1
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Willige BC, Yoo CY, Saldierna Guzmán JP. What is going on inside of phytochrome B photobodies? THE PLANT CELL 2024; 36:2065-2085. [PMID: 38511271 PMCID: PMC11132900 DOI: 10.1093/plcell/koae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 12/20/2023] [Accepted: 01/08/2024] [Indexed: 03/22/2024]
Abstract
Plants exhibit an enormous phenotypic plasticity to adjust to changing environmental conditions. For this purpose, they have evolved mechanisms to detect and measure biotic and abiotic factors in their surroundings. Phytochrome B exhibits a dual function, since it serves as a photoreceptor for red and far-red light as well as a thermosensor. In 1999, it was first reported that phytochromes not only translocate into the nucleus but also form subnuclear foci upon irradiation by red light. It took more than 10 years until these phytochrome speckles received their name; these foci were coined photobodies to describe unique phytochrome-containing subnuclear domains that are regulated by light. Since their initial discovery, there has been much speculation about the significance and function of photobodies. Their presumed roles range from pure experimental artifacts to waste deposits or signaling hubs. In this review, we summarize the newest findings about the meaning of phyB photobodies for light and temperature signaling. Recent studies have established that phyB photobodies are formed by liquid-liquid phase separation via multivalent interactions and that they provide diverse functions as biochemical hotspots to regulate gene expression on multiple levels.
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Affiliation(s)
- Björn Christopher Willige
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
| | - Chan Yul Yoo
- School of Biological Sciences, University of Utah, UT 84112, USA
| | - Jessica Paola Saldierna Guzmán
- Department of Soil and Crop Sciences, College of Agricultural Sciences, Colorado State University, Fort Collins, CO 80521, USA
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2
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Huq E, Lin C, Quail PH. Light signaling in plants-a selective history. PLANT PHYSIOLOGY 2024; 195:213-231. [PMID: 38431282 PMCID: PMC11060691 DOI: 10.1093/plphys/kiae110] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Revised: 12/15/2023] [Accepted: 02/16/2024] [Indexed: 03/05/2024]
Abstract
In addition to providing the radiant energy that drives photosynthesis, sunlight carries signals that enable plants to grow, develop and adapt optimally to the prevailing environment. Here we trace the path of research that has led to our current understanding of the cellular and molecular mechanisms underlying the plant's capacity to perceive and transduce these signals into appropriate growth and developmental responses. Because a fully comprehensive review was not possible, we have restricted our coverage to the phytochrome and cryptochrome classes of photosensory receptors, while recognizing that the phototropin and UV classes also contribute importantly to the full scope of light-signal monitoring by the plant.
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Affiliation(s)
- Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Chentao Lin
- Basic Forestry and Plant Proteomics Research Center, Fujian Agriculture and Forestry University, Fuzhou 350002, China
| | - Peter H Quail
- Department of Plant and Microbial Biology, University of California, Berkeley, Berkeley, CA 94720, USA
- Plant Gene Expression Center, Agricultural Research Service, US Department of Agriculture, Albany, CA 94710, USA
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3
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions of PIF5 degradation and stabilization. Nat Commun 2024; 15:3519. [PMID: 38664420 PMCID: PMC11045832 DOI: 10.1038/s41467-024-47790-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2023] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear membraneless organelles named photobodies (PBs). However, the function of PBs in PHYB signaling remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR 5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. Conversely, reducing PB size by dim light, which enhanced PB dynamics and nucleoplasmic PHYB and PIF5, switched the balance towards PIF5 degradation. Together, these results reveal that PB formation spatially segregates two antagonistic PHYB signaling actions - PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm - which could enable an environmentally sensitive, counterbalancing mechanism to titrate nucleoplasmic PIF5 and environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
- Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju, 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA, 92521, USA.
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4
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Chang HH, Huang LC, Browning KS, Huq E, Cheng MC. The phosphorylation of carboxyl-terminal eIF2α by SPA kinases contributes to enhanced translation efficiency during photomorphogenesis. Nat Commun 2024; 15:3467. [PMID: 38658612 PMCID: PMC11043401 DOI: 10.1038/s41467-024-47848-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2023] [Accepted: 04/11/2024] [Indexed: 04/26/2024] Open
Abstract
Light triggers an enhancement of global translation during photomorphogenesis in Arabidopsis, but little is known about the underlying mechanisms. The phosphorylation of the α-subunit of eukaryotic initiation factor 2 (eIF2α) at a conserved serine residue in the N-terminus has been shown as an important mechanism for the regulation of protein synthesis in mammalian and yeast cells. However, whether the phosphorylation of this residue in plant eIF2α plays a role in regulation of translation remains elusive. Here, we show that the quadruple mutant of SUPPRESSOR OF PHYA-105 family members (SPA1-SPA4) display repressed translation efficiency after light illumination. Moreover, SPA1 directly phosphorylates the eIF2α C-terminus under light conditions. The C-term-phosphorylated eIF2α promotes translation efficiency and photomorphogenesis, whereas the C-term-unphosphorylated eIF2α results in a decreased translation efficiency. We also demonstrate that the phosphorylated eIF2α enhances ternary complex assembly by promoting its affinity to eIF2β and eIF2γ. This study reveals a unique mechanism by which light promotes translation via SPA1-mediated phosphorylation of the C-terminus of eIF2α in plants.
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Affiliation(s)
- Hui-Hsien Chang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Lin-Chen Huang
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan
| | - Karen S Browning
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, Austin, TX, 78712, USA
| | - Mei-Chun Cheng
- Department of Biochemical Science and Technology, National Taiwan University, Taipei, 10617, Taiwan.
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5
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Wang W, Kim J, Martinez TS, Huq E, Sung S. COP1 controls light-dependent chromatin remodeling. Proc Natl Acad Sci U S A 2024; 121:e2312853121. [PMID: 38349881 PMCID: PMC10895365 DOI: 10.1073/pnas.2312853121] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2023] [Accepted: 01/03/2024] [Indexed: 02/15/2024] Open
Abstract
Light is a crucial environmental factor that impacts various aspects of plant development. Phytochromes, as light sensors, regulate myriads of downstream genes to mediate developmental reprogramming in response to changes in environmental conditions. CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) is an E3 ligase for a number of substrates in light signaling, acting as a central repressor of photomorphogenesis. The interplay between phytochrome B (phyB) and COP1 forms an antagonistic regulatory module that triggers extensive gene expression reprogramming when exposed to light. Here, we uncover a role of COP1 in light-dependent chromatin remodeling through the regulation of VIL1 (VIN3-LIKE 1)/VERNALIZATION 5, a Polycomb protein. VIL1 directly interacts with phyB and regulates photomorphogenesis through the formation of repressive chromatin loops at downstream growth-promoting genes in response to light. Furthermore, we reveal that COP1 governs light-dependent formation of chromatin loop and limiting a repressive histone modification to fine-tune expressions of growth-promoting genes during photomorphogenesis through VIL1.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Teresa S Martinez
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712
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6
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Liu W, Giuriani G, Havlikova A, Li D, Lamont DJ, Neugart S, Velanis CN, Petersen J, Hoecker U, Christie JM, Jenkins GI. Phosphorylation of Arabidopsis UVR8 photoreceptor modulates protein interactions and responses to UV-B radiation. Nat Commun 2024; 15:1221. [PMID: 38336824 PMCID: PMC10858049 DOI: 10.1038/s41467-024-45575-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/09/2023] [Accepted: 01/27/2024] [Indexed: 02/12/2024] Open
Abstract
Exposure of plants to ultraviolet-B (UV-B) radiation initiates transcriptional responses that modify metabolism, physiology and development to enhance viability in sunlight. Many of these regulatory responses to UV-B radiation are mediated by the photoreceptor UV RESISTANCE LOCUS 8 (UVR8). Following photoreception, UVR8 interacts directly with multiple proteins to regulate gene expression, but the mechanisms that control differential protein binding to initiate distinct responses are unknown. Here we show that UVR8 is phosphorylated at several sites and that UV-B stimulates phosphorylation at Serine 402. Site-directed mutagenesis to mimic Serine 402 phosphorylation promotes binding of UVR8 to REPRESSOR OF UV-B PHOTOMORPHOGENESIS (RUP) proteins, which negatively regulate UVR8 action. Complementation of the uvr8 mutant with phosphonull or phosphomimetic variants suggests that phosphorylation of Serine 402 modifies UVR8 activity and promotes flavonoid biosynthesis, a key UV-B-stimulated response that enhances plant protection and crop nutritional quality. This research provides a basis to understand how UVR8 interacts differentially with effector proteins to regulate plant responses to UV-B radiation.
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Affiliation(s)
- Wei Liu
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Giovanni Giuriani
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Anezka Havlikova
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Dezhi Li
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Douglas J Lamont
- FingerPrints Proteomics Facility, School of Life Sciences, Discovery Centre, University of Dundee, Dow Street, Dundee, DD1 5EH, UK
| | - Susanne Neugart
- Department of Crop Sciences, Division Quality and Sensory of Plant Products, Georg-August-Universität Göttingen, D-37075, Göttingen, Germany
| | - Christos N Velanis
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
- School of Life, Health and Chemical Sciences, Faculty of Science, Technology, Engineering and Maths, Venables Building, The Open University, Walton Hall Campus, Milton Keynes, MK7 6AA, UK
| | - Jan Petersen
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
- Matthias Schleiden Institute of Genetics, Bioinformatics and Molecular Botany, Friedrich Schiller University, 07743, Jena, Germany
| | - Ute Hoecker
- Botanical Institute and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Köln, 50923, Köln, Germany
| | - John M Christie
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK
| | - Gareth I Jenkins
- School of Molecular Biosciences, College of Medical, Veterinary and Life Sciences, Bower Building, University of Glasgow, Glasgow, G12 8QQ, UK.
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7
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Ranjan A, Michael R, Gautam S, Trivedi PK. HY5-dependent light-mediated regulation of galactinol synthase gene, AtGolS1, modulates galactinol biosynthesis in Arabidopsis. Biochem Biophys Res Commun 2024; 695:149423. [PMID: 38157630 DOI: 10.1016/j.bbrc.2023.149423] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2023] [Accepted: 12/20/2023] [Indexed: 01/03/2024]
Abstract
The Raffinose Family of Oligosaccharides (RFOs), including Galactinol, Raffinose, and Stachyose, are pivotal carbohydrates with significant roles in abiotic stress tolerance and growth within dynamic environments. Plant development is profoundly influenced by light, a major environmental signal. Despite this, the interconnections between the biosynthesis of secondary sugars and light signaling have remained unexplored. This study reveals that exposure to light induces the expression of Galactinol synthase (AtGolS1), a key enzyme in the RFO biosynthesis pathway. The light-inducible response of AtGolS1 operates downstream of ELONGATED HYPOCOTYL 5 (HY5), a central regulator in light signaling. Mutant seedlings with disrupted HY5 function (hy5-215) exhibit reduced AtGolS1 transcript accumulation compared to wild-type (WT) and HY5 overexpression seedlings. DNA-protein interaction studies demonstrate that HY5 directly binds to light-responsive cis-elements in the promoter region of AtGolS1, thereby mediating its light responsiveness. Quantification of galactinol revealed a diminished accumulation in the hy5-215 mutant compared to wild-type (WT) and HY5 overexpression seedlings. Consequently, these findings shed light on the intricate crosstalk between RFO biosynthesis and light signaling in Arabidopsis.
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Affiliation(s)
- Avriti Ranjan
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India
| | - Rahul Michael
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Swati Gautam
- CSIR-National Botanical Research Institute, Council of Scientific and Industrial Research (CSIR-NBRI), Rana Pratap Marg, Lucknow, 226001, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India
| | - Prabodh Kumar Trivedi
- Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, 201002, India; CSIR-Central Institute of Medicinal and Aromatic Plants, Lucknow, 226015, India.
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8
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Kim RJA, Fan D, He J, Kim K, Du J, Chen M. Photobody formation spatially segregates two opposing phytochrome B signaling actions to titrate plant environmental responses. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2023.11.12.566724. [PMID: 38014306 PMCID: PMC10680666 DOI: 10.1101/2023.11.12.566724] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/29/2023]
Abstract
Photoactivation of the plant photoreceptor and thermosensor phytochrome B (PHYB) triggers its condensation into subnuclear photobodies (PBs). However, the function of PBs remains frustratingly elusive. Here, we found that PHYB recruits PHYTOCHROME-INTERACTING FACTOR5 (PIF5) to PBs. Surprisingly, PHYB exerts opposing roles in degrading and stabilizing PIF5. Perturbing PB size by overproducing PHYB provoked a biphasic PIF5 response: while a moderate increase in PHYB enhanced PIF5 degradation, further elevating the PHYB level stabilized PIF5 by retaining more of it in enlarged PBs. These results reveal a PB-mediated light and temperature sensing mechanism, in which PHYB condensation confers the co-occurrence and competition of two antagonistic phase-separated PHYB signaling actions-PIF5 stabilization in PBs and PIF5 degradation in the surrounding nucleoplasm-thereby enabling an environmentally-sensitive counterbalancing mechanism to titrate nucleoplasmic PIF5 and its transcriptional output. This PB-enabled signaling mechanism provides a framework for regulating a plethora of PHYB-interacting signaling molecules in diverse plant environmental responses.
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Affiliation(s)
- Ruth Jean Ae Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - De Fan
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - Jiangman He
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- These authors contributed equally
| | - Keunhwa Kim
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
- Current address: Plant Molecular Biology and Biotechnology Research Center, Gyeongsang National University, Jinju 52828, Republic of Korea
| | - Juan Du
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
| | - Meng Chen
- Department of Botany and Plant Sciences, Institute for Integrative Genome Biology, University of California, Riverside, CA 92521, USA
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9
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Lee S, Huq E. Characterization of PIF4 Phosphorylation by SPA1. Methods Mol Biol 2024; 2795:161-167. [PMID: 38594537 DOI: 10.1007/978-1-0716-3814-9_16] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/11/2024]
Abstract
The PHYTOCHROME INTERACTING FACTORs (PIFs) play pivotal roles in regulating thermo- and photo-morphogenesis in Arabidopsis. One of the main hubs in thermomorphogenesis is PIF4, which regulates plant development under high ambient temperature along with other PIFs. PIF4 enhances its own transcription and PIF4 protein is stabilized under high ambient temperature. However, the mechanisms of thermo-stabilization of PIF4 are less understood. Recently, it was shown that SUPPRESSOR OF PHYA-105 1 (SPA1) can function as a serine/threonine kinase to phosphorylate PIF4 in vitro, and the phosphorylated form of PIF4 is more stable under high ambient temperature conditions. In this chapter, we describe the in vitro kinase assay of PIF4 by SPA1. In principle, this protocol can be applied for other putative substrates and kinases.
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Affiliation(s)
- Sanghwa Lee
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
- Plant Molecular and Cellular Biology Laboratory, Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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10
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Kinmonth-Schultz H, Walker SM, Bingol K, Hoyt DW, Kim YM, Markillie LM, Mitchell HD, Nicora CD, Taylor R, Ward JK. Oligosaccharide production and signaling correlate with delayed flowering in an Arabidopsis genotype grown and selected in high [CO2]. PLoS One 2023; 18:e0287943. [PMID: 38153952 PMCID: PMC10754469 DOI: 10.1371/journal.pone.0287943] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Accepted: 12/05/2023] [Indexed: 12/30/2023] Open
Abstract
Since industrialization began, atmospheric CO2 ([CO2]) has increased from 270 to 415 ppm and is projected to reach 800-1000 ppm this century. Some Arabidopsis thaliana (Arabidopsis) genotypes delayed flowering in elevated [CO2] relative to current [CO2], while others showed no change or accelerations. To predict genotype-specific flowering behaviors, we must understand the mechanisms driving flowering response to rising [CO2]. [CO2] changes alter photosynthesis and carbohydrates in plants. Plants sense carbohydrate levels, and exogenous carbohydrate application influences flowering time and flowering transcript levels. We asked how organismal changes in carbohydrates and transcription correlate with changes in flowering time under elevated [CO2]. We used a genotype (SG) of Arabidopsis that was selected for high fitness at elevated [CO2] (700 ppm). SG delays flowering under elevated [CO2] (700 ppm) relative to current [CO2] (400 ppm). We compared SG to a closely related control genotype (CG) that shows no [CO2]-induced flowering change. We compared metabolomic and transcriptomic profiles in these genotypes at current and elevated [CO2] to assess correlations with flowering in these conditions. While both genotypes altered carbohydrates in response to elevated [CO2], SG had higher levels of sucrose than CG and showed a stronger increase in glucose and fructose in elevated [CO2]. Both genotypes demonstrated transcriptional changes, with CG increasing genes related to fructose 1,6-bisphosphate breakdown, amino acid synthesis, and secondary metabolites; and SG decreasing genes related to starch and sugar metabolism, but increasing genes involved in oligosaccharide production and sugar modifications. Genes associated with flowering regulation within the photoperiod, vernalization, and meristem identity pathways were altered in these genotypes. Elevated [CO2] may alter carbohydrates to influence transcription in both genotypes and delayed flowering in SG. Changes in the oligosaccharide pool may contribute to delayed flowering in SG. This work extends the literature exploring genotypic-specific flowering responses to elevated [CO2].
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Affiliation(s)
- Hannah Kinmonth-Schultz
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
- Departiment of Biology, Tennessee Technological University, Cookeville, TN, United States of America
| | - Stephen Michael Walker
- Department of Ecology and Evolutionary Biology, University of Kansas, Lawrence, KS, United States of America
| | - Kerem Bingol
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - David W. Hoyt
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Young-Mo Kim
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Lye Meng Markillie
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Hugh D. Mitchell
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Carrie D. Nicora
- Department of Energy, Environmental Molecular Sciences Laboratory, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Ronald Taylor
- Biological Sciences Division, Pacific Northwest National Laboratory, Richland, WA, United States of America
| | - Joy K. Ward
- Department of Biology, College of Arts and Sciences, Case Western Reserve University, Cleveland, OH, United States of America
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11
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Li S, Sun Z, Sang Q, Qin C, Kong L, Huang X, Liu H, Su T, Li H, He M, Fang C, Wang L, Liu S, Liu B, Liu B, Fu X, Kong F, Lu S. Soybean reduced internode 1 determines internode length and improves grain yield at dense planting. Nat Commun 2023; 14:7939. [PMID: 38040709 PMCID: PMC10692089 DOI: 10.1038/s41467-023-42991-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2023] [Accepted: 10/26/2023] [Indexed: 12/03/2023] Open
Abstract
Major cereal crops have benefitted from Green Revolution traits such as shorter and more compact plants that permit high-density planting, but soybean has remained relatively overlooked. To balance ideal soybean yield with plant height under dense planting, shortening of internodes without reducing the number of nodes and pods is desired. Here, we characterized a short-internode soybean mutant, reduced internode 1 (rin1). Partial loss of SUPPRESSOR OF PHYA 105 3a (SPA3a) underlies rin1. RIN1 physically interacts with two homologs of ELONGATED HYPOCOTYL 5 (HY5), STF1 and STF2, to promote their degradation. RIN1 regulates gibberellin metabolism to control internode development through a STF1/STF2-GA2ox7 regulatory module. In field trials, rin1 significantly enhances grain yield under high-density planting conditions comparing to its wild type of elite cultivar. rin1 mutants therefore could serve as valuable resources for improving grain yield under high-density cultivation and in soybean-maize intercropping systems.
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Affiliation(s)
- Shichen Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China
| | - Zhihui Sun
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Qing Sang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Qin
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Lingping Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xin Huang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Huan Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Tong Su
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Haiyang Li
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Milan He
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Chao Fang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Lingshuang Wang
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Shuangrong Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China.
| | - Baohui Liu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Xiangdong Fu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing, 100101, China.
| | - Fanjiang Kong
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
- The Innovative Academy of Seed Design, Key Laboratory of Soybean Molecular Design Breeding, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Harbin, 150081, China.
| | - Sijia Lu
- Guangdong Key Laboratory of Plant Adaptation and Molecular Design, Guangzhou Key Laboratory of Crop Gene Editing, Innovative Center of Molecular Genetics and Evolution, School of Life Sciences, Guangzhou University, Guangzhou, 510006, China.
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12
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Zhao Y, Zheng X, Zhang X, Wang W, Cai G, Bi G, Chen S, Sun C, Zhou JM. PIF3 is phosphorylated by MAPK to modulate plant immunity. THE NEW PHYTOLOGIST 2023; 240:372-381. [PMID: 37475167 DOI: 10.1111/nph.19139] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2022] [Accepted: 06/27/2023] [Indexed: 07/22/2023]
Abstract
Surface-localized pattern recognition receptors perceive pathogen-associated molecular patterns (PAMPs) to activate pattern-triggered immunity (PTI). Activation of mitogen-activated protein kinases (MAPKs) represents a major PTI response. Here, we report that Arabidopsis thaliana PIF3 negatively regulates plant defense gene expression and resistance to Pseudomonas syringae DC3000. PAMPs trigger phosphorylation of PIF3. Further study reveals that PIF3 interacts with and is phosphorylated by MPK3/6. By mass spectrometry and site-directed mutagenesis, we identified the corresponding phosphorylation sites which fit for SP motif. We further show that a phospho-mimicking PIF3 variant (PIF36D /pifq) conferred increased susceptibility to P. syringae DC3000 and caused lower levels of defense gene expression in plants. Together, this study reveals that PIF3 is phosphorylated by MPK3/6 and phosphorylation of the SP motif residues is required for its negative regulation on plant immunity.
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Affiliation(s)
- Yan Zhao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Xiaojuan Zheng
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Xiaojuan Zhang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Wei Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
| | - Gaihong Cai
- National Institute of Biological Sciences, Beijing, 100101, China
| | - Guozhi Bi
- College of Biological Sciences, China Agricultural University, Beijing, 100193, China
| | - She Chen
- National Institute of Biological Sciences, Beijing, 100101, China
| | - Chuanqing Sun
- State Key Laboratory of Hybrid Rice, Hunan Hybrid Rice Research Center, Hunan Academy of Agricultural Sciences, Changsha, 410125, China
| | - Jian-Min Zhou
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
- CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
- Hainan Yazhou Bay Seed Laboratory, Sanya, Hainan, 572025, China
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13
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Bhatnagar A, Burman N, Sharma E, Tyagi A, Khurana P, Khurana JP. Two splice forms of OsbZIP1, a homolog of AtHY5, function to regulate skotomorphogenesis and photomorphogenesis in rice. PLANT PHYSIOLOGY 2023; 193:426-447. [PMID: 37300540 DOI: 10.1093/plphys/kiad334] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/24/2023] [Revised: 04/24/2023] [Accepted: 05/05/2023] [Indexed: 06/12/2023]
Abstract
Plants possess well-developed light sensing mechanisms and signal transduction systems for regulating photomorphogenesis. ELONGATED HYPOCOTYL5 (HY5), a basic leucine zipper (bZIP) transcription factor, has been extensively characterized in dicots. In this study, we show that OsbZIP1 is a functional homolog of Arabidopsis (Arabidopsis thaliana) HY5 (AtHY5) and is important for light-mediated regulation of seedling and mature plant development in rice (Oryza sativa). Ectopic expression of OsbZIP1 in rice reduced plant height and leaf length without affecting plant fertility, which contrasts with OsbZIP48, a previously characterized HY5 homolog. OsbZIP1 is alternatively spliced, and the OsbZIP1.2 isoform lacking the CONSTITUTIVELY PHOTOMORPHOGENIC1 (COP1)-binding domain regulated seedling development in the dark. Rice seedlings overexpressing OsbZIP1 were shorter than the vector control under white and monochromatic light conditions, whereas RNAi knockdown seedlings displayed the opposite phenotype. While OsbZIP1.1 was light-regulated, OsbZIP1.2 showed a similar expression profile in both light and dark conditions. Due to its interaction with OsCOP1, OsbZIP1.1 undergoes 26S proteasome-mediated degradation under dark conditions. Also, OsbZIP1.1 interacted with and was phosphorylated by CASEIN KINASE2 (OsCK2α3). In contrast, OsbZIP1.2 did not show any interaction with OsCOP1 or OsCK2α3. We propose that OsbZIP1.1 likely regulates seedling development in the light, while OsbZIP1.2 is the dominant player under dark conditions. The data presented in this study reveal that AtHY5 homologs in rice have undergone neofunctionalization, and alternative splicing of OsbZIP1 has increased the repertoire of its functions.
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Affiliation(s)
- Akanksha Bhatnagar
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Naini Burman
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
- Regional Centre for Biotechnology, Faridabad, Haryana 121001, India
| | - Eshan Sharma
- Interdisciplinary Centre for Plant Genomics & Department of Plant Molecular Biology, University of Delhi South Campus, New Delhi 110021, India
| | - Akhilesh Tyagi
- 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
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14
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Han R, Ma L, Lv Y, Qi L, Peng J, Li H, Zhou Y, Song P, Duan J, Li J, Li Z, Terzaghi W, Guo Y, Li J. SALT OVERLY SENSITIVE2 stabilizes phytochrome-interacting factors PIF4 and PIF5 to promote Arabidopsis shade avoidance. THE PLANT CELL 2023; 35:2972-2996. [PMID: 37119311 PMCID: PMC10396385 DOI: 10.1093/plcell/koad119] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Sun-loving plants trigger the shade avoidance syndrome (SAS) to compete against their neighbors for sunlight. Phytochromes are plant red (R) and far-red (FR) light photoreceptors that play a major role in perceiving the shading signals and triggering SAS. Shade induces a reduction in the level of active phytochrome B (phyB), thus increasing the abundance of PHYTOCHROME-INTERACTING FACTORS (PIFs), a group of growth-promoting transcription factors. However, whether other factors are involved in modulating PIF activity in the shade remains largely obscure. Here, we show that SALT OVERLY SENSITIVE2 (SOS2), a protein kinase essential for salt tolerance, positively regulates SAS in Arabidopsis thaliana. SOS2 directly phosphorylates PIF4 and PIF5 at a serine residue close to their conserved motif for binding to active phyB. This phosphorylation thus decreases their interaction with phyB and posttranslationally promotes PIF4 and PIF5 protein accumulation. Notably, the role of SOS2 in regulating PIF4 and PIF5 protein abundance and SAS is more prominent under salt stress. Moreover, phyA and phyB physically interact with SOS2 and promote SOS2 kinase activity in the light. Collectively, our study uncovers an unexpected role of salt-activated SOS2 in promoting SAS by modulating the phyB-PIF module, providing insight into the coordinated response of plants to salt stress and shade.
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Affiliation(s)
- Run Han
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liang Ma
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yang Lv
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Peng
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Pengyu Song
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianfang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, PA 18766, USA
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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15
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Ma L, Han R, Yang Y, Liu X, Li H, Zhao X, Li J, Fu H, Huo Y, Sun L, Yan Y, Zhang H, Li Z, Tian F, Li J, Guo Y. Phytochromes enhance SOS2-mediated PIF1 and PIF3 phosphorylation and degradation to promote Arabidopsis salt tolerance. THE PLANT CELL 2023; 35:2997-3020. [PMID: 37119239 PMCID: PMC10396371 DOI: 10.1093/plcell/koad117] [Citation(s) in RCA: 22] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2022] [Revised: 03/08/2023] [Accepted: 04/10/2023] [Indexed: 06/19/2023]
Abstract
Soil salinity is one of the most detrimental abiotic stresses affecting plant survival, and light is a core environmental signal regulating plant growth and responses to abiotic stress. However, how light modulates the plant's response to salt stress remains largely obscure. Here, we show that Arabidopsis (Arabidopsis thaliana) seedlings are more tolerant to salt stress in the light than in the dark, and that the photoreceptors phytochrome A (phyA) and phyB are involved in this tolerance mechanism. We further show that phyA and phyB physically interact with the salt tolerance regulator SALT OVERLY SENSITIVE2 (SOS2) in the cytosol and nucleus, and enhance salt-activated SOS2 kinase activity in the light. Moreover, SOS2 directly interacts with and phosphorylates PHYTOCHROME-INTERACTING FACTORS PIF1 and PIF3 in the nucleus. Accordingly, PIFs act as negative regulators of plant salt tolerance, and SOS2 phosphorylation of PIF1 and PIF3 decreases their stability and relieves their repressive effect on plant salt tolerance in both light and dark conditions. Together, our study demonstrates that photoactivated phyA and phyB promote plant salt tolerance by increasing SOS2-mediated phosphorylation and degradation of PIF1 and PIF3, thus broadening our understanding of how plants adapt to salt stress according to their dynamic light environment.
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Affiliation(s)
- Liang Ma
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Run Han
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yongqing Yang
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiangning Liu
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoyun Zhao
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jianfang Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Haiqi Fu
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yandan Huo
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Liping Sun
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Yan
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hongyan Zhang
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Zhen Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Feng Tian
- National Maize Improvement Center, Key Laboratory of Biology and Genetic Improvement of Maize (MOA), Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing 100193, China
| | - Jigang Li
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yan Guo
- State Key Laboratory of Plant Environmental Resilience (SKLPER), College of Biological Sciences, China Agricultural University, Beijing 100193, China
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16
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Chen L, Li Q, Wang M, Xiao F, Li K, Yang R, Sun M, Zhang H, Guo J, Chen J, Jiao F. ZmCOP1 Regulates Maize Mesocotyl Length and Plant Height through the Phytohormone Pathways. Life (Basel) 2023; 13:1522. [PMID: 37511897 PMCID: PMC10381158 DOI: 10.3390/life13071522] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2023] [Revised: 06/27/2023] [Accepted: 06/30/2023] [Indexed: 07/30/2023] Open
Abstract
The morphogenesis of crops is critical to their yield performance. COP1 (constitutively photomorphogenic1) is one of the core regulators in plant morphogenesis and has been deeply studied in Arabidopsis thaliana. However, the function of COP1 in maize is still unclear. Here, we found that the mesocotyl lengths of zmcop1 loss-of-function mutants were shorter than those of wild-type B73 in darkness, while the mesocotyl lengths of lines with ZmCOP1 overexpression were longer than those of wild-type B104. The plant height with zmcop1 was shorter than that of B73 in both short- and long-day photoperiods. Using transcriptome RNA sequencing technology, we identified 33 DEGs (differentially expressed genes) between B73's etiolated seedlings and those featuring zmcop1, both in darkness. The DEGs were mainly enriched in the plant phytohormone pathways. Our results provide direct evidence that ZmCOP1 functions in the elongation of etiolated seedlings in darkness and affects plant height in light. Our data can be applied in the improvement of maize plant architecture.
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Affiliation(s)
- Liping Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Qiuhua Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Ming Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Feng Xiao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Kangshi Li
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Ran Yang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Meng Sun
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Haiyan Zhang
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Jinjie Guo
- State Key Laboratory of North China Crop Improvement and Regulation, Hebei Sub-Center for National Maize Improvement Center, College of Agronomy, Hebei Agricultural University, Baoding 071001, China
| | - Jingtang Chen
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
| | - Fuchao Jiao
- College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
- The Characteristic Laboratory of Crop Germplasm Innovation and Application, Provincial Department of Education, College of Agronomy, Qingdao Agricultural University, Qingdao 266109, China
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17
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Shor E, Skaliter O, Sharon E, Kitsberg Y, Bednarczyk D, Kerzner S, Vainstein D, Tabach Y, Vainstein A. Developmental and temporal changes in petunia petal transcriptome reveal scent-repressing plant-specific RING-kinase-WD40 protein. FRONTIERS IN PLANT SCIENCE 2023; 14:1180899. [PMID: 37360732 PMCID: PMC10286513 DOI: 10.3389/fpls.2023.1180899] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/06/2023] [Accepted: 05/05/2023] [Indexed: 06/28/2023]
Abstract
In moth-pollinated petunias, production of floral volatiles initiates when the flower opens and occurs rhythmically during the day, for optimal flower-pollinator interaction. To characterize the developmental transcriptomic response to time of day, we generated RNA-Seq databases for corollas of floral buds and mature flowers in the morning and in the evening. Around 70% of transcripts accumulating in petals demonstrated significant changes in expression levels in response to the flowers' transition from a 4.5-cm bud to a flower 1 day postanthesis (1DPA). Overall, 44% of the petal transcripts were differentially expressed in the morning vs. evening. Morning/evening changes were affected by flower developmental stage, with a 2.5-fold larger transcriptomic response to daytime in 1DPA flowers compared to buds. Analyzed genes known to encode enzymes in volatile organic compound biosynthesis were upregulated in 1DPA flowers vs. buds-in parallel with the activation of scent production. Based on analysis of global changes in the petal transcriptome, PhWD2 was identified as a putative scent-related factor. PhWD2 is a protein that is uniquely present in plants and has a three-domain structure: RING-kinase-WD40. Suppression of PhWD2 (termed UPPER - Unique Plant PhEnylpropanoid Regulator) resulted in a significant increase in the levels of volatiles emitted from and accumulated in internal pools, suggesting that it is a negative regulator of petunia floral scent production.
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Affiliation(s)
- Ekaterina Shor
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Oded Skaliter
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Elad Sharon
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Yaarit Kitsberg
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Dominika Bednarczyk
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Shane Kerzner
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
| | - Danny Vainstein
- School of Computer Science, Tel Aviv University, Tel Aviv, Israel
| | - Yuval Tabach
- The Institute for Medical Research, Israel-Canada, Hadassah Medical School, The Hebrew University of Jerusalem, Jerusalem, Israel
| | - Alexander Vainstein
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, The Hebrew University of Jerusalem, Rehovot, Israel
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18
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Sharma A, Samtani H, Sahu K, Sharma AK, Khurana JP, Khurana P. Functions of Phytochrome-Interacting Factors (PIFs) in the regulation of plant growth and development: A comprehensive review. Int J Biol Macromol 2023:125234. [PMID: 37290549 DOI: 10.1016/j.ijbiomac.2023.125234] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2023] [Revised: 06/02/2023] [Accepted: 06/04/2023] [Indexed: 06/10/2023]
Abstract
Transcription factors play important roles in governing plant responses upon changes in their ambient conditions. Any fluctuation in the supply of critical requirements for plants, such as optimum light, temperature, and water leads to the reprogramming of gene-signaling pathways. At the same time, plants also evaluate and shift their metabolism according to the various stages of development. Phytochrome-Interacting Factors are one of the most important classes of transcription factors that regulate both developmental and external stimuli-based growth of plants. This review focuses on the identification of PIFs in various organisms, regulation of PIFs by various proteins, functions of PIFs of Arabidopsis in diverse developmental pathways such as seed germination, photomorphogenesis, flowering, senescence, seed and fruit development, and external stimuli-induced plant responses such as shade avoidance response, thermomorphogenesis, and various abiotic stress responses. Recent advances related to the functional characterization of PIFs of crops such as rice, maize, and tomato have also been incorporated in this review, to ascertain the potential of PIFs as key regulators to enhance the agronomic traits of these crops. Thus, an attempt has been made to provide a holistic view of the function of PIFs in various processes in plants.
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Affiliation(s)
- Aishwarye Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Harsha Samtani
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Karishma Sahu
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Arun Kumar Sharma
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Jitendra Paul Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India
| | - Paramjit Khurana
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi 110021, India.
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19
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Fraikin GY, Belenikina NS, Rubin AB. Molecular Bases of Signaling Processes Regulated by Cryptochrome Sensory Photoreceptors in Plants. BIOCHEMISTRY. BIOKHIMIIA 2023; 88:770-782. [PMID: 37748873 DOI: 10.1134/s0006297923060056] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2023] [Revised: 04/28/2023] [Accepted: 05/02/2023] [Indexed: 09/27/2023]
Abstract
The blue-light sensors, cryptochromes, compose the extensive class of flavoprotein photoreceptors, regulating signaling processes in plants underlying their development, growth, and metabolism. In several algae, cryptochromes may act not only as sensory photoreceptors but also as photolyases, catalyzing repair of the UV-induced DNA lesions. Cryptochromes bind FAD as the chromophore at the photolyase homologous region (PHR) domain and contain the cryptochrome C-terminal extension (CCE), which is absent in photolyases. Photosensory process in cryptochrome is initiated by photochemical chromophore conversions, including formation of the FAD redox forms. In the state with the chromophore reduced to neutral radical (FADH×), the photoreceptor protein undergoes phosphorylation, conformational changes, and disengagement from the PHR domain and CCE with subsequent formation of oligomers of cryptochrome molecules. Photooligomerization is a structural basis of the functional activities of cryptochromes, since it ensures formation of their complexes with a variety of signaling proteins, including transcriptional factors and regulators of transcription. Interactions in such complexes change the protein signaling activities, leading to regulation of gene expression and plant photomorphogenesis. In recent years, multiple papers, reporting novel, more detailed information about the molecular mechanisms of above-mentioned processes were published. The present review mainly focuses on analysis of the data contained in these publications, particularly regarding structural aspects of the cryptochrome transitions into photoactivated states and regulatory signaling processes mediated by the cryptochrome photoreceptors in plants.
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Affiliation(s)
| | | | - Andrey B Rubin
- Lomonosov Moscow State University, Moscow, 119991, Russia
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20
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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.
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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
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Orthologs of Human-Disease-Associated Genes in Plants Are Involved in Regulating Leaf Senescence. Life (Basel) 2023; 13:life13020559. [PMID: 36836919 PMCID: PMC9965218 DOI: 10.3390/life13020559] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2023] [Revised: 02/10/2023] [Accepted: 02/14/2023] [Indexed: 02/19/2023] Open
Abstract
As eukaryotes, plants and animals have many commonalities on the genetic level, although they differ greatly in appearance and physiological habits. The primary goal of current plant research is to improve the crop yield and quality. However, plant research has a wider aim, exploiting the evolutionary conservatism similarities between plants and animals, and applying discoveries in the field of botany to promote zoological research that will ultimately serve human health, although very few studies have addressed this aspect. Here, we analyzed 35 human-disease-related gene orthologs in plants and characterized the genes in depth. Thirty-four homologous genes were found to be present in the herbaceous annual plant Arabidopsis thaliana and the woody perennial plant Populus trichocarpa, with most of the genes having more than two exons, including the ATM gene with 78 exons. More surprisingly, 27 (79.4%) of the 34 homologous genes in Arabidopsis were found to be senescence-associated genes (SAGs), further suggesting a close relationship between human diseases and cellular senescence. Protein-protein interaction network analysis revealed that the 34 genes formed two main subnetworks, and genes in the first subnetwork interacted with 15 SAGs. In conclusion, our results show that most of the 34 homologs of human-disease-associated genes in plants are involved in the leaf senescence process, suggesting that leaf senescence may offer a means to study the pathogenesis of human diseases and to screen drugs for the treat of diseases.
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22
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Zhu X, Chen S, Hu X, Zhao L, Wang Y, Huang J, Chen J, Qiu Y, Zhang X, Wang M, Yang X, Zhang Y, Zhu Y. Near-Infrared Nano-Optogenetic Activation of Cancer Immunotherapy via Engineered Bacteria. ADVANCED MATERIALS (DEERFIELD BEACH, FLA.) 2023; 35:e2207198. [PMID: 36314411 DOI: 10.1002/adma.202207198] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2022] [Revised: 10/01/2022] [Indexed: 06/16/2023]
Abstract
Certain anaerobic microbes with the capability to colonize the tumor microenvironment tend to express the heterologous gene in a sustainable manner, which will inevitably compromise the therapeutic efficacy and induce off-tumor toxicity in vivo. To improve the therapeutic precision and controllability of bacteria-based therapeutics, Escherichia coli Nissle 1917 (EcN), engineered to sense blue light and release the encoded flagellin B (flaB), is conjugated with lanthanide upconversion nanoparticles (UCNPs) for near-infrared (NIR) nano-optogenetic cancer immunotherapy. Upon 808 nm photoirradiation, UCNPs emit at the blue region to photoactivate the EcN for secretion of flaB, which subsequently binds to Toll-like receptor 5 expressed on the membrane of macrophages for activating immune response via MyD88-dependent signal pathway. Such synergism leads to significant tumor regression in different tumor models and metastatic tumors with negligible side effects. These studies based on the NIR nano-optogenetic platform highlight the rational of leveraging the optogenetic tools combined with natural propensity of certain bacteria for cancer immunotherapy.
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Affiliation(s)
- Xiaoqiang Zhu
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Sihan Chen
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Xiuwen Hu
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Lijun Zhao
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Yiqian Wang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Jinzhao Huang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Jiawen Chen
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Yuzhi Qiu
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Xuefei Zhang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Mengdie Wang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
- Department of Neurology, Union Hospital, Tongji Medical College, Huazhong University of Science and Technology, Jiefang Avenue, Wuhan, 430022, P. R. China
| | - Xiangliang Yang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Yan Zhang
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
| | - Yanhong Zhu
- National Engineering Research Centre for Nanomedicine, College of Life Science and Technology, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
- Hubei Key Laboratory of Bioinorganic Chemistry and Materia Medica, Huazhong University of Science and Technology, 1037 Luoyu Road, Wuhan, 430074, P. R. China
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23
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Choi DM, Kim SH, Han YJ, Kim JI. Regulation of Plant Photoresponses by Protein Kinase Activity of Phytochrome A. Int J Mol Sci 2023; 24:ijms24032110. [PMID: 36768431 PMCID: PMC9916439 DOI: 10.3390/ijms24032110] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2022] [Revised: 01/17/2023] [Accepted: 01/18/2023] [Indexed: 01/25/2023] Open
Abstract
Extensive research has been conducted for decades to elucidate the molecular and regulatory mechanisms for phytochrome-mediated light signaling in plants. As a result, tens of downstream signaling components that physically interact with phytochromes are identified, among which negative transcription factors for photomorphogenesis, PHYTOCHROME-INTERACTING FACTORs (PIFs), are well known to be regulated by phytochromes. In addition, phytochromes are also shown to inactivate an important E3 ligase complex consisting of CONSTITUTIVELY PHOTOMORPHOGENIC 1 (COP1) and SUPPRESSORs OF phyA-105 (SPAs). This inactivation induces the accumulation of positive transcription factors for plant photomorphogenesis, such as ELONGATED HYPOCOTYL 5 (HY5). Although many downstream components of phytochrome signaling have been studied thus far, it is not fully elucidated which intrinsic activity of phytochromes is necessary for the regulation of these components. It should be noted that phytochromes are autophosphorylating protein kinases. Recently, the protein kinase activity of phytochrome A (phyA) has shown to be important for its function in plant light signaling using Avena sativa phyA mutants with reduced or increased kinase activity. In this review, we highlight the function of phyA as a protein kinase to explain the regulation of plant photoresponses by phyA.
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Affiliation(s)
- Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seong-Hyeon Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju 61186, Republic of Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju 61186, Republic of Korea
- Correspondence:
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24
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Mardani Korrani F, Amooaghaie R, Ahadi A. He-Ne Laser Enhances Seed Germination and Salt Acclimation in Salvia officinalis Seedlings in a Manner Dependent on Phytochrome and H 2O 2. PROTOPLASMA 2023; 260:103-116. [PMID: 35471709 DOI: 10.1007/s00709-022-01762-1] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
In the current study the role of H2O2 in He-Ne laser-induced effects on seed germination and post-germinative performance of Salvia officinalis seedlings was assessed under both non-stress and saline conditions. Salinity had adverse impacts on seed germination and root length and decreased seed germination tolerance index. Seed priming with H2O2 and He-Ne laser impacted the seed germination and vigoration in a dose-dependent manner. The optimal effects were gathered by energy dose of 6 J/cm2 laser and concentration of 5 mM H2O2. These pre-treatments enhanced seed germination due to increasing contents of total soluble and reducing sugars and the amylase activity in seeds and improved seedling performance under saline and non-saline conditions. Furthermore, Phy B transcripts were upregulated, salt-accrued oxidative stress was mitigated, and the activities of POD and CAT increased in seedlings primed with H2O2 and laser. Interestingly, applying diphenyleneiodonium (DPI as an inhibitor of NADPH oxidase activity) and N, N-dimethyl thiourea (DMTU as a H2O2 scavenger) arrested the upregulation of phy B gene and abolished stimulatory impact of laser priming on the aforementioned attributes under both non-stress and saline conditions. These novel findings suggest that H2O2 as a downstream signal modulates the impacts of He-Ne laser on seed germination, seedling performance and salt acclimation in sage seedlings, and likely phy B also is involved in these responses.
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Affiliation(s)
| | - Rayhaneh Amooaghaie
- Plant Science Department, Science Faculty, Shahrekord University, Shahrekord, Iran.
- Biotechnology Research Institute, Shahrekord University, Shahrekord, Iran.
| | - Alimohammad Ahadi
- Genetic Department, Science Faculty, Shahrekord University, Shahrekord, Iran
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25
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Zhang L, Song C, Guo D, Guo L, Hou X, Wang H. Identification of differentially expressed miRNAs and their target genes in response to brassinolide treatment on flowering of tree peony ( Paeonia ostii). PLANT SIGNALING & BEHAVIOR 2022; 17:2056364. [PMID: 35343364 PMCID: PMC8959526 DOI: 10.1080/15592324.2022.2056364] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/20/2022] [Revised: 03/16/2022] [Accepted: 03/16/2022] [Indexed: 06/14/2023]
Abstract
Tree peony is a famous flower plant in China, but the short and concentrated flowering period limits its ornamental value and economic value. Brassinolide (BR) plays an important role in plant growth and development including flowering. There have been a large number of reports on the molecular aspects of the flowering process, but the genetic mechanism that was responsible for miRNA-guided regulation of tree peony is almost unclear. In this study, the leaves of tree peony cultivar, 'Feng Dan', were sprayed with different concentrations of BR, and the obvious bloom delay was found at the treatment with BR 50 μg/L. The small RNA sequencing and transcriptome sequencing were performed on the petals of tree peony under an untreated control (CK) and the treatment with BR 50 μg/L during four consecutive flowering development stages. A total of 22 known miRNAs belonging to 12 families were identified and 84 novel miRNAs were predicted. Combined with transcriptome data, a total of 376 target genes were predicted for the 18 differentially expressed known miRNAs and 177 target genes were predicted for the 23 differentially expressed novel miRNAs. Additionally, the potential miRNAs and their target genes were identified, including miR156b targeting SPL, miR172a_4 targeting AP2 and four novel miRNAs targeting SPA1, and revealed that they might affect the flowering time in tree peony. Collectively, these results would provide a theoretical basis for further analysis of miRNA-guided regulation on flowering period in tree peony.
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Affiliation(s)
- Lin Zhang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, Henan sheng, China
| | - Chengwei Song
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, Henan sheng, China
| | - Dalong Guo
- College of Horticulture and Plant Protection, Henan University of Science and Technology, Luoyang, Henan sheng, China
| | - Lili Guo
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, Henan sheng, China
| | - Xiaogai Hou
- College of Agriculture/Tree Peony, Henan University of Science and Technology, Luoyang, Henan sheng, China
| | - Huafang Wang
- College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
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26
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Wang Q, Zhu Z. Light signaling-mediated growth plasticity in Arabidopsis grown under high-temperature conditions. STRESS BIOLOGY 2022; 2:53. [PMID: 37676614 PMCID: PMC10441904 DOI: 10.1007/s44154-022-00075-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/24/2022] [Accepted: 11/11/2022] [Indexed: 09/08/2023]
Abstract
Growing concern around global warming has led to an increase in research focused on plant responses to increased temperature. In this review, we highlight recent advances in our understanding of plant adaptation to high ambient temperature and heat stress, emphasizing the roles of plant light signaling in these responses. We summarize how high temperatures regulate plant cotyledon expansion and shoot and root elongation and explain how plants use light signaling to combat severe heat stress. Finally, we discuss several future avenues for this research and identify various unresolved questions within this field.
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Affiliation(s)
- Qi Wang
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China
| | - Ziqiang Zhu
- College of Life Sciences, Nanjing Normal University, Nanjing, 210023, China.
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27
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Stafen CF, Kleine-Vehn J, Maraschin FDS. Signaling events for photomorphogenic root development. TRENDS IN PLANT SCIENCE 2022; 27:1266-1282. [PMID: 36057533 DOI: 10.1016/j.tplants.2022.08.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/28/2021] [Revised: 07/26/2022] [Accepted: 08/02/2022] [Indexed: 06/15/2023]
Abstract
A germinating seedling incorporates environmental signals such as light into developmental outputs. Light is not only a source of energy, but also a central coordinative signal in plants. Traditionally, most research focuses on aboveground organs' response to light; therefore, our understanding of photomorphogenesis in roots is relatively scarce. However, root development underground is highly responsive to light signals from the shoot and understanding these signaling mechanisms will give a better insight into early seedling development. Here, we review the central light signaling hubs and their role in root growth promotion of Arabidopsis thaliana seedlings.
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Affiliation(s)
- Cássia Fernanda Stafen
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil
| | - Jürgen Kleine-Vehn
- Institute of Biology II, Chair of Molecular Plant Physiology (MoPP), University of Freiburg, Freiburg, Germany; Center for Integrative Biological Signalling Studies (CIBSS), University of Freiburg, 79104 Freiburg, Germany
| | - Felipe Dos Santos Maraschin
- PPGBM - Programa de Pós-Graduação em Genética e Biologia Molecular, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil; Departamento de Botânica, Universidade Federal do Rio Grande do Sul - UFRGS, Porto Alegre, RS, Brazil.
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28
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Zhang YX, Niu YQ, Wang XF, Wang ZH, Wang ML, Yang J, Wang YG, Zhang WJ, Song ZP, Li LF. Phenotypic and transcriptomic responses of the shade-grown species Panax ginseng to variable light conditions. ANNALS OF BOTANY 2022; 130:749-762. [PMID: 35961674 PMCID: PMC9670753 DOI: 10.1093/aob/mcac105] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/08/2022] [Accepted: 08/10/2022] [Indexed: 06/15/2023]
Abstract
BACKGROUND AND AIMS Elucidating how plant species respond to variable light conditions is important to understand the ecological adaptation to heterogeneous natural habitats. Plant performance and its underlying gene regulatory network have been well documented in sun-grown plants. However, the phenotypic and molecular responses of shade-grown plants under variable light conditions have remained largely unclear. METHODS We assessed the differences in phenotypic performance between Panax ginseng (shade-grown) and Arabidopsis thaliana (sun-grown) under sunlight, shade and deep-shade conditions. To further address the molecular bases underpinning the phenotypic responses, we compared time-course transcriptomic expression profiling and candidate gene structures between the two species. KEY RESULTS Our results show that, compared with arabidopsis, ginseng plants not only possess a lower degree of phenotypic plasticity among the three light conditions, but also exhibit higher photosynthetic efficiency under shade and deep-shade conditions. Further comparisons of the gene expression and structure reveal that differential transcriptional regulation together with increased copy number of photosynthesis-related genes (e.g. electron transfer and carbon fixation) may improve the photosynthetic efficiency of ginseng plants under the two shade conditions. In contrast, the inactivation of phytochrome-interacting factors (i.e. absent and no upregulation of the PIF genes) are potentially associated with the observed low degree of phenotypic plasticity of ginseng plants under variable light conditions. CONCLUSIONS Our study provides new insights into how shade-grown plants respond to variable light conditions. Candidate genes related to shade adaptation in ginseng provide valuable genetic resources for future molecular breeding of high-density planting crops.
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Affiliation(s)
- Yu-Xin Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Qian Niu
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Xin-Feng Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhen-Hui Wang
- Department of Agronomy, Jilin Agricultural University, Changchun 130118, China
| | - Meng-Li Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Ji Yang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Yu-Guo Wang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Wen-Ju Zhang
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Zhi-Ping Song
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
| | - Lin-Feng Li
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai 200438, China
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29
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Zhao H, Zhang Y, Zheng Y. Integration of ABA, GA, and light signaling in seed germination through the regulation of ABI5. FRONTIERS IN PLANT SCIENCE 2022; 13:1000803. [PMID: 36092418 PMCID: PMC9449724 DOI: 10.3389/fpls.2022.1000803] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/22/2022] [Accepted: 08/08/2022] [Indexed: 06/01/2023]
Abstract
Seed germination is precisely controlled by a variety of signals, among which light signals and the phytohormones abscisic acid (ABA) and gibberellin (GA) play crucial roles. New findings have greatly increased our understanding of the mechanisms by which these three signals regulate seed germination and the close connections between them. Although much work has been devoted to ABA, GA, and light signal interactions, there is still no systematic description of their combination, especially in seed germination. In this review, we integrate ABA, GA, and light signaling in seed germination through the direct and indirect regulation of ABSCISIC ACID INSENSITIVE5 (ABI5), the core transcription factor that represses seed germination in ABA signaling, into our current understanding of the regulatory mechanism of seed germination.
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Affiliation(s)
- Hongyun Zhao
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, China
| | - Yamei Zhang
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, China
| | - Yuan Zheng
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Sciences, Henan University, Kaifeng, China
- Sanya Institute of Henan University, Sanya, China
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30
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Genetic Dissection of Light-Regulated Adventitious Root Induction in Arabidopsis thaliana Hypocotyls. Int J Mol Sci 2022; 23:ijms23105301. [PMID: 35628112 PMCID: PMC9140560 DOI: 10.3390/ijms23105301] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 05/05/2022] [Accepted: 05/06/2022] [Indexed: 01/27/2023] Open
Abstract
Photomorphogenic responses of etiolated seedlings include the inhibition of hypocotyl elongation and opening of the apical hook. In addition, dark-grown seedlings respond to light by the formation of adventitious roots (AR) on the hypocotyl. How light signaling controls adventitious rooting is less well understood. Hereto, we analyzed adventitious rooting under different light conditions in wild type and photomorphogenesis mutants in Arabidopsis thaliana. Etiolation was not essential for AR formation but raised the competence to form AR under white and blue light. The blue light receptors CRY1 and PHOT1/PHOT2 are key elements contributing to the induction of AR formation in response to light. Furthermore, etiolation-controlled competence for AR formation depended on the COP9 signalosome, E3 ubiquitin ligase CONSTITUTIVELY PHOTOMORPHOGENIC (COP1), the COP1 interacting SUPPRESSOR OF PHYA-105 (SPA) kinase family members (SPA1,2 and 3) and Phytochrome-Interacting Factors (PIF). In contrast, ELONGATED HYPOCOTYL5 (HY5), suppressed AR formation. These findings provide a genetic framework that explains the high and low AR competence of Arabidopsis thaliana hypocotyls that were treated with dark, and light, respectively. We propose that light-induced auxin signal dissipation generates a transient auxin maximum that explains AR induction by a dark to light switch.
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31
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Liu Y, Zhang XW, Liu X, Zheng PF, Su L, Wang GL, Wang XF, Li YY, You CX, An JP. Phytochrome interacting factor MdPIF7 modulates anthocyanin biosynthesis and hypocotyl growth in apple. PLANT PHYSIOLOGY 2022; 188:2342-2363. [PMID: 34983053 PMCID: PMC8968312 DOI: 10.1093/plphys/kiab605] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/04/2021] [Accepted: 11/26/2021] [Indexed: 06/10/2023]
Abstract
Light affects many physiological and developmental processes of plants by regulating the expression and activity of light-responsive proteins. Among them, phytochrome interacting factors (PIFs) play pivotal roles in the regulation of anthocyanin accumulation and hypocotyl growth. However, the molecular mechanism is not well understood, especially in woody plants, such as apple (Malus × domestica). In this study, we identified a light-responsive PIF protein, MdPIF7, in apple and investigated the molecular mechanism of its regulation of anthocyanin biosynthesis and hypocotyl growth. We found that overexpression of MdPIF7 decreased anthocyanin accumulation in transgenic apple materials and promoted hypocotyl elongation in ectopically expressed Arabidopsis (Arabidopsis thaliana). Further investigation showed that MdPIF7 functioned by interacting with B-box 23 (MdBBX23), a positive regulator of anthocyanin biosynthesis in apple and hypocotyl growth inhibition in ectopically expressed Arabidopsis, and attenuating the transcriptional activation of MdBBX23 on LONG HYPOCOTYL 5 (MdHY5). In addition, MdPIF7 interacted with basic region leucine zipper 44 (MdbZIP44) and ethylene response factor 38 (MdERF38), two positive regulators of anthocyanin biosynthesis, and it negatively regulated MdbZIP44- and MdERF38-promoted anthocyanin accumulation by interfering with the interaction between MdbZIP44/MdERF38 and MdMYB1. Taken together, our results reveal that MdPIF7 regulates anthocyanin biosynthesis in apple and hypocotyl growth in ectopically expressed Arabidopsis through MdPIF7-MdBBX23-MdHY5 and MdPIF7-MdbZIP44/MdERF38-MdMYB1 modules. Our findings enrich the functional studies of PIF proteins and provide insights into the molecular mechanism of PIF-mediated anthocyanin biosynthesis and hypocotyl growth.
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Affiliation(s)
| | | | - Xin Liu
- Beijing Academy of Forestry and Pomology Sciences, Beijing Academy of Agriculture and Forestry Sciences, Beijing, 100093, China
| | - Peng-Fei Zheng
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Ling Su
- Shandong Academy of Grape, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
| | - Gui-Luan Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Xiao-Fei Wang
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
| | - Yuan-Yuan Li
- State Key Laboratory of Crop Biology, College of Horticulture Science and Engineering, Shandong Agricultural University, Tai’an 271018, Shandong, China
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Ponnu J, Hoecker U. Signaling Mechanisms by Arabidopsis Cryptochromes. FRONTIERS IN PLANT SCIENCE 2022; 13:844714. [PMID: 35295637 PMCID: PMC8918993 DOI: 10.3389/fpls.2022.844714] [Citation(s) in RCA: 22] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/28/2021] [Accepted: 02/04/2022] [Indexed: 05/29/2023]
Abstract
Cryptochromes (CRYs) are blue light photoreceptors that regulate growth, development, and metabolism in plants. In Arabidopsis thaliana (Arabidopsis), CRY1 and CRY2 possess partially redundant and overlapping functions. Upon exposure to blue light, the monomeric inactive CRYs undergo phosphorylation and oligomerization, which are crucial to CRY function. Both the N- and C-terminal domains of CRYs participate in light-induced interaction with multiple signaling proteins. These include the COP1/SPA E3 ubiquitin ligase, several transcription factors, hormone signaling intermediates and proteins involved in chromatin-remodeling and RNA N6 adenosine methylation. In this review, we discuss the mechanisms of Arabidopsis CRY signaling in photomorphogenesis and the recent breakthroughs in Arabidopsis CRY research.
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Affiliation(s)
| | - Ute Hoecker
- *Correspondence: Ute Hoecker, , orcid.org/0000-0002-5636-9777
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Pay ML, Kim DW, Somers DE, Kim JK, Foo M. Modelling of plant circadian clock for characterizing hypocotyl growth under different light quality conditions. IN SILICO PLANTS 2022; 4:diac001. [PMID: 35369361 PMCID: PMC8963510 DOI: 10.1093/insilicoplants/diac001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Accepted: 01/13/2022] [Indexed: 06/14/2023]
Abstract
To meet the ever-increasing global food demand, the food production rate needs to be increased significantly in the near future. Speed breeding is considered as a promising agricultural technology solution to achieve the zero-hunger vision as specified in the United Nations Sustainable Development Goal 2. In speed breeding, the photoperiod of the artificial light has been manipulated to enhance crop productivity. In particular, regulating the photoperiod of different light qualities rather than solely white light can further improve speed breading. However, identifying the optimal light quality and the associated photoperiod simultaneously remains a challenging open problem due to complex interactions between multiple photoreceptors and proteins controlling plant growth. To tackle this, we develop a first comprehensive model describing the profound effect of multiple light qualities with different photoperiods on plant growth (i.e. hypocotyl growth). The model predicts that hypocotyls elongated more under red light compared to both red and blue light. Drawing similar findings from previous related studies, we propose that this might result from the competitive binding of red and blue light receptors, primarily Phytochrome B (phyB) and Cryptochrome 1 (cry1) for the core photomorphogenic regulator, CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1). This prediction is validated through an experimental study on Arabidopsis thaliana. Our work proposes a potential molecular mechanism underlying plant growth under different light qualities and ultimately suggests an optimal breeding protocol that takes into account light quality.
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Affiliation(s)
- Miao Lin Pay
- Institute for Future Transport and Cities, Coventry University, Coventry CV1 2TE, UK
| | - Dae Wook Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - David E Somers
- Department of Molecular Genetics, The Ohio State University, Columbus, OH 43210, USA
- Center for Applied Plant Sciences, The Ohio State University, Columbus, OH 43210, USA
| | - Jae Kyoung Kim
- Department of Mathematical Sciences, Korea Advanced Institute of Science and Technology, Daejeon 34141, Republic of Korea
- Biomedical Mathematics Group, Institute for Basic Science, Daejeon 34126, Republic of Korea
| | - Mathias Foo
- School of Engineering, University of Warwick, Coventry CV4 7AL, UK
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PIF7 controls leaf cell proliferation through an AN3 substitution repression mechanism. Proc Natl Acad Sci U S A 2022; 119:2115682119. [PMID: 35086930 PMCID: PMC8812563 DOI: 10.1073/pnas.2115682119] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/07/2021] [Indexed: 01/09/2023] Open
Abstract
Phytochrome photoreceptors can markedly alter leaf blade growth in response to far-red (FR) rich neighbor shade, yet we have a limited understanding of how this is accomplished. This study identifies ANGUSTIFOLIA3 (AN3) as a central component in phytochrome promotion of leaf cell proliferation and PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) as a potent repressor. AN3 and PIF7 impose opposing regulation on a shared suite of genes through common cis-acting promoter elements. In response to FR light, activated PIF7 blocks AN3 action by evicting and substituting for AN3 at target promoters. This molecular switch module provides a mechanism through which changes in external light quality can dynamically manipulate gene expression, cell division, and leaf size. Plants are agile, plastic organisms able to adapt to everchanging circumstances. Responding to far-red (FR) wavelengths from nearby vegetation, shade-intolerant species elicit the adaptive shade-avoidance syndrome (SAS), characterized by elongated petioles, leaf hyponasty, and smaller leaves. We utilized end-of-day FR (EODFR) treatments to interrogate molecular processes that underlie the SAS leaf response. Genetic analysis established that PHYTOCHROME-INTERACTING FACTOR 7 (PIF7) is required for EODFR-mediated constraint of leaf blade cell division, while EODFR messenger RNA sequencing data identified ANGUSTIFOLIA3 (AN3) as a potential PIF7 target. We show that PIF7 can suppress AN3 transcription by directly interacting with and sequestering AN3. We also establish that PIF7 and AN3 impose antagonistic control of gene expression via common cis-acting promoter motifs in several cell-cycle regulator genes. EODFR triggers the molecular substitution of AN3 to PIF7 at G-box/PBE-box promoter regions and a switch from promotion to repression of gene expression.
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Li C, Qi L, Zhang S, Dong X, Jing Y, Cheng J, Feng Z, Peng J, Li H, Zhou Y, Wang X, Han R, Duan J, Terzaghi W, Lin R, Li J. Mutual upregulation of HY5 and TZP in mediating phytochrome A signaling. THE PLANT CELL 2022; 34:633-654. [PMID: 34741605 PMCID: PMC8774092 DOI: 10.1093/plcell/koab254] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2021] [Accepted: 10/08/2021] [Indexed: 05/25/2023]
Abstract
Phytochrome A (phyA) is the far-red (FR) light photoreceptor in plants that is essential for seedling de-etiolation under FR-rich environments, such as canopy shade. TANDEM ZINC-FINGER/PLUS3 (TZP) was recently identified as a key component of phyA signal transduction in Arabidopsis thaliana; however, how TZP is integrated into the phyA signaling networks remains largely obscure. Here, we demonstrate that ELONGATED HYPOCOTYL5 (HY5), a well-characterized transcription factor promoting photomorphogenesis, mediates FR light induction of TZP expression by directly binding to a G-box motif in the TZP promoter. Furthermore, TZP physically interacts with CONSTITUTIVE PHOTOMORPHOGENIC1 (COP1), an E3 ubiquitin ligase targeting HY5 for 26S proteasome-mediated degradation, and this interaction inhibits COP1 interaction with HY5. Consistent with those results, TZP post-translationally promotes HY5 protein stability in FR light, and in turn, TZP protein itself is destabilized by COP1 in both dark and FR light conditions. Moreover, tzp hy5 double mutants display an additive phenotype relative to their respective single mutants under high FR light intensities, indicating that TZP and HY5 also function in largely independent pathways. Together, our data demonstrate that HY5 and TZP mutually upregulate each other in transmitting the FR light signal, thus providing insights into the complicated but delicate control of phyA signaling networks.
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Affiliation(s)
- Cong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Lijuan Qi
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Shaoman Zhang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaojing Dong
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yanjun Jing
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jinkui Cheng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Ziyi Feng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jing Peng
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Hong Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Yangyang Zhou
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Xiaoji Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Run Han
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Jie Duan
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - William Terzaghi
- Department of Biology, Wilkes University, Wilkes-Barre, Pennsylvania 18766, USA
| | - Rongcheng Lin
- Key Laboratory of Photobiology, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China
| | - Jigang Li
- State Key Laboratory of Plant Physiology and Biochemistry, College of Biological Sciences, China Agricultural University, Beijing 100193, China
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Lin F, Cao J, Yuan J, Liang Y, Li J. Integration of Light and Brassinosteroid Signaling during Seedling Establishment. Int J Mol Sci 2021; 22:12971. [PMID: 34884771 PMCID: PMC8657978 DOI: 10.3390/ijms222312971] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2021] [Revised: 11/27/2021] [Accepted: 11/27/2021] [Indexed: 01/02/2023] Open
Abstract
Light and brassinosteroid (BR) are external stimuli and internal cue respectively, that both play critical roles in a wide range of developmental and physiological process. Seedlings grown in the light exhibit photomorphogenesis, while BR promotes seedling etiolation. Light and BR oppositely control the development switch from shotomorphogenesis in the dark to photomorphogenesis in the light. Recent progress report that substantial components have been identified as hubs to integrate light and BR signals. Photomorphogenic repressors including COP1, PIFs, and AGB1 have been reported to elevate BR response, while photomorphogenesis-promoting factors such as HY5, BZS1, and NF-YCs have been proven to repress BR signal. In addition, BR components also modulate light signal. Here, we review the current research on signaling network associated with light and brassinosteroids, with a focus on the integration of light and BR signals enabling plants to thrive in the changeable environment.
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Affiliation(s)
- Fang Lin
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China; (J.C.); (J.Y.); (Y.L.); (J.L.)
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Kerner K, Nagano S, Lübbe A, Hoecker U. Functional comparison of the WD-repeat domains of SPA1 and COP1 in suppression of photomorphogenesis. PLANT, CELL & ENVIRONMENT 2021; 44:3273-3282. [PMID: 34251043 DOI: 10.1111/pce.14148] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2021] [Revised: 06/30/2021] [Accepted: 06/30/2021] [Indexed: 06/13/2023]
Abstract
The Arabidopsis COP1/SPA complex acts as a cullin4-based E3 ubiquitin ligase to suppress photomorphogenesis in darkness. It is a tetrameric complex of two COP1 and two SPA proteins. Both COP1 and SPA are essential for the activity of this complex, and they both contain a C-terminal WD-repeat domain responsible for substrate recruitment and binding of DDB1. Here, we used a WD domain swap-approach to address the cooperativity of COP1 and SPA proteins. We found that expression of a chimeric COP1 carrying the WD-repeat domain of SPA1 mostly complemented the cop1-4-mutant phenotype in darkness, indicating that the WD repeat of SPA1 can replace the WD repeat of COP1. In the light, SPA1-WD partially substituted for COP1-WD. In contrast, expression of a chimeric SPA1 protein carrying the WD repeat of COP1 did not rescue the spa-mutant phenotype. Together, our findings demonstrate that a SPA1-type WD repeat is essential for COP1/SPA activity, while a COP1-type WD is in part dispensible. Moreover, a complex with four SPA1-WDs is more active than a complex with only two SPA1-WDs. A homology model of SPA1-WD based on the crystal structure of COP1-WD uncovered two insertions and several amino acid substitutions at the predicted substrate-binding pocket of SPA1-WD.
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Affiliation(s)
- Konstantin Kerner
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
| | - Soshichiro Nagano
- Institute for Plant Physiology, Justus Liebig-University Gießen, Gießen, Germany
| | - Annika Lübbe
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
| | - Ute Hoecker
- Institute for Plant Sciences and Cluster of Excellence on Plant Sciences (CEPLAS), Biocenter, University of Cologne, Cologne, Germany
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38
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Xu Y, Zhu Z. PIF4 and PIF4-Interacting Proteins: At the Nexus of Plant Light, Temperature and Hormone Signal Integrations. Int J Mol Sci 2021; 22:10304. [PMID: 34638641 PMCID: PMC8509071 DOI: 10.3390/ijms221910304] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2021] [Revised: 09/19/2021] [Accepted: 09/21/2021] [Indexed: 11/16/2022] Open
Abstract
Basic helix-loop-helix (bHLH) family transcription factor PHYTOCHROME INTERACTING FACTOR 4 (PIF4) is necessary for plant adaption to light or high ambient temperature. PIF4 directly associates with plenty of its target genes and modulates the global transcriptome to induce or reduce gene expression levels. However, PIF4 activity is tightly controlled by its interacting proteins. Until now, twenty-five individual proteins have been reported to physically interact with PIF4. These PIF4-interacting proteins act together with PIF4 and form a unique nexus for plant adaption to light or temperature change. In this review, we will discuss the different categories of PIF4-interacting proteins, including photoreceptors, circadian clock regulators, hormone signaling components, and transcription factors. These distinct PIF4-interacting proteins either integrate light and/or temperature cues with endogenous hormone signaling, or control PIF4 abundances and transcriptional activities. Taken together, PIF4 and PIF4-interacting proteins play major roles for exogenous and endogenous signal integrations, and therefore establish a robust network for plants to cope with their surrounding environmental alterations.
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Affiliation(s)
- Yang Xu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
| | - Ziqiang Zhu
- Jiangsu Key Laboratory for Biodiversity and Biotechnology, College of Life Sciences, Nanjing Normal University, Nanjing 210023, China;
- Key Laboratory of Molecular Design for Plant Cell Factory of Guangdong Higher Education Institutes, Department of Biology, Institute of Plant and Food Science, Southern University of Science and Technology, Shenzhen 518055, China
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Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 2021; 12:5614. [PMID: 34556672 PMCID: PMC8460787 DOI: 10.1038/s41467-021-25909-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022] Open
Abstract
Photoactivated phytochrome B (PHYB) binds to antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to regulate hundreds of light responsive genes in Arabidopsis by promoting PIF degradation. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (AD) consisting of a hydrophobic activator motif flanked by acidic residues. A PIF3mAD mutant, in which the activator motif is replaced with alanines, fails to activate PIF3 target genes in Arabidopsis, validating the functions of the PIF3 AD in vivo. Intriguingly, the N-terminal photosensory module of PHYB binds immediately adjacent to the PIF3 AD to repress PIF3’s transactivation activity, demonstrating a novel PHYB signaling mechanism through direct interference of the transactivation activity of PIF3. Our findings indicate that PHYB, likely also PHYA, controls the stability and activity of PIFs via structurally separable dual signaling mechanisms. Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.
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40
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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.
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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
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Kim J, Bordiya Y, Kathare PK, Zhao B, Zong W, Huq E, Sung S. Phytochrome B triggers light-dependent chromatin remodelling through the PRC2-associated PHD finger protein VIL1. NATURE PLANTS 2021; 7:1213-1219. [PMID: 34354260 PMCID: PMC8448934 DOI: 10.1038/s41477-021-00986-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2021] [Accepted: 07/12/2021] [Indexed: 05/16/2023]
Abstract
To compensate for a sessile nature, plants have developed sophisticated mechanisms to sense varying environmental conditions. Phytochromes (phys) are light and temperature sensors that regulate downstream genes to render plants responsive to environmental stimuli1-4. Here, we show that phyB directly triggers the formation of a repressive chromatin loop by physically interacting with VERNALIZATION INSENSITIVE 3-LIKE1/VERNALIZATION 5 (VIL1/VRN5), a component of Polycomb Repressive Complex 2 (PRC2)5,6, in a light-dependent manner. VIL1 and phyB cooperatively contribute to the repression of growth-promoting genes through the enrichment of Histone H3 Lys27 trimethylation (H3K27me3), a repressive histone modification. In addition, phyB and VIL1 mediate the formation of a chromatin loop to facilitate the repression of ATHB2. Our findings show that phyB directly utilizes chromatin remodelling to regulate the expression of target genes in a light-dependent manner.
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Affiliation(s)
- Junghyun Kim
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Yogendra Bordiya
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Bo Zhao
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Wei Zong
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA
| | - Sibum Sung
- Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX, USA.
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Hoang QTN, Cho JY, Choi DM, Shin AY, Kim JA, Han YJ, Kim JI. Protein Kinase Activity of Phytochrome A Positively Correlates With Photoresponses in Arabidopsis. FRONTIERS IN PLANT SCIENCE 2021; 12:706316. [PMID: 34394163 PMCID: PMC8362889 DOI: 10.3389/fpls.2021.706316] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/07/2021] [Accepted: 07/12/2021] [Indexed: 06/13/2023]
Abstract
Plant phytochromes are known as autophosphorylating serine/threonine protein kinases. However, the functional importance of their kinase activity is not fully elucidated. Previously, the kinase activity is shown to be necessary for the function of Avena sativa phytochrome A (AsphyA) using transgenic plants with mutants displaying reduced kinase activity, such as K411L and T418D. In this study, we isolated and analyzed two AsphyA mutants, K411R and T418V, that showed increased kinase activity. Transgenic phyA-201 plants with these mutants showed hypersensitive responses to far-red (FR) light, such as shorter hypocotyls and more expanded cotyledons than those of control plant (i.e., transgenic phyA-201 plant with wild-type AsphyA). Contrary to the mutants with reduced kinase activity, these mutants accelerated FR-induced phosphorylation and subsequent degradation of phytochrome-interacting factor 3 (PIF3) in Arabidopsis. Moreover, elongated hypocotyl 5 (HY5), a critical positive regulator of photoresponses in plants, accumulated in higher amounts in the transgenic plants under FR light than in the control plant. In addition, PIF1 degradation was accelerated in the transgenic plants. Consequently, the transgenic plants exhibit higher germination frequencies than the control plant. Collectively, our results demonstrate that the AsphyA mutants with increased kinase activity are hyperactive in plants, supporting a positive relationship between the kinase activity of phytochromes and photoresponses in plants.
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Affiliation(s)
- Quyen T. N. Hoang
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Jae-Yong Cho
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Da-Min Choi
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
| | - Ah-Young Shin
- Plant Systems Engineering Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon, South Korea
| | - Jin A. Kim
- National Academy of Agricultural Science, Rural Development Administration, Jeollabuk-do, South Korea
| | - Yun-Jeong Han
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
| | - Jeong-Il Kim
- Department of Integrative Food, Bioscience and Biotechnology, Chonnam National University, Gwangju, South Korea
- Kumho Life Science Laboratory, Chonnam National University, Gwangju, South Korea
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43
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Praat M, De Smet I, van Zanten M. Protein kinase and phosphatase control of plant temperature responses. JOURNAL OF EXPERIMENTAL BOTANY 2021:erab345. [PMID: 34283227 DOI: 10.1093/jxb/erab345] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Indexed: 06/13/2023]
Abstract
Plants must cope with ever-changing temperature conditions in their environment. Suboptimal high and low temperatures, and stressful extreme temperatures, induce adaptive mechanisms that allow optimal performance and survival, respectively. These processes have been extensively studied at the physiological, transcriptional and (epi)genetic level. Cellular temperature signalling cascades and tolerance mechanisms also involve post-translational modifications (PTMs), particularly protein phosphorylation. Many protein kinases are known to be involved in cold acclimation and heat stress responsiveness but research on the role and importance of kinases and phosphatases in triggering responses to mild changes in temperature such as thermomorphogenesis is inadequately understood. In this review, we summarize the current knowledge on the roles of kinases and phosphatases in plant temperature responses. We discuss how kinases can function over a range of temperatures in different signalling pathways and provide an outlook to the application of PTM-modifying factors for the development of thermotolerant crops.
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Affiliation(s)
- Myrthe Praat
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
| | - Ive De Smet
- Ghent University, Department of Plant Biotechnology and Bioinformatics, B-9052 Ghent, Belgium
- VIB Center for Plant Systems Biology, B-9052 Ghent, Belgium
| | - Martijn van Zanten
- Molecular Plant Physiology, Institute of Environmental Biology, Utrecht University. Padualaan 8, 3584CH Utrecht, the Netherlands
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Abstract
The perception of light signals by the phytochrome family of photoreceptors has a crucial influence on almost all aspects of growth and development throughout a plant's life cycle. The holistic regulatory networks orchestrated by phytochromes, including conformational switching, subcellular localization, direct protein-protein interactions, transcriptional and posttranscriptional regulations, and translational and posttranslational controls to promote photomorphogenesis, are highly coordinated and regulated at multiple levels. During the past decade, advances using innovative approaches have substantially broadened our understanding of the sophisticated mechanisms underlying the phytochrome-mediated light signaling pathways. This review discusses and summarizes these discoveries of the role of the modular structure of phytochromes, phytochrome-interacting proteins, and their functions; the reciprocal modulation of both positive and negative regulators in phytochrome signaling; the regulatory roles of phytochromes in transcriptional activities, alternative splicing, and translational regulation; and the kinases and E3 ligases that modulate PHYTOCHROME INTERACTING FACTORs to optimize photomorphogenesis.
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Affiliation(s)
- Mei-Chun Cheng
- Department of Biochemical Science and Technology, National Taiwan University, Taipei 10617, Taiwan
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Praveen Kumar Kathare
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Inyup Paik
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
| | - Enamul Huq
- Department of Molecular Biosciences, University of Texas at Austin, Austin, Texas 78712, USA;
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45
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Lee S, Wang W, Huq E. Spatial regulation of thermomorphogenesis by HY5 and PIF4 in Arabidopsis. Nat Commun 2021; 12:3656. [PMID: 34135347 PMCID: PMC8209091 DOI: 10.1038/s41467-021-24018-7] [Citation(s) in RCA: 42] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2020] [Accepted: 05/29/2021] [Indexed: 12/13/2022] Open
Abstract
Plants respond to high ambient temperature by implementing a suite of morphological changes collectively termed thermomorphogenesis. Here we show that the above and below ground tissue-response to high ambient temperature are mediated by distinct transcription factors. While the central hub transcription factor, PHYTOCHROME INTERCTING FACTOR 4 (PIF4) regulates the above ground tissue response, the below ground root elongation is primarily regulated by ELONGATED HYPOCOTYL 5 (HY5). Plants respond to high temperature by largely expressing distinct sets of genes in a tissue-specific manner. HY5 promotes root thermomorphogenesis via directly controlling the expression of many genes including the auxin and BR pathway genes. Strikingly, the above and below ground thermomorphogenesis is impaired in spaQ. Because SPA1 directly phosphorylates PIF4 and HY5, SPAs might control the stability of PIF4 and HY5 to regulate thermomorphogenesis in both tissues. These data collectively suggest that plants employ distinct combination of SPA-PIF4-HY5 module to regulate tissue-specific thermomorphogenesis. Plants undergo morphological changes collectively termed thermomorphogenesis when exposed to elevated temperature. Here the authors show that the SPA1 kinase regulates distinct thermomorphogenic responses according to tissue type by interactions with PIF4 and HY5 in shoots and roots, respectively.
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Affiliation(s)
- Sanghwa Lee
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Wenli Wang
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, USA.
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46
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Lee S, Zhu L, Huq E. An autoregulatory negative feedback loop controls thermomorphogenesis in Arabidopsis. PLoS Genet 2021; 17:e1009595. [PMID: 34061850 PMCID: PMC8195427 DOI: 10.1371/journal.pgen.1009595] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2021] [Revised: 06/11/2021] [Accepted: 05/11/2021] [Indexed: 12/13/2022] Open
Abstract
Plant growth and development are acutely sensitive to high ambient temperature caused in part due to climate change. However, the mechanism of high ambient temperature signaling is not well defined. Here, we show that HECATEs (HEC1 and HEC2), two helix-loop-helix transcription factors, inhibit thermomorphogenesis. While the expression of HEC1 and HEC2 is increased and HEC2 protein is stabilized at high ambient temperature, hec1hec2 double mutant showed exaggerated thermomorphogenesis. Analyses of the four PHYTOCHROME INTERACTING FACTOR (PIF1, PIF3, PIF4 and PIF5) mutants and overexpression lines showed that they all contribute to promote thermomorphogenesis. Furthermore, genetic analysis showed that pifQ is epistatic to hec1hec2. HECs and PIFs oppositely control the expression of many genes in response to high ambient temperature. PIFs activate the expression of HECs in response to high ambient temperature. HEC2 in turn interacts with PIF4 both in yeast and in vivo. In the absence of HECs, PIF4 binding to its own promoter as well as the target gene promoters was enhanced, indicating that HECs control PIF4 activity via heterodimerization. Overall, these data suggest that PIF4-HEC forms an autoregulatory composite negative feedback loop that controls growth genes to modulate thermomorphogenesis.
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Affiliation(s)
- Sanghwa Lee
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Ling Zhu
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, Texas, United States of America
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47
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Wang W, Paik I, Kim J, Hou X, Sung S, Huq E. Direct phosphorylation of HY5 by SPA kinases to regulate photomorphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:2311-2326. [PMID: 33686674 PMCID: PMC8641065 DOI: 10.1111/nph.17332] [Citation(s) in RCA: 23] [Impact Index Per Article: 7.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/03/2021] [Indexed: 05/25/2023]
Abstract
Elongated hypocotyl5 (HY5) is a key transcription factor that promotes photomorphogenesis. Constitutive photomorphogenic1 (COP1)-Suppressor of phytochrome A-105 (SPA) E3 ubiquitin ligase complex promotes ubiquitination and degradation of HY5 to repress photomorphogenesis in darkness. HY5 is also regulated by phosphorylation at serine 36 residue. However, the kinase responsible for phosphorylation of HY5 remains unknown. Here, using extensive in vitro and in vivo biochemical, genetic, and photobiological techniques, we have identified a new kinase that phosphorylates HY5 and demonstrated the significance of phosphorylation of HY5 in Arabidopsis thaliana. We show that SPA proteins are the missing kinases necessary for HY5 phosphorylation. SPAs can directly phosphorylate HY5 in vitro, and the phosphorylated HY5 is absent in the spaQ background in vivo. We also demonstrate that the unphosphorylated HY5 interacts strongly with both COP1 and SPA1 and is the preferred substrate for degradation, whereas the phosphorylated HY5 is more stable in the dark. In addition, the unphosphorylated HY5 actively binds to the target promoters and is the physiologically more active form. Consistently, the transgenic plants expressing the unphosphorylated form of HY5 display enhanced photomorphogenesis. Collectively, our study revealed the missing kinase responsible for direct phosphorylation of HY5 that fine-tunes its stability and activity to regulate photomorphogenesis.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Inyup Paik
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Sibum Sung
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA
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48
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Wang W, Paik I, Kim J, Hou X, Sung S, Huq E. Direct phosphorylation of HY5 by SPA kinases to regulate photomorphogenesis in Arabidopsis. THE NEW PHYTOLOGIST 2021; 230:2311-2326. [PMID: 33686674 DOI: 10.1101/2020.09.10.291773] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 03/03/2021] [Indexed: 05/23/2023]
Abstract
Elongated hypocotyl5 (HY5) is a key transcription factor that promotes photomorphogenesis. Constitutive photomorphogenic1 (COP1)-Suppressor of phytochrome A-105 (SPA) E3 ubiquitin ligase complex promotes ubiquitination and degradation of HY5 to repress photomorphogenesis in darkness. HY5 is also regulated by phosphorylation at serine 36 residue. However, the kinase responsible for phosphorylation of HY5 remains unknown. Here, using extensive in vitro and in vivo biochemical, genetic, and photobiological techniques, we have identified a new kinase that phosphorylates HY5 and demonstrated the significance of phosphorylation of HY5 in Arabidopsis thaliana. We show that SPA proteins are the missing kinases necessary for HY5 phosphorylation. SPAs can directly phosphorylate HY5 in vitro, and the phosphorylated HY5 is absent in the spaQ background in vivo. We also demonstrate that the unphosphorylated HY5 interacts strongly with both COP1 and SPA1 and is the preferred substrate for degradation, whereas the phosphorylated HY5 is more stable in the dark. In addition, the unphosphorylated HY5 actively binds to the target promoters and is the physiologically more active form. Consistently, the transgenic plants expressing the unphosphorylated form of HY5 display enhanced photomorphogenesis. Collectively, our study revealed the missing kinase responsible for direct phosphorylation of HY5 that fine-tunes its stability and activity to regulate photomorphogenesis.
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Affiliation(s)
- Wenli Wang
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Inyup Paik
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Junghyun Kim
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Xilin Hou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in East China, Ministry of Agriculture, Nanjing Agricultural University, Nanjing, 210095, China
| | - Sibum Sung
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
| | - Enamul Huq
- Department of Molecular Biosciences and The Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX, 78712, USA
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49
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Current Understanding of bHLH Transcription Factors in Plant Abiotic Stress Tolerance. Int J Mol Sci 2021; 22:ijms22094921. [PMID: 34066424 PMCID: PMC8125693 DOI: 10.3390/ijms22094921] [Citation(s) in RCA: 54] [Impact Index Per Article: 18.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Revised: 04/28/2021] [Accepted: 05/01/2021] [Indexed: 01/20/2023] Open
Abstract
Named for the characteristic basic helix-loop-helix (bHLH) region in their protein structure, bHLH proteins are a widespread transcription factor class in eukaryotes. bHLHs transcriptionally regulate their target genes by binding to specific positions on their promoters and thereby direct a variety of plant developmental and metabolic processes, such as photomorphogenesis, flowering induction, shade avoidance, and secondary metabolite biosynthesis, which are important for promoting plant tolerance or adaptation to adverse environments. In this review, we discuss the vital roles of bHLHs in plant responses to abiotic stresses, such as drought, salinity, cold, and iron deficiency. We suggest directions for future studies into the roles of bHLH genes in plant and discuss their potential applications in crop breeding.
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50
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Iqbal Z, Iqbal MS, Hashem A, Abd_Allah EF, Ansari MI. Plant Defense Responses to Biotic Stress and Its Interplay With Fluctuating Dark/Light Conditions. FRONTIERS IN PLANT SCIENCE 2021; 12:631810. [PMID: 33763093 PMCID: PMC7982811 DOI: 10.3389/fpls.2021.631810] [Citation(s) in RCA: 49] [Impact Index Per Article: 16.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/21/2020] [Accepted: 02/08/2021] [Indexed: 05/24/2023]
Abstract
Plants are subjected to a plethora of environmental cues that cause extreme losses to crop productivity. Due to fluctuating environmental conditions, plants encounter difficulties in attaining full genetic potential for growth and reproduction. One such environmental condition is the recurrent attack on plants by herbivores and microbial pathogens. To surmount such attacks, plants have developed a complex array of defense mechanisms. The defense mechanism can be either preformed, where toxic secondary metabolites are stored; or can be inducible, where defense is activated upon detection of an attack. Plants sense biotic stress conditions, activate the regulatory or transcriptional machinery, and eventually generate an appropriate response. Plant defense against pathogen attack is well understood, but the interplay and impact of different signals to generate defense responses against biotic stress still remain elusive. The impact of light and dark signals on biotic stress response is one such area to comprehend. Light and dark alterations not only regulate defense mechanisms impacting plant development and biochemistry but also bestow resistance against invading pathogens. The interaction between plant defense and dark/light environment activates a signaling cascade. This signaling cascade acts as a connecting link between perception of biotic stress, dark/light environment, and generation of an appropriate physiological or biochemical response. The present review highlights molecular responses arising from dark/light fluctuations vis-à-vis elicitation of defense mechanisms in plants.
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Affiliation(s)
- Zahra Iqbal
- Molecular Crop Research Unit, Department of Biochemistry, Chulalongkorn University, Bangkok, Thailand
| | | | - Abeer Hashem
- Botany and Microbiology Department, College of Science, King Saud University, Riyadh, Saudi Arabia
- Mycology and Plant Disease Survey Department, Plant Pathology Research Institute, ARC, Giza, Egypt
| | - Elsayed Fathi Abd_Allah
- Plant Production Department, College of Food and Agricultural Sciences, King Saud University, Riyadh, Saudi Arabia
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