectroscopy and Western blot analysis. Application of methyl-JA (MeJA) can rescue the delayed phyA photodestruction in the mutant in a time- and dose-dependent manner. Light regulation of phyA transcripts thought to be under control of stable phytochrome B (phyB) is still functional. The delayed photodestruction is accompanied by an elevated sensitivity of phytochrome-dependent growth responses to red and far-red light.
Collapse
Affiliation(s)
- Michael Riemann
- Institute of Botany 1, Universität Karlsruhe, Kaiserstrasse 2, 76128 Karlsruhe, Germany.
| | | | | | | | | | | | | | | | | |
Collapse
|
34
|
Clack T, Shokry A, Moffet M, Liu P, Faul M, Sharrock RA. Obligate heterodimerization of Arabidopsis phytochromes C and E and interaction with the PIF3 basic helix-loop-helix transcription factor. THE PLANT CELL 2009; 21:786-99. [PMID: 19286967 PMCID: PMC2671712 DOI: 10.1105/tpc.108.065227] [Citation(s) in RCA: 42] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2008] [Revised: 02/17/2009] [Accepted: 03/02/2009] [Indexed: 05/18/2023]
Abstract
Phytochromes are dimeric chromoproteins that regulate plant responses to red (R) and far-red (FR) light. The Arabidopsis thaliana genome encodes five phytochrome apoproteins: type I phyA mediates responses to FR, and type II phyB-phyE mediate shade avoidance and classical R/FR-reversible responses. In this study, we describe the complete in vivo complement of homodimeric and heterodimeric type II phytochromes. Unexpectedly, phyC and phyE do not homodimerize and are present in seedlings only as heterodimers with phyB and phyD. Roles in light regulation of hypocotyl length, leaf area, and flowering time are demonstrated for heterodimeric phytochromes containing phyC or phyE. Heterodimers of phyC and chromophoreless phyB are inactive, indicating that phyC subunits require spectrally intact dimer partners to be active themselves. Consistent with the obligate heterodimerization of phyC and phyE, phyC is made unstable by removal of its phyB binding partner, and overexpression of phyE results in accumulation of phyE monomers. Following a pulse of red light, phyA, phyB, phyC, and phyD interact in vivo with the PHYTOCHROME INTERACTING FACTOR3 basic helix-loop-helix transcription factor, and this interaction is FR reversible. Therefore, most or all of the type I and type II phytochromes, including heterodimeric forms, appear to function through PIF-mediated pathways. These findings link an unanticipated diversity of plant R/FR photoreceptor structures to established phytochrome signaling mechanisms.
Collapse
Affiliation(s)
- Ted Clack
- Department of Plant Sciences and Plant Pathology, Montana State University, Bozeman, Montana 59717, USA
| | | | | | | | | | | |
Collapse
|
35
|
Lin R, Teng Y, Park HJ, Ding L, Black C, Fang P, Wang H. Discrete and essential roles of the multiple domains of Arabidopsis FHY3 in mediating phytochrome A signal transduction. PLANT PHYSIOLOGY 2008; 148:981-92. [PMID: 18715961 PMCID: PMC2556831 DOI: 10.1104/pp.108.120436] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/03/2008] [Accepted: 08/15/2008] [Indexed: 05/20/2023]
Abstract
Phytochrome A is the primary photoreceptor for mediating various far-red light-induced responses in higher plants. We recently showed that Arabidopsis (Arabidopsis thaliana) FAR-RED ELONGATED HYPOCOTYL3 (FHY3) and FAR-RED-IMPAIRED RESPONSE1 (FAR1), a pair of homologous proteins sharing significant sequence homology to Mutator-like transposases, act as novel transcription factors essential for activating the expression of FHY1 and FHL (for FHY1-like), whose products are required for light-induced phytochrome A nuclear accumulation and subsequent light responses. FHY3, FAR1, and Mutator-like transposases also share a similar domain structure, including an N-terminal C2H2 zinc finger domain, a central putative core transposase domain, and a C-terminal SWIM motif (named after SWI2/SNF and MuDR transposases). In this study, we performed a promoter-swapping analysis of FHY3 and FAR1. Our results suggest that the partially overlapping functions of FHY3 and FAR1 entail divergence of their promoter activities and protein subfunctionalization. To gain a better understanding of the molecular mode of FHY3 function, we performed a structure-function analysis, using site-directed mutagenesis and transgenic approaches. We show that the conserved N-terminal C2H2 zinc finger domain is essential for direct DNA binding and biological function of FHY3 in mediating light signaling, whereas the central core transposase domain and C-terminal SWIM domain are essential for the transcriptional regulatory activity of FHY3 and its homodimerization or heterodimerization with FAR1. Furthermore, the ability to form homodimers or heterodimers largely correlates with the transcriptional regulatory activity of FHY3 in plant cells. Together, our results reveal discrete roles of the multiple domains of FHY3 and provide functional support for the proposition that FHY3 and FAR1 represent transcription factors derived from a Mutator-like transposase(s).
Collapse
Affiliation(s)
- Rongcheng Lin
- Boyce Thompson Institute for Plant Research, Cornell University, Ithaca, NY 14853, USA
| | | | | | | | | | | | | |
Collapse
|
36
|
Hwang YS, Quail PH. Phytochrome-Regulated PIL1 Derepression is Developmentally Modulated. ACTA ACUST UNITED AC 2008; 49:501-11. [DOI: 10.1093/pcp/pcn024] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
|
37
|
Leivar P, Monte E, Al-Sady B, Carle C, Storer A, Alonso JM, Ecker JR, Quail PH. The Arabidopsis phytochrome-interacting factor PIF7, together with PIF3 and PIF4, regulates responses to prolonged red light by modulating phyB levels. THE PLANT CELL 2008; 20:337-52. [PMID: 18252845 PMCID: PMC2276449 DOI: 10.1105/tpc.107.052142] [Citation(s) in RCA: 286] [Impact Index Per Article: 17.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2007] [Revised: 11/19/2007] [Accepted: 01/15/2008] [Indexed: 05/18/2023]
Abstract
We show that a previously uncharacterized Arabidopsis thaliana basic helix-loop-helix (bHLH) phytochrome interacting factor (PIF), designated PIF7, interacts specifically with the far-red light-absorbing Pfr form of phyB through a conserved domain called the active phyB binding motif. Similar to PIF3, upon light exposure, PIF7 rapidly migrates to intranuclear speckles, where it colocalizes with phyB. However, in striking contrast to PIF3, this process is not accompanied by detectable light-induced phosphorylation or degradation of PIF7, suggesting that the consequences of interaction with photoactivated phyB may differ among PIFs. Nevertheless, PIF7 acts similarly to PIF3 in prolonged red light as a weak negative regulator of phyB-mediated seedling deetiolation. Examination of pif3, pif4, and pif7 double mutant combinations shows that their moderate hypersensitivity to extended red light is additive. We provide evidence that the mechanism by which these PIFs operate on the phyB signaling pathway under prolonged red light is through maintaining low phyB protein levels, in an additive or synergistic manner, via a process likely involving the proteasome pathway. These data suggest that the role of these phyB-interacting bHLH factors in modulating seedling deetiolation in prolonged red light may not be as phy-activated signaling intermediates, as proposed previously, but as direct modulators of the abundance of the photoreceptor.
Collapse
Affiliation(s)
- Pablo Leivar
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | | | | | | | | | | | | |
Collapse
|
38
|
Mechanistic duality of transcription factor function in phytochrome signaling. Proc Natl Acad Sci U S A 2008; 105:2232-7. [PMID: 18245378 DOI: 10.1073/pnas.0711675105] [Citation(s) in RCA: 96] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The phytochrome (phy) family of sensory photoreceptors (phyA-E in Arabidopsis) elicit changes in gene expression after light-induced migration to the nucleus, where they interact with basic helix-loop-helix transcription factors, such as phytochrome-interacting factor 3 (PIF3). The mechanism by which PIF3 relays phy signals, both early after initial light exposure and later during long-term irradiation, is not understood. Using transgenically expressed PIF3 variants, carrying site-specific amino acid substitutions that block the protein from binding either to DNA, phyA, and/or phyB, we examined the involvement of PIF3 in early, phy-induced marker gene expression and in modulating long-term, phy-imposed inhibition of hypocotyl cell elongation under prolonged, continuous irradiation. We describe an unanticipated dual mechanism of PIF3 action that involves the temporal uncoupling of its two most central molecular functions. We find that in early signaling, PIF3 acts positively as a transcription factor, exclusively requiring its DNA-binding capacity. Contrary to previous proposals, PIF3 functions as a constitutive coactivator in this process, without the need for phy binding and subsequent phy-induced modifications. This finding implies that another factor(s) is conditionally activated by phy and functions in concert with PIF3, to induce target gene transcription. In contrast, during long-term irradiations, PIF3 acts exclusively through its phyB-interacting capacity to control hypocotyl cell elongation, independently of its ability to bind DNA. Unexpectedly, PIF3 uses this capacity to regulate phyB protein abundance (and thereby global photosensory sensitivity) to modulate this long-term response rather than participating directly in the transduction chain as a signaling intermediate.
Collapse
|
39
|
Khanna R, Shen Y, Marion CM, Tsuchisaka A, Theologis A, Schäfer E, Quail PH. The basic helix-loop-helix transcription factor PIF5 acts on ethylene biosynthesis and phytochrome signaling by distinct mechanisms. THE PLANT CELL 2007; 19:3915-29. [PMID: 18065691 PMCID: PMC2217642 DOI: 10.1105/tpc.107.051508] [Citation(s) in RCA: 79] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/05/2007] [Revised: 10/09/2007] [Accepted: 11/14/2007] [Indexed: 05/19/2023]
Abstract
PHYTOCHROME-INTERACTING FACTOR5 (PIF5), a basic helix-loop-helix transcription factor, interacts specifically with the photoactivated form of phytochrome B (phyB). Here, we report that dark-grown Arabidopsis thaliana seedlings overexpressing PIF5 (PIF5-OX) exhibit exaggerated apical hooks and short hypocotyls, reminiscent of the triple response induced by elevated ethylene levels, whereas pif5 mutants fail to maintain tight hooks like those of wild-type seedlings. Silver ions, an ethylene receptor blocker, rescued the triple-response phenotype, and we show that PIF5-OX seedlings express enhanced levels of key ethylene biosynthesis enzymes and produce elevated ethylene levels. Exposure of PIF5-OX seedlings to prolonged continuous red light (Rc) promotes hypocotyl elongation relative to dark controls, the reciprocal of the Rc-imposed hypocotyl inhibition displayed by wild-type seedlings. In contrast with this PIF5-OX hyposensitivity to Rc, pif5 mutant seedlings are hypersensitive relative to wild-type seedlings. We show that this contrast is due to reciprocal changes in phyB protein levels in prolonged Rc. Compared with wild-type seedlings, PIF5-OX seedlings have reduced, whereas pif5 mutants have increased, phyB (and phyC) levels in Rc. The phyB degradation in the overexpressors depends on a functional phyB binding motif in PIF5 and involves the 26S proteasome pathway. Our data thus indicate that overexpressed PIF5 causes altered ethylene levels, which promote the triple response in darkness, whereas in the light, the interaction of photoactivated phyB with PIF5 causes degradation of the photoreceptor protein. The evidence suggests that endogenous PIF5 negatively regulates phyB-imposed hypocotyl inhibition in prolonged Rc by reducing photoreceptor abundance, and thereby photosensory capacity, rather than functioning as a signaling intermediate.
Collapse
Affiliation(s)
- Rajnish Khanna
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | | | | | | | | | | |
Collapse
|
40
|
Shen Y, Khanna R, Carle CM, Quail PH. Phytochrome induces rapid PIF5 phosphorylation and degradation in response to red-light activation. PLANT PHYSIOLOGY 2007; 145:1043-51. [PMID: 17827270 PMCID: PMC2048774 DOI: 10.1104/pp.107.105601] [Citation(s) in RCA: 206] [Impact Index Per Article: 12.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The phytochrome (phy) family of sensory photoreceptors (phyA-phyE in Arabidopsis thaliana) induces changes in target-gene expression upon light-induced translocation to the nucleus, where certain members interact with selected members of the constitutively nuclear basic helix-loop-helix transcription factor family, such as PHYTOCHROME-INTERACTING FACTOR3 (PIF3). Previous evidence indicates that the binding of the photoactivated photoreceptor molecule to PIF3 induces rapid phosphorylation of the transcription factor in the cell prior to its degradation via the ubiqitin-proteosome system. To investigate whether this apparent primary signaling mechanism can be generalized to other phy-interacting partners, we have examined the molecular behavior of a second related phy-interacting member of the basic helix-loop-helix family, PIF5, during early deetiolation, immediately following initial exposure of dark-grown seedlings to light. The data show that red light induces very rapid phosphorylation and subsequent degradation (t(1/2) < 5 min) of PIF5 via the proteosome system upon irradiation. Photobiological and genetic evidence indicates that the photoactivated phy molecule acts within 60 s to induce this phosphorylation of PIF5, and that phyA and phyB redundantly dominate this process, with phyD playing an apparently minor role. Collectively, the data support the proposal that the rapid phy-induced phosphorylation of PIF3 and PIF5 may represent the biochemical mechanism of primary signal transfer from photoactivated photoreceptor to binding partner, and that phyA and phyB (and possibly phyD) may signal to multiple, shared partners utilizing this common mechanism.
Collapse
Affiliation(s)
- Yu Shen
- Department of Plant and Microbial Biology, University of California, Berkeley, California 94720, USA
| | | | | | | |
Collapse
|
41
|
|
42
|
Franklin KA, Allen T, Whitelam GC. Phytochrome A is an irradiance-dependent red light sensor. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 50:108-17. [PMID: 17346261 DOI: 10.1111/j.1365-313x.2007.03036.x] [Citation(s) in RCA: 56] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/04/2023]
Abstract
Plants perceive red (R) and far-red (FR) light signals using the phytochrome family of photoreceptors. In Arabidopsis thaliana, five phytochromes (phyA-phyE) have been identified and characterized. Unlike other family members, phyA is subject to rapid light-induced proteolytic degradation and so accumulates to relatively high levels in dark-grown seedlings. The insensitivity of phyA mutant seedlings to prolonged FR and wild-type appearance in R has led to suggestions that phyA functions predominantly as an FR sensor during the early stages of seedling establishment. The majority of published photomorphogenesis experiments have, however, used <50 micromol m(-2) sec(-1) of R when characterizing phytochrome functions. Here we reveal considerable phyA activity in R at higher (>160 micromol m(-2) sec(-1)) photon irradiances. Under these conditions, plant architecture was observed to be largely regulated by the redundant actions of phytochromes A, B and D. Moreover, quadruple phyBphyCphyDphyE mutants containing only functional phyA displayed R-mediated de-etiolation and survived to flowering. The enhanced activity of phyA in continuous R (Rc) of high photon irradiance correlates with retarded degradation of the endogenous protein in wild-type plants and prolonged epifluorescence of nuclear-localized phyA:YFP in transgenic lines. Such observations suggest irradiance-dependent 'photoprotection' of nuclear phyA in R, providing a possible explanation for the increased activity observed. The discovery that phyA can function as an effective irradiance sensor, even in light environments that establish a high Pfr concentration, raises the possibility that phyA may contribute significantly to the regulation of growth and development in daylight-grown plants.
Collapse
Affiliation(s)
- Keara A Franklin
- Department of Biology, University of Leicester, Leicester LE1 7RH, UK.
| | | | | |
Collapse
|
43
|
Abstract
A method is presented for the extraction of total protein from Arabidopsis thaliana tissue. The protocol was designed for the solubilization of a range of proteins and their efficient and quantitative recovery. It is especially compatible with the small quantities of available tissue often associated with this species and was originally intended for Western blot preparations. Samples extracted using this method can be quantitated directly using a commercially available kit.
Collapse
|
44
|
Sheehan MJ, Kennedy LM, Costich DE, Brutnell TP. Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2007; 49:338-53. [PMID: 17181778 DOI: 10.1111/j.1365-313x.2006.02962.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/13/2023]
Abstract
Phytochromes are the primary red/far-red photoreceptors of higher plants, mediating numerous developmental processes throughout the life cycle, from germination to flowering. In seed plants, phytochromes are encoded by a small gene family with each member performing both distinct and redundant roles in mediating physiological responses to light cues. Studies in both eudicot and monocot species have defined a central role for phytochrome B in mediating responses to light in the control of several agronomically important traits, including plant height, transitions to flowering and axillary branch meristem development. Here we characterize Mutator-induced alleles of PhyB1 and a naturally occurring deletion allele of PhyB2 in Zea mays (maize). Using single and double mutants, we show that the highly similar PhyB1 and PhyB2 genes encode proteins with both overlapping and non-redundant functions that control seedling and mature plant traits. PHYB1 and PHYB2 regulate elongation of sheath and stem tissues of mature plants and contribute to the light-mediated regulation of PhyA and Cab gene transcripts. However, PHYB1 and not PHYB2 contributes significantly to the inhibition of mesocotyl elongation under red light, whereas PHYB2 and to a lesser extent PHYB1 mediate the photoperiod-dependent floral transition. This sub functionalization of PHYB activities in maize has probably occurred since the tetraploidization of maize, and may contribute to flowering time variation in modern-day varieties.
Collapse
Affiliation(s)
- Moira J Sheehan
- Department of Plant Biology, Cornell University, Tower Road, Ithaca, NY 14853, USA
| | | | | | | |
Collapse
|
45
|
Husaineid SSH, Kok RA, Schreuder MEL, Hanumappa M, Cordonnier-Pratt MM, Pratt LH, van der Plas LHW, van der Krol AR. Overexpression of homologous phytochrome genes in tomato: exploring the limits in photoperception. JOURNAL OF EXPERIMENTAL BOTANY 2007; 58:615-26. [PMID: 17251177 DOI: 10.1093/jxb/erl253] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Transgenic tomato [Lycopersicon esculentum (=Solanum lycopersicum)] lines overexpressing tomato PHYA, PHYB1, or PHYB2, under control of the constitutive double-35S promoter from cauliflower mosaic virus (CaMV) have been generated to test the level of saturation in individual phytochrome-signalling pathways in tomato. Western blot analysis confirmed the elevated phytochrome protein levels in dark-grown seedlings of the respective PHY overexpressing (PHYOE) lines. Exposure to 4 h of red light resulted in a decrease in phytochrome A protein level in the PHYAOE lines, indicating that the chromophore availability is not limiting for assembly into holoprotein and that the excess of phytochrome A protein is also targeted for light-regulated destruction. The elongation and anthocyanin accumulation responses of plants grown under white light, red light, far-red light, and end-of-day far-red light were used for characterization of selected PHYOE lines. In addition, the anthocyanin accumulation response to different fluence rates of red light of 4-d-old dark-grown seedlings was studied. The elevated levels of phyA in the PHYAOE lines had little effect on seedling and adult plant phenotype. Both PHYAOE in the phyA mutant background and PHYB2OE in the double-mutant background rescued the mutant phenotype, proving that expression of the transgene results in biologically active phytochrome. The PHYB1OE lines showed mild effects on the inhibition of stem elongation and anthocyanin accumulation and little or no effect on the red light high irradiance response. By contrast, the PHYB2OE lines showed a strong inhibition of elongation, enhancement of anthocyanin accumulation, and a strong amplification of the red light high irradiance response.
Collapse
Affiliation(s)
- Said S H Husaineid
- Laboratory of Plant Physiology, Graduate School of Experimental Plant Sciences, Wageningen University, Arboretumlaan 4, NL 6703 BD Wageningen, The Netherlands
| | | | | | | | | | | | | | | |
Collapse
|
46
|
Tepperman JM, Hwang YS, Quail PH. phyA dominates in transduction of red-light signals to rapidly responding genes at the initiation of Arabidopsis seedling de-etiolation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2006; 48:728-42. [PMID: 17076805 DOI: 10.1111/j.1365-313x.2006.02914.x] [Citation(s) in RCA: 117] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
Contrary to expectations based on the visible phenotypic behavior of seedlings undergoing de-etiolation in response to continuous red light (Rc), previous gene expression profiling showed that one or more of the five-membered phytochrome (phy) family of Arabidopsis, other than phyB, is predominantly responsible for transducing the Rc signals to light-responsive genes. To begin to identify which phys are involved, and to define potential primary targets of phy signaling, we have examined the genome-wide expression profiles of genes responding to Rc within 1 h (early response genes) of initial exposure of dark-grown wild-type, phyA, phyB and phyAphyB double mutant seedlings to the light signal. The data show that phyA has a quantitatively dominant role in Rc-induced expression of these early response genes, that phyB has minimal detectable regulatory activity in the presence of phyA, but assumes a quantitatively larger role in its absence, and that phyA and phyB combined are responsible for the full extent of Rc responsiveness of 96% of these genes. No evidence was obtained of a significant role for the remaining family members, phyC, phyD or phyE, in this process. In striking contrast, Rc-imposed repression of early response gene expression remains quantitatively strong in the phyAphyB double mutant, as well as the monogenic mutants, suggesting a significant role for one or more of the other three phys in this response. Examination of the established or predicted functional roles of the early response genes indicates that genes encoding transcription factors represent the largest single category, at a frequency three times their prevalence genome-wide. This dominance is particularly striking among those genes responding most robustly to the Rc signal, where >50% are classified as involved in transcriptional regulation, suggesting that these may have potentially primary regulatory roles at the interface between phy signaling and the light-responsive transcriptional network. Integration of the present data with those of a previous genome-scale transcriptional analysis of a pif3 mutant, suggests a complex network involving perception and transduction of inductive Rc signals by both phyA and phyB through both PIF3 and other undefined signaling partners to early response genes.
Collapse
Affiliation(s)
- James M Tepperman
- Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720, USA
| | | | | |
Collapse
|
47
|
Khanna R, Shen Y, Toledo-Ortiz G, Kikis EA, Johannesson H, Hwang YS, Quail PH. Functional profiling reveals that only a small number of phytochrome-regulated early-response genes in Arabidopsis are necessary for optimal deetiolation. THE PLANT CELL 2006; 18:2157-71. [PMID: 16891401 PMCID: PMC1560915 DOI: 10.1105/tpc.106.042200] [Citation(s) in RCA: 82] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/11/2023]
Abstract
In previous time-resolved microarray-based expression profiling, we identified 32 genes encoding putative transcription factors, signaling components, and unknown proteins that are rapidly and robustly induced by phytochrome (phy)-mediated light signals. Postulating that they are the most likely to be direct targets of phy signaling and to function in the primary phy regulatory circuitry, we examined the impact of targeted mutations in these genes on the phy-induced seedling deetiolation process in Arabidopsis thaliana. Using light-imposed concomitant inhibition of hypocotyl and stimulation of cotyledon growth as diagnostic criteria for normal deetiolation, we identified three major mutant response categories. Seven (22%) lines displayed statistically significant, reciprocal, aberrant photoresponsiveness in the two organs, suggesting disruption of normal deetiolation; 13 (41%) lines displayed significant defects either unidirectionally in both organs or in hypocotyls only, suggesting global effects not directly related to photomorphogenic signaling; and 12 (37%) lines displayed no significant difference in photoresponsiveness from the wild type. Potential reasons for the high proportion of rapidly light-responsive genes apparently unnecessary for the deetiolation phenotype are discussed. One of the seven disrupted genes displaying a significant mutant phenotype, the basic helix-loop-helix factor-encoding PHYTOCHROME-INTERACTING FACTOR3-LIKE1 gene, was found to be necessary for rapid light-induced expression of the photomorphogenesis- and circadian-related PSEUDO-RESPONSE REGULATOR9 gene, indicating a regulatory function in the early phy-induced transcriptional network.
Collapse
Affiliation(s)
- Rajnish Khanna
- Department of Plant and Microbial Biology, University of California, Berkeley, 94720, USA
| | | | | | | | | | | | | |
Collapse
|
48
|
Garg AK, Sawers RJH, Wang H, Kim JK, Walker JM, Brutnell TP, Parthasarathy MV, Vierstra RD, Wu RJ. Light-regulated overexpression of an Arabidopsis phytochrome A gene in rice alters plant architecture and increases grain yield. PLANTA 2006; 223:627-36. [PMID: 16136335 DOI: 10.1007/s00425-005-0101-3] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/07/2005] [Accepted: 07/15/2005] [Indexed: 05/04/2023]
Abstract
The phytochromes are a family of red/far-red light absorbing photoreceptors that control plant developmental and metabolic processes in response to changes in the light environment. We report here the overexpression of Arabidopsis thaliana PHYTOCHROME A (PHYA) gene in a commercially important indica rice variety (Oryza sativa L. Pusa Basmati-1). The expression of the transgene was driven by the light-regulated and tissue-specific rice rbcS promoter. Several independent homozygous sixth generation (T(5)) transgenic lines were characterized and shown to accumulate relatively high levels of PHYA protein in the light. Under both far-red and red light, PHYA-overexpressing lines showed inhibition of the coleoptile extension in comparison to non-transgenic seedlings. Furthermore, compared with non-transgenic rice plants, mature transgenic plants showed significant reduction in plant height, internode length and internode diameter (including differences in cell size and number), and produced an increased number of panicles per plant. Under greenhouse conditions, rice grain yield was 6-21% higher in three PHYA-overexpressing lines than in non-transgenic plants. These results demonstrate the potential of manipulating light signal-transduction pathways to minimize the problems of lodging in basmati/aromatic rice and to enhance grain productivity.
Collapse
Affiliation(s)
- Ajay K Garg
- Department of Molecular Biology and Genetics, Cornell University, Ithaca, New York 14853, USA
| | | | | | | | | | | | | | | | | |
Collapse
|
49
|
Takano M, Inagaki N, Xie X, Yuzurihara N, Hihara F, Ishizuka T, Yano M, Nishimura M, Miyao A, Hirochika H, Shinomura T. Distinct and cooperative functions of phytochromes A, B, and C in the control of deetiolation and flowering in rice. THE PLANT CELL 2005; 17:3311-25. [PMID: 16278346 PMCID: PMC1315371 DOI: 10.1105/tpc.105.035899] [Citation(s) in RCA: 224] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/05/2023]
Abstract
We have isolated phytochrome B (phyB) and phyC mutants from rice (Oryza sativa) and have produced all combinations of double mutants. Seedlings of phyB and phyB phyC mutants exhibited a partial loss of sensitivity to continuous red light (Rc) but still showed significant deetiolation responses. The responses to Rc were completely canceled in phyA phyB double mutants. These results indicate that phyA and phyB act in a highly redundant manner to control deetiolation under Rc. Under continuous far-red light (FRc), phyA mutants showed partially impaired deetiolation, and phyA phyC double mutants showed no significant residual phytochrome responses, indicating that not only phyA but also phyC is involved in the photoperception of FRc in rice. Interestingly, the phyB phyC double mutant displayed clear R/FR reversibility in the pulse irradiation experiments, indicating that both phyA and phyB can mediate the low-fluence response for gene expression. Rice is a short-day plant, and we found that mutation in either phyB or phyC caused moderate early flowering under the long-day photoperiod, while monogenic phyA mutation had little effect on the flowering time. The phyA mutation, however, in combination with phyB or phyC mutation caused dramatic early flowering.
Collapse
Affiliation(s)
- Makoto Takano
- Department of Plant Physiology, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki, Japan.
| | | | | | | | | | | | | | | | | | | | | |
Collapse
|
50
|
Shen Y, Feng S, Ma L, Lin R, Qu LJ, Chen Z, Wang H, Deng XW. Arabidopsis FHY1 protein stability is regulated by light via phytochrome A and 26S proteasome. PLANT PHYSIOLOGY 2005; 139:1234-43. [PMID: 16244150 PMCID: PMC1283761 DOI: 10.1104/pp.105.067645] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2005] [Revised: 08/29/2005] [Accepted: 09/08/2005] [Indexed: 05/05/2023]
Abstract
Phytochrome A (phyA) is the primary photoreceptor mediating responses to far-red light. Among the phyA downstream signaling components, Far-red Elongated Hypocotyl 1 (FHY1) is a genetically defined positive regulator of photomorphogenesis in far-red light. Both physiological and genomic characterization of the fhy1 mutants indicated a close functional relationship of FHY1 with phyA. Here, we showed that FHY1 is most abundant in young seedlings grown in darkness and is quickly down-regulated during further seedling development and by light exposure. By using light-insensitive 35S promoter-driven functional beta-glucuronidase-FHY1 and green fluorescent protein-FHY1 fusion proteins, we showed that this down-regulation of FHY1 protein abundance by light is largely at posttranscriptional level and most evident in the nuclei. The light-triggered FHY1 protein reduction is primarily mediated through the 26S proteasome-dependent protein degradation. Further, phyA is directly involved in mediating the light-triggered down-regulation of FHY1, and the dark accumulation of FHY1 requires functional pleiotropic Constitutive Photomorphogenic/De-Etiolated/Fusca proteins. Our data indicate that phyA, the 26S proteasome, and the Constitutive Photomorphogenic/De-Etiolated/Fusca proteins are all involved in the light regulation of FHY1 protein abundance during Arabidopsis (Arabidopsis thaliana) seedling development.
Collapse
Affiliation(s)
- Yunping Shen
- Peking-Yale Joint Center of Plant Molecular Genetics and Agrobiotechnology, College of Life Sciences, Peking University, Beijing 100871, China
| | | | | | | | | | | | | | | |
Collapse
|