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Serson WR, Gishini MFS, Stupar RM, Stec AO, Armstrong PR, Hildebrand D. Identification and Candidate Gene Evaluation of a Large Fast Neutron-Induced Deletion Associated with a High-Oil Phenotype in Soybean Seeds. Genes (Basel) 2024; 15:892. [PMID: 39062671 PMCID: PMC11276498 DOI: 10.3390/genes15070892] [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: 06/06/2024] [Revised: 06/29/2024] [Accepted: 07/03/2024] [Indexed: 07/28/2024] Open
Abstract
Since the dawn of agriculture, crops have been genetically altered for desirable characteristics. This has included the selection of natural and induced mutants. Increasing the production of plant oils such as soybean (Glycine max) oil as a renewable resource for food and fuel is valuable. Successful breeding for higher oil levels in soybeans, however, usually results in reduced seed protein. A soybean fast neutron population was screened for oil content, and three high oil mutants with minimal reductions in protein levels were found. Three backcross F2 populations derived from these mutants exhibited segregation for seed oil content. DNA was pooled from the high-oil and normal-oil plants within each population and assessed by comparative genomic hybridization. A deletion encompassing 20 gene models on chromosome 14 was found to co-segregate with the high-oil trait in two of the three populations. Eighteen genes in the deleted region have known functions that appear unrelated to oil biosynthesis and accumulation pathways, while one of the unknown genes (Glyma.14G101900) may contribute to the regulation of lipid droplet formation. This high-oil trait can facilitate the breeding of high-oil soybeans without protein reduction, resulting in higher meal protein levels.
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Affiliation(s)
- William R. Serson
- Department of Biology, Penn State University, Lehigh Valley, Center Valley, PA 18034, USA
| | | | - Robert M. Stupar
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Adrian O. Stec
- Department of Agronomy and Plant Genetics, University of Minnesota, Saint Paul, MN 55108, USA; (R.M.S.); (A.O.S.)
| | - Paul R. Armstrong
- United States Department of Agriculture-Agricultural Research Service, Manhattan, KS 66502, USA
| | - David Hildebrand
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546, USA;
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2
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Wang G, Mao J, Ji M, Wang W, Fu J. A comprehensive assessment of photosynthetic acclimation to shade in C4 grass (Cynodon dactylon (L.) Pers.). BMC PLANT BIOLOGY 2024; 24:591. [PMID: 38902617 PMCID: PMC11191358 DOI: 10.1186/s12870-024-05242-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Accepted: 06/03/2024] [Indexed: 06/22/2024]
Abstract
BACKGROUND Light deficit in shaded environment critically impacts the growth and development of turf plants. Despite this fact, past research has predominantly concentrated on shade avoidance rather than shade tolerance. To address this, our study examined the photosynthetic adjustments of Bermudagrass when exposed to varying intensities of shade to gain an integrative understanding of the shade response of C4 turfgrass. RESULTS We observed alterations in photosynthetic pigment-proteins, electron transport and its associated carbon and nitrogen assimilation, along with ROS-scavenging enzyme activity in shaded conditions. Mild shade enriched Chl b and LHC transcripts, while severe shade promoted Chl a, carotenoids and photosynthetic electron transfer beyond QA- (ET0/RC, φE0, Ψ0). The study also highlighted differential effects of shade on leaf and root components. For example, Soluble sugar content varied between leaves and roots as shade diminished SPS, SUT1 but upregulated BAM. Furthermore, we observed that shading decreased the transcriptional level of genes involving in nitrogen assimilation (e.g. NR) and SOD, POD, CAT enzyme activities in leaves, even though it increased in roots. CONCLUSIONS As shade intensity increased, considerable changes were noted in light energy conversion and photosynthetic metabolism processes along the electron transport chain axis. Our study thus provides valuable theoretical groundwork for understanding how C4 grass acclimates to shade tolerance.
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Affiliation(s)
- Guangyang Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, 264025, Shandong, China
| | - Jinyan Mao
- College of Agriculture, Ludong University, Yantai, 264025, Shandong, China
| | - Mingxia Ji
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, 264025, Shandong, China
| | - Wei Wang
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, 264025, Shandong, China
| | - Jinmin Fu
- Coastal Salinity Tolerant Grass Engineering and Technology Research Center, Ludong University, Yantai, 264025, Shandong, China.
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3
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Zhou Y, Kusmec A, Schnable PS. Genetic regulation of self-organizing azimuthal canopy orientations and their impacts on light interception in maize. THE PLANT CELL 2024; 36:1600-1621. [PMID: 38252634 PMCID: PMC11062469 DOI: 10.1093/plcell/koae007] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2023] [Revised: 12/06/2023] [Accepted: 12/14/2023] [Indexed: 01/24/2024]
Abstract
The efficiency of solar radiation interception contributes to the photosynthetic efficiency of crop plants. Light interception is a function of canopy architecture, including plant density; leaf number, length, width, and angle; and azimuthal canopy orientation. We report on the ability of some maize (Zea mays) genotypes to alter the orientations of their leaves during development in coordination with adjacent plants. Although the upper canopies of these genotypes retain the typical alternate-distichous phyllotaxy of maize, their leaves grow parallel to those of adjacent plants. A genome-wide association study (GWAS) on this parallel canopy trait identified candidate genes, many of which are associated with shade avoidance syndrome, including phytochromeC2. GWAS conducted on the fraction of photosynthetically active radiation (PAR) intercepted by canopies also identified multiple candidate genes, including liguleless1 (lg1), previously defined by its role in ligule development. Under high plant densities, mutants of shade avoidance syndrome and liguleless genes (lg1, lg2, and Lg3) exhibit altered canopy patterns, viz, the numbers of interrow leaves are greatly reduced as compared to those of nonmutant controls, resulting in dramatically decreased PAR interception. In at least the case of lg2, this phenotype is not a consequence of abnormal ligule development. Instead, liguleless gene functions are required for normal light responses, including azimuth canopy re-orientation.
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Affiliation(s)
- Yan Zhou
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
| | - Aaron Kusmec
- Department of Agronomy, Iowa State University, Ames, IA 50011, USA
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4
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Huang S, Ma Y, Xu Y, Lu P, Yang J, Xie Y, Gan J, Li L. Shade-induced RTFL/DVL peptides negatively regulate the shade response by directly interacting with BSKs in Arabidopsis. Nat Commun 2023; 14:6898. [PMID: 37898648 PMCID: PMC10613268 DOI: 10.1038/s41467-023-42618-3] [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: 01/24/2023] [Accepted: 10/17/2023] [Indexed: 10/30/2023] Open
Abstract
For shade-intolerant species, shade light indicates the close proximity of neighboring plants and triggers the shade avoidance syndrome (SAS), which causes exaggerated growth and reduced crop yield. Here, we report that non-secreted ROT FOUR LIKE (RTFL)/DEVIL (DVL) peptides negatively regulate SAS by interacting with BRASSINOSTEROID SIGNALING KINASEs (BSKs) and reducing the protein level of PHYTOCHROME INTERACTING FACTOR 4 (PIF4) in Arabidopsis. The transcription of at least five RTFLs (RTFL13/16/17/18/21) is induced by low R:FR light. The RTFL18 (DVL1) protein is stabilized under low R:FR conditions and localized to the plasma membrane. A phenotype analysis reveals that RTFL18 negatively regulates low R:FR-promoted petiole elongation. BSK3 and BSK6 are identified as partners of RTFL18 through binding assays and structural modeling. The overexpression of RTFL18 or knockdown of BSK3/6 reduces BRASSINOSTEROID signaling and reduces low R:FR-stabilized PIF4 levels. Genetically, the overexpression of BSK3/6 and PIF4 restores the petiole phenotype acquired by RTFL18-overexpressing lines. Collectively, our work characterizes a signaling cascade (the RTFLs-BSK3/6-PIF4 pathway) that prevents the excessive activation of the shade avoidance response in Arabidopsis.
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Affiliation(s)
- Sha Huang
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu Ma
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yitian Xu
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Pengfei Lu
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jie Yang
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Yu Xie
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Jianhua Gan
- Shanghai Public Health Clinical Center, State Key Laboratory of Genetic Engineering, Department of Physiology and Biophysics, School of Life Sciences, Fudan University, Shanghai, 200438, China
| | - Lin Li
- State Key Laboratory of Genetic Engineering, Institute of Plants Biology, School of Life Sciences, Fudan University, Shanghai, 200438, China.
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5
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Brooks CJ, Atamian HS, Harmer SL. Multiple light signaling pathways control solar tracking in sunflowers. PLoS Biol 2023; 21:e3002344. [PMID: 37906610 PMCID: PMC10617704 DOI: 10.1371/journal.pbio.3002344] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/21/2023] [Indexed: 11/02/2023] Open
Abstract
Sunflowers are famous for their ability to track the sun throughout the day and then reorient at night to face east the following morning. This occurs by differential growth patterns, with the east sides of stems growing more during the day and the west sides of stems growing more at night. This process, termed heliotropism, is generally believed to be a specialized form of phototropism; however, the underlying mechanism is unknown. To better understand heliotropism, we compared gene expression patterns in plants undergoing phototropism in a controlled environment and in plants initiating and maintaining heliotropic growth in the field. We found the expected transcriptome signatures of phototropin-mediated phototropism in sunflower stems bending towards monochromatic blue light. Surprisingly, the expression patterns of these phototropism-regulated genes are quite different in heliotropic plants. Most genes rapidly induced during phototropism display only minor differences in expression across solar tracking stems. However, some genes that are both rapidly induced during phototropism and are implicated in growth responses to foliar shade are rapidly induced on the west sides of stems at the onset of heliotropism, suggesting a possible role for red light photoreceptors in solar tracking. To test the involvement of different photoreceptor signaling pathways in heliotropism, we modulated the light environment of plants initiating solar tracking. We found that depletion of either red and far-red light or blue light did not hinder the initiation or maintenance of heliotropism in the field. Together, our results suggest that the transcriptional regulation of heliotropism is distinct from phototropin-mediated phototropism and likely involves inputs from multiple light signaling pathways.
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Affiliation(s)
- Christopher J. Brooks
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Hagop S. Atamian
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
- Schmid College of Science and Technology, Chapman University, Orange, California, United States of America
| | - Stacey L. Harmer
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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6
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Wallner ES, Tonn N, Shi D, Luzzietti L, Wanke F, Hunziker P, Xu Y, Jung I, Lopéz-Salmerón V, Gebert M, Wenzl C, Lohmann JU, Harter K, Greb T. OBERON3 and SUPPRESSOR OF MAX2 1-LIKE proteins form a regulatory module driving phloem development. Nat Commun 2023; 14:2128. [PMID: 37059727 PMCID: PMC10104830 DOI: 10.1038/s41467-023-37790-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2021] [Accepted: 03/31/2023] [Indexed: 04/16/2023] Open
Abstract
Spatial specificity of cell fate decisions is central for organismal development. The phloem tissue mediates long-distance transport of energy metabolites along plant bodies and is characterized by an exceptional degree of cellular specialization. How a phloem-specific developmental program is implemented is, however, unknown. Here we reveal that the ubiquitously expressed PHD-finger protein OBE3 forms a central module with the phloem-specific SMXL5 protein for establishing the phloem developmental program in Arabidopsis thaliana. By protein interaction studies and phloem-specific ATAC-seq analyses, we show that OBE3 and SMXL5 proteins form a complex in nuclei of phloem stem cells where they promote a phloem-specific chromatin profile. This profile allows expression of OPS, BRX, BAM3, and CVP2 genes acting as mediators of phloem differentiation. Our findings demonstrate that OBE3/SMXL5 protein complexes establish nuclear features essential for determining phloem cell fate and highlight how a combination of ubiquitous and local regulators generate specificity of developmental decisions in plants.
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Affiliation(s)
- Eva-Sophie Wallner
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- Gilbert Biological Sciences, Stanford University, Stanford, CA, 94305-5020, USA
| | - Nina Tonn
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Dongbo Shi
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- Japan RIKEN Center for Sustainable Resource Science (CSRS), Yokohama, 230-0045, Japan
- Institute for Biochemistry and Biology (IBB), University of Potsdam, Potsdam, 14476, Germany
- Japan Science and Technology Agency (JST), Saitama, Kawaguchi, Japan
| | - Laura Luzzietti
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Friederike Wanke
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Pascal Hunziker
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Yingqiang Xu
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Ilona Jung
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Vadir Lopéz-Salmerón
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
- BD Bioscience, 69126, Heidelberg, Germany
| | - Michael Gebert
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Christian Wenzl
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Jan U Lohmann
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany
| | - Klaus Harter
- Center for Plant Molecular Biology (ZMBP), University of Tübingen, 72076, Tübingen, Germany
| | - Thomas Greb
- Centre for Organismal Studies (COS), Heidelberg University, 69120, Heidelberg, Germany.
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7
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Chen E, Yang X, Liu R, Zhang M, Zhang M, Zhou F, Li D, Hu H, Li C. GhBEE3-Like gene regulated by brassinosteroids is involved in cotton drought tolerance. FRONTIERS IN PLANT SCIENCE 2022; 13:1019146. [PMID: 36311136 PMCID: PMC9606830 DOI: 10.3389/fpls.2022.1019146] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/14/2022] [Accepted: 09/26/2022] [Indexed: 06/16/2023]
Abstract
Brassinosteroids (BRs) are important phytohormones that play a vital role in plant drought tolerance, but their mechanisms in cotton (Gossypium hirsutum L.) are poorly understood. Numerous basic helix-loop-helix (bHLH) family genes are involved in the responses to both BRs and drought stress. GhBEE3-Like, a bHLH transcription factor, is repressed by both 24-epi-BL (an active BR substance) and PEG8000 (drought simulation) treatments in cotton. Moreover, GhBZR1, a crucial transcription factor in BR signaling pathway, directly binds to the E-box element in GhBEE3-Like promoter region and inhibits its expression, which has been confirmed by electrophoretic mobility shift assay (EMSA) and dual luciferase reporter assay. Functional analysis revealed that Arabidopsis with GhBEE3-Like overexpression had drought sensitive phenotype, while GhBEE3-Like knock-down cotton plants obtained by virus-induced gene silencing (VIGS) technology were more tolerant to drought stress. Furthermore, the expression levels of three stress-related genes, GhERD10, GhCDPK1 and GhRD26, were significantly higher in GhBEE3-Like knock-down cotton than in control cotton after drought treatment. These results suggest that GhBEE3-Like is inhibited by BRs which elevates the expressions of stress-related genes to enhance plant drought tolerance. This study lays the foundation for understanding the mechanisms of BR-regulated drought tolerance and establishment of drought-resistant cotton lines.
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Affiliation(s)
- Eryong Chen
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Xiaobei Yang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Ruie Liu
- Shanghai Center for Plant Stress Biology, National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai, China
| | - Mengke Zhang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Meng Zhang
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Feng Zhou
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Dongxiao Li
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Haiyan Hu
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- International Joint Laboratory of Plant Genetic Improvement and Soil Remediation, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
| | - Chengwei Li
- Henan Engineering Research Center of Crop Genome Editing, School of Life Science and Technology, Henan Institute of Science and Technology, Xinxiang, China
- College of Biological Engineering, Henan University of Technology, Zhengzhou, China
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8
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A combination of plasma membrane sterol biosynthesis and autophagy is required for shade-induced hypocotyl elongation. Nat Commun 2022; 13:5659. [PMID: 36216814 PMCID: PMC9550796 DOI: 10.1038/s41467-022-33384-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2021] [Accepted: 09/15/2022] [Indexed: 12/04/2022] Open
Abstract
Plant growth ultimately depends on fixed carbon, thus the available light for photosynthesis. Due to canopy light absorption properties, vegetative shade combines low blue (LB) light and a low red to far-red ratio (LRFR). In shade-avoiding plants, these two conditions independently trigger growth adaptations to enhance light access. However, how these conditions, differing in light quality and quantity, similarly promote hypocotyl growth remains unknown. Using RNA sequencing we show that these two features of shade trigger different transcriptional reprogramming. LB induces starvation responses, suggesting a switch to a catabolic state. Accordingly, LB promotes autophagy. In contrast, LRFR induced anabolism including expression of sterol biosynthesis genes in hypocotyls in a manner dependent on PHYTOCHROME-INTERACTING FACTORs (PIFs). Genetic analyses show that the combination of sterol biosynthesis and autophagy is essential for hypocotyl growth promotion in vegetative shade. We propose that vegetative shade enhances hypocotyl growth by combining autophagy-mediated recycling and promotion of specific lipid biosynthetic processes. Plants subject to vegetative shade receive a low quantity of blue light (LB) and a low ratio of red to far-red light (LFLR). Here the authors show that while LB induces autophagy, LFLR leads to changes in lipid metabolism, and propose that these processes may contribute to shade avoidance responses.
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9
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Arias D, Ortega A, González-Calquin C, Quiroz LF, Moreno-Romero J, Martínez-García JF, Stange C. Development and carotenoid synthesis in dark-grown carrot taproots require PHYTOCHROME RAPIDLY REGULATED1. PLANT PHYSIOLOGY 2022; 189:1450-1465. [PMID: 35266544 PMCID: PMC9237741 DOI: 10.1093/plphys/kiac097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Accepted: 02/04/2022] [Indexed: 05/16/2023]
Abstract
Light stimulates carotenoid synthesis in plants during photomorphogenesis through the expression of PHYTOENE SYNTHASE (PSY), a key gene in carotenoid biosynthesis. The orange carrot (Daucus carota) synthesizes and accumulates high amounts of carotenoids in the taproot that grows underground. Contrary to other organs, light impairs carrot taproot development and represses the expression of carotenogenic genes, such as DcPSY1 and DcPSY2, reducing carotenoid accumulation. By means of RNA sequencing, in a previous analysis, we observed that carrot PHYTOCHROME RAPIDLY REGULATED1 (DcPAR1) is more highly expressed in the underground grown taproot compared with those grown in light. PAR1 is a transcriptional cofactor with a negative role in shade avoidance syndrome regulation in Arabidopsis (Arabidopsis thaliana) through the dimerization with PHYTOCHROME-INTERACTING FACTORs (PIFs), allowing a moderate synthesis of carotenoids. Here, we show that overexpressing AtPAR1 in carrot increases carotenoid production in taproots grown underground as well as DcPSY1 expression. The high expression of AtPAR1 and DcPAR1 led us to hypothesize a functional role of DcPAR1 that was verified through in vivo binding to AtPIF7 and overexpression in Arabidopsis, where AtPSY expression and carotenoid accumulation increased together with a photomorphogenic phenotype. Finally, DcPAR1 antisense carrot lines presented a dramatic decrease in carotenoid levels and in relative expression of key carotenogenic genes as well as impaired taproot development. These results suggest that DcPAR1 is a key factor for secondary root development and carotenoid synthesis in carrot taproot grown underground.
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Affiliation(s)
- Daniela Arias
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Angélica Ortega
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | | | - Luis Felipe Quiroz
- Centro de Biología Molecular Vegetal, Facultad de Ciencias, Universidad de Chile, Santiago, Chile
| | - Jordi Moreno-Romero
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, Universitat Politècnica de València, València, Spain
| | - Jaime F Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Barcelona, Spain
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, Universitat Politècnica de València, València, Spain
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10
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Cao J, Liang Y, Yan T, Wang X, Zhou H, Chen C, Zhang Y, Zhang B, Zhang S, Liao J, Cheng S, Chu J, Huang X, Xu D, Li J, Deng XW, Lin F. The photomorphogenic repressors BBX28 and BBX29 integrate light and brassinosteroid signaling to inhibit seedling development in Arabidopsis. THE PLANT CELL 2022; 34:2266-2285. [PMID: 35294019 PMCID: PMC9134050 DOI: 10.1093/plcell/koac092] [Citation(s) in RCA: 11] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/04/2022] [Accepted: 02/27/2022] [Indexed: 05/20/2023]
Abstract
B-box containing proteins (BBXs) integrate light and various hormonal signals to regulate plant growth and development. Here, we demonstrate that the photomorphogenic repressors BBX28 and BBX29 positively regulate brassinosteroid (BR) signaling in Arabidopsis thaliana seedlings. Treatment with the BR brassinolide stabilized BBX28 and BBX29, which partially depended on BR INSENSITIVE1 (BRI1) and BIN2. bbx28 bbx29 seedlings exhibited larger cotyledon aperture than the wild-type when treated with brassinazole in the dark, which partially suppressed the closed cotyledons of brassinazole resistant 1-1D (bzr1-1D). Consistently, overexpressing BBX28 and BBX29 partially rescued the short hypocotyls of bri1-5 and bin2-1 in both the dark and light, while the loss-of-function of BBX28 and BBX29 partially suppressed the long hypocotyls of bzr1-1D in the light. BBX28 and BBX29 physically interacted with BR-ENHANCED EXPRESSION1 (BEE1), BEE2, and BEE3 and enhanced their binding to and activation of their target genes. Moreover, BBX28 and BBX29 as well as BEE1, BEE2, and BEE3 increased BZR1 accumulation to promote the BR signaling pathway. Therefore, both BBX28 and BBX29 interact with BEE1, BEE2, and BEE3 to orchestrate light and BR signaling by facilitating the transcriptional activity of BEE target genes. Our study provides insights into the pivotal roles of BBX28 and BBX29 as signal integrators in ensuring normal seedling development.
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Affiliation(s)
| | | | | | - Xuncheng Wang
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
| | - Hua Zhou
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen 518055, China
| | - Chen Chen
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Yingli Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Beihong Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shuhao Zhang
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Juncheng Liao
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
| | - Shujing Cheng
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
| | - Jinfang Chu
- National Centre for Plant Gene Research (Beijing), Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 100039, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen 361102, China
| | - Dongqing Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Jia Li
- Ministry of Education Key Laboratory of Cell Activities and Stress Adaptations, School of Life Sciences, Lanzhou University, Lanzhou 730000, China
- School of Life Sciences, Guangzhou University, Guangzhou 510006, China
| | - Xing Wang Deng
- Department of Biology, Institute of Plant and Food Sciences, Southern University of Science and Technology, Shenzhen 518055, China
- State Key Laboratory of Protein and Plant Gene Research, Peking-Tsinghua Center for Life Sciences, School of Advanced Agriculture Sciences and School of Life Sciences, Peking University, Beijing 100871, China
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11
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Shi Y, Ke X, Yang X, Liu Y, Hou X. Plants response to light stress. J Genet Genomics 2022; 49:735-747. [DOI: 10.1016/j.jgg.2022.04.017] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 04/13/2022] [Accepted: 04/26/2022] [Indexed: 11/30/2022]
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12
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Wu Q, Zhong S, Shi H. MicroProteins: Dynamic and accurate regulation of protein activity. JOURNAL OF INTEGRATIVE PLANT BIOLOGY 2022; 64:812-820. [PMID: 35060666 DOI: 10.1111/jipb.13229] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/17/2022] [Indexed: 06/14/2023]
Abstract
Proteins usually assemble oligomers or high-order complexes to increase their efficiency and specificity in biological processes. The dynamic equilibrium of complex formation and disruption imposes reversible regulation of protein function. MicroProteins are small, single-domain proteins that directly bind target protein complexes and disrupt their assembly. Growing evidence shows that microProteins are efficient regulators of protein activity at the post-translational level. In the last few decades, thousands of plant microProteins have been predicted by computational approaches, but only a few have been experimentally validated. Recent studies highlighted the mechanistic working modes of newly-identified microProteins in Arabidopsis and other plant species. Here, we review characterized microProteins, including their biological roles, regulatory targets, and modes of action. In particular, we focus on microProtein-directed allosteric modulation of key components in light signaling pathways, and we summarize the biogenesis and evolutionary trajectory of known microProteins in plants. Understanding the regulatory mechanisms of microProteins is an important step towards potential utilization of microProteins as versatile biotechnological tools in crop bioengineering.
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Affiliation(s)
- Qingqing Wu
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
- National Engineering Laboratory of Crop Stress Resistance Breeding, School of Life Sciences, Anhui Agricultural University, Hefei, 230036, China
| | - Shangwei Zhong
- State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, Peking University, Beijing, 100871, China
| | - Hui Shi
- College of Life Sciences, Capital Normal University, and Beijing Key Laboratory of Plant Gene Resources and Biotechnology for Carbon Reduction and Environmental Improvement, Beijing, 100048, China
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13
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Albertos P, Wlk T, Griffiths J, Pimenta Lange MJ, Unterholzner SJ, Rozhon W, Lange T, Jones AM, Poppenberger B. Brassinosteroid-regulated bHLH transcription factor CESTA induces the gibberellin 2-oxidase GA2ox7. PLANT PHYSIOLOGY 2022; 188:2012-2025. [PMID: 35148416 PMCID: PMC8968292 DOI: 10.1093/plphys/kiac008] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/25/2021] [Accepted: 12/10/2021] [Indexed: 05/14/2023]
Abstract
Brassinosteroids (BRs) are plant steroids that have growth-promoting capacities, which are partly enabled by an ability to induce biosynthesis of gibberellins (GAs), a second class of plant hormones. In addition, BRs can also activate GA catabolism; here we show that in Arabidopsis (Arabidopsis thaliana) the basic helix-loop-helix transcription factor CESTA (CES) and its homologues BRASSINOSTEROID-ENHANCED EXPRESSION (BEE) 1 and 3 contribute to this activity. CES and the BEEs are BR-regulated at the transcriptional and posttranslational level and participate in different physiological processes, including vegetative and reproduction development, shade avoidance, and cold stress responses. We show that CES/BEEs can induce the expression of the class III GA 2-oxidase GA2ox7 and that this activity is increased by BRs. In BR signaling - and CES/BEE-deficient mutants, GA2ox7 expression decreased, yielding reduced levels of GA110, a product of GA2ox7 activity. In plants that over-express CES, GA2ox7 expression is hyper-responsive to BR, GA110 levels are elevated and amounts of bioactive GA are reduced. We provide evidence that CES directly binds to the GA2ox7 promoter and is activated by BRs, but can also act by BR-independent means. Based on these results, we propose a model for CES activity in GA catabolism where CES can be recruited for GA2ox7 induction not only by BR, but also by other factors.
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Affiliation(s)
| | | | | | - Maria J Pimenta Lange
- Institute of Plant Biology, Technical University of Braunschweig, Braunschweig, Germany
| | | | | | - Theo Lange
- Institute of Plant Biology, Technical University of Braunschweig, Braunschweig, Germany
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14
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Pathak AK, Singh SP, Sharma R, Nath V, Tuli R. Transcriptome analysis at mid-stage seed development in litchi with contrasting seed size. 3 Biotech 2022; 12:47. [PMID: 35127302 PMCID: PMC8783947 DOI: 10.1007/s13205-021-03098-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2021] [Accepted: 12/18/2021] [Indexed: 02/03/2023] Open
Abstract
Litchi is a sub-tropical fruit crop with genotypes that bear fruits with variable seed size. Small seed size is a desirable trait in litchi, as it improves consumers' preference and facilitates fruit processing. Seed specific transcriptome analysis was performed in two litchi genotypes with contrasting seed size to identify the genes associated with seed development. The transcriptomic sequence data from seeds at mid-development stages (16-28 days after anthesis) were de-novo assembled into 1,39,608 Trinity transcripts. Out of these, 6325 transcripts expressed differentially between the two contrasting genotypes. Several putative genes for salicylic acid, jasmonic acid and brassinosteriod pathways were down-regulated in seeds of the small-seeded litchi. The putative regulators of seed maturation and seed storage were down-regulated in the small-seeded genotype. Embryogenesis, cell expansion, seed size and stress related Trinity transcripts exhibited differential expression. Further studies on gene characterization will reveal the early regulators of seed size in litchi. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s13205-021-03098-8.
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Affiliation(s)
- Ashish K. Pathak
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.261674.00000 0001 2174 5640Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
| | - Sudhir P. Singh
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.454774.1Center of Innovative and Applied Bioprocessing (DBT-CIAB), Sector 81, SAS Nagar, Mohali, India
| | - Ritika Sharma
- grid.473732.6Sardar Swaran Singh National Institute of Bioenergy, Jalandhar, India
| | - Vishal Nath
- grid.506047.0ICAR-National Research Centre of Litchi, Muzaffarpur, India
| | - Rakesh Tuli
- grid.452674.60000 0004 1757 6145National Agri-Food Biotechnology Institute (DBT-NABI), Sector 81, SAS Nagar, Mohali, India ,grid.261674.00000 0001 2174 5640Department of Biotechnology, University Institute of Engineering and Technology, Panjab University, Chandigarh, India
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15
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Tian Q, Luan J, Guo C, Shi X, Deng P, Zhou Z, Zhang W, Shen L. A bHLH protein, OsBIM1, positively regulates rice leaf angle by promoting brassinosteroid signaling. Biochem Biophys Res Commun 2021; 578:129-135. [PMID: 34562652 DOI: 10.1016/j.bbrc.2021.09.035] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Accepted: 09/16/2021] [Indexed: 11/16/2022]
Abstract
Rice leaf angle is an important agronomic trait determining plant architecture and crop yield. Brassinosteroids (BRs) play crucial roles in controlling rice leaf angle, thus an increasing number of researches were focused on the BR signaling pathway in rice. However, the orthologs of some important components in Arabidopsis BR signaling have not yet been characterized in rice. In this study, we identified a rice bHLH transcription factor named OsBIM1, as the closest rice homolog of AtBIM1 (BES1-Interacting MYC-like Protein1). Overexpression of OsBIM1 significantly increases rice leaf angles, whereas the T-DNA knock-out mutant osbim1 and wide type (WT) showed similar leaf inclination. OsBIM1 overexpression enhances the sensitivity and response to BR treatment in rice. Gene expression analysis showed that the overexpression of OsBIM1 significantly increased the transcripts of INCREASED LEAF INCLINATION1 (OsILI1) that functions as a key transcription factor promoting BR signaling and response. Meanwhile, OsBIM1 inhibited the expression of DWARF2 (OsD2, a key enzyme in BR biosynthesis pathway). OsBIM1 can bind with OsILI1 promoter and enhance OsILI1 expression in response to BR treatment. The promoting effect of OsBIM1 overexpression on leaf angle can still be observed at harvest stage, but overexpression of OsBIM1 resulted in smaller grain size and reduced yield. These results indicate that OsBIM1 functions as a positive regulator in BR signaling, and its overexpression increases rice lamina inclination by promoting BR sensitivity and response.
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Affiliation(s)
- Quanxiang Tian
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China; College of Life and Environmental Science, Hangzhou Normal University, Hangzhou, 311121, China
| | - Junxia Luan
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chunxia Guo
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Xingyu Shi
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ping Deng
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhenzhen Zhou
- Excellence and Innovation Center, Jiangsu Academy of Agricultural Science, Nanjing, 210014, China.
| | - Wenhua Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China
| | - Like Shen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Life Sciences, Nanjing Agricultural University, Nanjing, 210095, China.
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Morelli L, Paulišić S, Qin W, Iglesias-Sanchez A, Roig-Villanova I, Florez-Sarasa I, Rodriguez-Concepcion M, Martinez-Garcia JF. Light signals generated by vegetation shade facilitate acclimation to low light in shade-avoider plants. PLANT PHYSIOLOGY 2021; 186:2137-2151. [PMID: 34618102 PMCID: PMC8331150 DOI: 10.1093/plphys/kiab206] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/23/2020] [Accepted: 04/08/2021] [Indexed: 05/27/2023]
Abstract
When growing in search for light, plants can experience continuous or occasional shading by other plants. Plant proximity causes a decrease in the ratio of R to far-red light (low R:FR) due to the preferential absorbance of R light and reflection of FR light by photosynthetic tissues of neighboring plants. This signal is often perceived before actual shading causes a reduction in photosynthetically active radiation (low PAR). Here, we investigated how several Brassicaceae species from different habitats respond to low R:FR and low PAR in terms of elongation, photosynthesis, and photoacclimation. Shade-tolerant plants such as hairy bittercress (Cardamine hirsuta) displayed a good adaptation to low PAR but a poor or null response to low R:FR exposure. In contrast, shade-avoider species, such as Arabidopsis (Arabidopsis thaliana), showed a weak photosynthetic performance under low PAR but they strongly elongated when exposed to low R:FR. These responses could be genetically uncoupled. Most interestingly, exposure to low R:FR of shade-avoider (but not shade-tolerant) plants improved their photoacclimation to low PAR by triggering changes in photosynthesis-related gene expression, pigment accumulation, and chloroplast ultrastructure. These results indicate that low R:FR signaling unleashes molecular, metabolic, and developmental responses that allow shade-avoider plants (including most crops) to adjust their photosynthetic capacity in anticipation of eventual shading by nearby plants.
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Affiliation(s)
- Luca Morelli
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Wenting Qin
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Ariadna Iglesias-Sanchez
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Irma Roig-Villanova
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Igor Florez-Sarasa
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Manuel Rodriguez-Concepcion
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
| | - Jaime F Martinez-Garcia
- Institute for Plant Molecular and Cell Biology (IBMCP), CSIC-UPV, València 46022, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, Campus UAB Bellaterra, Barcelona 08193, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Passeig Lluís Companys 23, Barcelona 08010, Spain
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17
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Hao Y, Zong X, Ren P, Qian Y, Fu A. Basic Helix-Loop-Helix (bHLH) Transcription Factors Regulate a Wide Range of Functions in Arabidopsis. Int J Mol Sci 2021; 22:ijms22137152. [PMID: 34281206 PMCID: PMC8267941 DOI: 10.3390/ijms22137152] [Citation(s) in RCA: 66] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2021] [Revised: 06/29/2021] [Accepted: 06/29/2021] [Indexed: 01/30/2023] Open
Abstract
The basic helix-loop-helix (bHLH) transcription factor family is one of the largest transcription factor gene families in Arabidopsis thaliana, and contains a bHLH motif that is highly conserved throughout eukaryotic organisms. Members of this family have two conserved motifs, a basic DNA binding region and a helix-loop-helix (HLH) region. These proteins containing bHLH domain usually act as homo- or heterodimers to regulate the expression of their target genes, which are involved in many physiological processes and have a broad range of functions in biosynthesis, metabolism and transduction of plant hormones. Although there are a number of articles on different aspects to provide detailed information on this family in plants, an overall summary is not available. In this review, we summarize various aspects of related studies that provide an overview of insights into the pleiotropic regulatory roles of these transcription factors in plant growth and development, stress response, biochemical functions and the web of signaling networks. We then provide an overview of the functional profile of the bHLH family and the regulatory mechanisms of other proteins.
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18
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Liu Y, Jafari F, Wang H. Integration of light and hormone signaling pathways in the regulation of plant shade avoidance syndrome. ABIOTECH 2021; 2:131-145. [PMID: 36304753 PMCID: PMC9590540 DOI: 10.1007/s42994-021-00038-1] [Citation(s) in RCA: 25] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 01/06/2021] [Accepted: 02/24/2021] [Indexed: 11/25/2022]
Abstract
As sessile organisms, plants are unable to move or escape from their neighboring competitors under high-density planting conditions. Instead, they have evolved the ability to sense changes in light quantity and quality (such as a reduction in photoactive radiation and drop in red/far-red light ratios) and evoke a suite of adaptative responses (such as stem elongation, reduced branching, hyponastic leaf orientation, early flowering and accelerated senescence) collectively termed shade avoidance syndrome (SAS). Over the past few decades, much progress has been made in identifying the various photoreceptor systems and light signaling components implicated in regulating SAS, and in elucidating the underlying molecular mechanisms, based on extensive molecular genetic studies with the model dicotyledonous plant Arabidopsis thaliana. Moreover, an emerging synthesis of the field is that light signaling integrates with the signaling pathways of various phytohormones to coordinately regulate different aspects of SAS. In this review, we present a brief summary of the various cross-talks between light and hormone signaling in regulating SAS. We also present a perspective of manipulating SAS to tailor crop architecture for breeding high-density tolerant crop cultivars.
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Affiliation(s)
- Yang Liu
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Fereshteh Jafari
- Biotechnology Research Institute, Chinese Academy of Agricultural Sciences, Beijing, 100081 China
| | - Haiyang Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, South China Agricultural University, Guangzhou, 510642 China
- Guangdong Laboratory for Lingnan Modern Agriculture, Guangzhou, 510642 China
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19
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Li W, Liu Y, Wang W, Liu J, Yao M, Guan M, Guan C, He X. Phytochrome-interacting factor (PIF) in rapeseed (Brassica napus L.): Genome-wide identification, evolution and expression analyses during abiotic stress, light quality and vernalization. Int J Biol Macromol 2021; 180:14-27. [PMID: 33722620 DOI: 10.1016/j.ijbiomac.2021.03.055] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2020] [Revised: 03/07/2021] [Accepted: 03/10/2021] [Indexed: 10/21/2022]
Abstract
Phytochrome-interacting factors (PIFs) are members of basic helix-loop-helix (bHLH) transcription factors and the primary partners of phytochromes (PHY) in light signaling. PIFs interact with the Pfr forms of phytochrome to play an important role in the pathways of response to light and temperature in plants. In this study, 30, 12, and 16 potential PIF genes were identified in Brassica napus, Brassica rapa, Brassica oleracea, respectively, which could be divided into three subgroups. The Br/Bo/BnaPIF genes are intron-rich and similar to the PIF genes in Arabidopsis. However, unlike the AtPIFs that exist in multiple alternative-splicing forms, the majority of Br/Bo/BnaPIF genes have no alternative-splicing forms. A total of 52 Br/Bo/BnaPIF proteins have both the conserved active PHYB binding (APB) and bHLH domains. The Ka/Ks ratio revealed that most BnaPIFs underwent purifying selection. A promoter analysis found that light-related, abscisic acid-related and MYB-binding sites were the most abundant in the promoters of BnaPIFs. BnaPIF genes displayed different spatiotemporal patterns of expression and were regulated by light quality, circadian rhythms, cold, heat, and vernalization. Our results are useful for understanding the biological functions of PIF proteins in rapeseed.
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Affiliation(s)
- Wenqian Li
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Yan Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Weiping Wang
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Juncen Liu
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mingyao Yao
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mei Guan
- Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Chunyun Guan
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China
| | - Xin He
- Southern Regional Collaborative Innovation Center for Grain and Oil Crops in China, Hunan Agricultural University, Changsha, Hunan 410128, China; Oil Crops Research, Hunan Agricultural University, Changsha, Hunan 410128, China; Hunan Branch of National Oilseed Crops Improvement Center, Changsha, Hunan 410128, China.
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20
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O’Rourke JA, Graham MA. Gene Expression Responses to Sequential Nutrient Deficiency Stresses in Soybean. Int J Mol Sci 2021; 22:1252. [PMID: 33513952 PMCID: PMC7866191 DOI: 10.3390/ijms22031252] [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: 12/17/2020] [Revised: 01/21/2021] [Accepted: 01/22/2021] [Indexed: 02/06/2023] Open
Abstract
Throughout the growing season, crops experience a multitude of short periods of various abiotic stresses. These stress events have long-term impacts on plant performance and yield. It is imperative to improve our understanding of the genes and biological processes underlying plant stress tolerance to mitigate end of season yield loss. The majority of studies examining transcriptional changes induced by stress focus on single stress events. Few studies have been performed in model or crop species to examine transcriptional responses of plants exposed to repeated or sequential stress exposure, which better reflect field conditions. In this study, we examine the transcriptional profile of soybean plants exposed to iron deficiency stress followed by phosphate deficiency stress (-Fe-Pi). Comparing this response to previous studies, we identified a core suite of genes conserved across all repeated stress exposures (-Fe-Pi, -Fe-Fe, -Pi-Pi). Additionally, we determined transcriptional response to sequential stress exposure (-Fe-Pi) involves genes usually associated with reproduction, not stress responses. These findings highlight the plasticity of the plant transcriptome and the complexity of unraveling stress response pathways.
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Affiliation(s)
- Jamie A. O’Rourke
- Corn Insects and Crop Genetics Research Unit, USDA—Agricultural Research Service, Ames, IA 50010, USA;
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21
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Paulišić S, Qin W, Arora Verasztó H, Then C, Alary B, Nogue F, Tsiantis M, Hothorn M, Martínez‐García JF. Adjustment of the PIF7-HFR1 transcriptional module activity controls plant shade adaptation. EMBO J 2021; 40:e104273. [PMID: 33264441 PMCID: PMC7780144 DOI: 10.15252/embj.2019104273] [Citation(s) in RCA: 26] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2019] [Revised: 10/01/2020] [Accepted: 10/16/2020] [Indexed: 01/29/2023] Open
Abstract
Shade caused by the proximity of neighboring vegetation triggers a set of acclimation responses to either avoid or tolerate shade. Comparative analyses between the shade-avoider Arabidopsis thaliana and the shade-tolerant Cardamine hirsuta revealed a role for the atypical basic-helix-loop-helix LONG HYPOCOTYL IN FR 1 (HFR1) in maintaining the shade tolerance in C. hirsuta, inhibiting hypocotyl elongation in shade and constraining expression profile of shade-induced genes. We showed that C. hirsuta HFR1 protein is more stable than its A. thaliana counterpart, likely due to its lower binding affinity to CONSTITUTIVE PHOTOMORPHOGENIC 1 (COP1), contributing to enhance its biological activity. The enhanced HFR1 total activity is accompanied by an attenuated PHYTOCHROME INTERACTING FACTOR (PIF) activity in C. hirsuta. As a result, the PIF-HFR1 module is differently balanced, causing a reduced PIF activity and attenuating other PIF-mediated responses such as warm temperature-induced hypocotyl elongation (thermomorphogenesis) and dark-induced senescence. By this mechanism and that of the already-known of phytochrome A photoreceptor, plants might ensure to properly adapt and thrive in habitats with disparate light amounts.
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Affiliation(s)
- Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Wenting Qin
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Harshul Arora Verasztó
- Structural Plant Biology LaboratorySection of BiologyDepartment of Botany and Plant BiologyUniversity of GenevaGenevaSwitzerland
| | - Christiane Then
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
- Present address:
Department for Epidemiology and Pathogen DiagnosticsJulius Kühn‐InstitutFederal Research Institute for Cultivated PlantsBraunschweigGermany
| | - Benjamin Alary
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
| | - Fabien Nogue
- Institut Jean‐Pierre BourginINRA, AgroParisTech, CNRSUniversité Paris‐SaclayVersaillesFrance
| | - Miltos Tsiantis
- Department of Comparative Development and GeneticsMax Planck Institute from Plant Breeding ResearchCologneGermany
| | - Michael Hothorn
- Structural Plant Biology LaboratorySection of BiologyDepartment of Botany and Plant BiologyUniversity of GenevaGenevaSwitzerland
| | - Jaime F Martínez‐García
- Centre for Research in Agricultural Genomics (CRAG)CSIC‐IRTA‐UAB‐UB, Cerdanyola del Vallès, Campus UABBarcelonaSpain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)BarcelonaSpain
- Institute for Plant Molecular and Cellular Biology (IBMCP)CSIC‐UPVValènciaSpain
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22
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Song B, Zhao H, Dong K, Wang M, Wu S, Li S, Wang Y, Chen P, Jiang L, Tao Y. Phytochrome A inhibits shade avoidance responses under strong shade through repressing the brassinosteroid pathway in Arabidopsis. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:1520-1534. [PMID: 33037720 DOI: 10.1111/tpj.15018] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/31/2020] [Accepted: 08/10/2020] [Indexed: 06/11/2023]
Abstract
In dense canopy, a reduction in red to far-red (R/FR) light ratio triggers shade avoidance responses (SARs) in Arabidopsis thaliana, a shade avoiding plant. Two red/far-red (R/FR) light photoreceptors, PHYB and PHYA, were reported to be key negative regulators of the SARs. PHYB represses the SARs under normal light conditions; however, the role of PHYA in the SARs remains elusive. We set up two shade conditions: Shade and strong Shade (s-Shade) with different R/FR ratios (0.7 and 0.1), which allowed us to observe phenotypes dominated by PHYB- and PHYA-mediated pathway, respectively. By comparing the hypocotyl growth under these two conditions with time, we found PHYA was predominantly activated in the s-Shade after prolonged shade treatment. We further showed that under s-Shade, PHYA inhibits hypocotyl elongation partially through repressing the brassinosteroid (BR) pathway. COP1 and PIF4,5 act downstream of PHYA. After prolonged shade treatment, the nuclear localization of COP1 was reduced, while the PIF4 protein level was much lower in the s-Shade than that in Shade. Both changes occurred in a PHYA-dependent manner. We propose that under deep canopy, the R/FR ratio is extremely low, which promotes the nuclear accumulation of PHYA. Activated PHYA reduces COP1 nuclear speckle, which may lead to changes of downstream targets, such as PIF4,5 and HY5. Together, these proteins regulate the BR pathway through modulating BES1/BZR1 and the expression of BR biosynthesis and BR target genes.
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Affiliation(s)
- Bin Song
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Hongli Zhao
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Kangmei Dong
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Meiling Wang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Shujuan Wu
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Si Li
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Yuxiang Wang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Peirui Chen
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Liangrong Jiang
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
| | - Yi Tao
- Xiamen Plant Genetics Key Laboratory and State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, Fujian Province, 361102, China
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23
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Holalu SV, Reddy SK, Blackman BK, Finlayson SA. Phytochrome interacting factors 4 and 5 regulate axillary branching via bud abscisic acid and stem auxin signalling. PLANT, CELL & ENVIRONMENT 2020; 43:2224-2238. [PMID: 32542798 DOI: 10.1111/pce.13824] [Citation(s) in RCA: 22] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Revised: 06/12/2020] [Accepted: 06/13/2020] [Indexed: 05/21/2023]
Abstract
The ratio of red light to far-red light (R:FR) is perceived by phytochrome B (phyB) and informs plants of nearby competition. A low R:FR indicative of competition induces the shade avoidance syndrome and suppresses branching by incompletely understood mechanisms. Phytochrome interacting factors (PIFs) are transcription factors targeted by phytochromes to evoke photomorphogenic responses. PIF4 and PIF5 promote shade avoidance responses and become inactivated by direct interaction with active phyB in the nucleus. Here, genetic and physiological assays show that PIF4 and PIF5 contribute to the suppression of branching resulting from phyB loss of function and a low R:FR, although roles for other PIFs or pathways may exist. The suppression of branching is associated with PIF4/PIF5 promotion of the expression of the branching inhibitor BRANCHED 1 and abscisic acid (ABA) accumulation in axillary buds and is dependent on the function of the key ABA biosynthetic enzyme Nine-cis-epoxycarotenoid dioxygenase 3. However, PIF4/PIF5 function is not confined to a single hormonal pathway, as they also promote stem indole-3-acetic acid accumulation and stimulate systemic auxin signalling, which contribute to the suppression of bud growth when phyB is inactive.
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Affiliation(s)
- Srinidhi V Holalu
- Department of Plant and Microbial Biology, University of California Berkeley, California, USA
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, USA
- Faculty of Molecular and Environmental Plant Sciences, Texas A&M University, College Station, Texas, USA
| | - Srirama K Reddy
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, USA
- Faculty of Molecular and Environmental Plant Sciences, Texas A&M University, College Station, Texas, USA
- Valent BioSciences LLC, Biorational Research Center, Libertyville, Illinois, USA
| | - Benjamin K Blackman
- Department of Plant and Microbial Biology, University of California Berkeley, California, USA
| | - Scott A Finlayson
- Department of Soil and Crop Sciences, Texas A&M University and Texas A&M AgriLife Research, College Station, Texas, USA
- Faculty of Molecular and Environmental Plant Sciences, Texas A&M University, College Station, Texas, USA
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24
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25
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Buti S, Hayes S, Pierik R. The bHLH network underlying plant shade-avoidance. PHYSIOLOGIA PLANTARUM 2020; 169:312-324. [PMID: 32053251 PMCID: PMC7383782 DOI: 10.1111/ppl.13074] [Citation(s) in RCA: 27] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Revised: 02/05/2020] [Accepted: 02/11/2020] [Indexed: 05/24/2023]
Abstract
Shade is a potential threat to many plant species. When shade-intolerant plants detect neighbours, they elongate their stems and leaves in an effort to maximise their light capture. This developmental programme, known as 'shade-avoidance' is tightly controlled by specialised photoreceptors and a suite of transcriptional regulators. The basic helix-loop-helix (bHLH) family of transcription factors are particularly important for shade-induced elongation. In recent years, it has become apparent that many members of this family heterodimerise and that together they form a complex regulatory network. This review summarises recent work into the structure of the bHLH network and how it regulates elongation growth. In addition to this, we highlight how photoreceptors modulate the function of the network via direct interaction with transcription factors. It is hoped that the information integrated in this review will provide a useful theoretical framework for future studies on the molecular basis of shade-avoidance in plants.
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Affiliation(s)
- Sara Buti
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
| | - Scott Hayes
- Centro Nacional de Biotecnología, CSICMadrid28049Spain
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental BiologyUtrecht UniversityUtrecht3584 CHThe Netherlands
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26
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Ma L, Li Y, Li X, Xu D, Lin X, Liu M, Li G, Qin X. FAR-RED ELONGATED HYPOCOTYLS3 negatively regulates shade avoidance responses in Arabidopsis. PLANT, CELL & ENVIRONMENT 2019; 42:3280-3292. [PMID: 31351015 DOI: 10.1111/pce.13630] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 07/18/2019] [Accepted: 07/19/2019] [Indexed: 06/10/2023]
Abstract
Light is a key limiting factor of plant growth and development under the canopy. Specific light signals, such as a low ratio of red : far-red (R:FR) light, trigger the shade avoidance response, which affects hypocotyl, stem, and leaf growth. Although multiple components mediating shade avoidance responses have been identified in the past few decades, the underlying regulatory mechanism remains unclear. In this study, we found that the far-red elongated hypocotyls 3 (fhy3) mutant exhibited longer hypocotyls and increased expression levels of core shade avoidance response genes under low R:FR shade conditions compared with the wild type No-0, suggesting that FHY3 negatively regulates shade avoidance responses. Yeast one-hybrid, chromatin immunoprecipitation, and RT-qPCR assays revealed that FHY3 directly binds to the promoters and gene body of PHYTOCHROME RAPIDLY REGULATED1 (PAR1) and PAR2 and activates their expression to inhibit shade responses. Furthermore, the overexpression of PAR1 or PAR2 rescued the enhanced shade avoidance responses of fhy3, indicating that both genes are direct downstream targets of FHY3 that mediate shade avoidance responses. Our findings demonstrate that the light-signalling protein FHY3 positively regulates the transcription of PAR1 and PAR2, which encode two key negative regulators of shade avoidance responses, thus repressing plant responses to shade signals.
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Affiliation(s)
- Lin Ma
- School of Biological Science and Technology, University of Jinan, Jinan, China
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Yang Li
- Photobiological Industry Institute, Fujian Sanan Sino-Science Photobiotech Co., Ltd., Quanzhou, China
| | - Xiuxiu Li
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Di Xu
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xueqiao Lin
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Mingmei Liu
- School of Biological Science and Technology, University of Jinan, Jinan, China
| | - Gang Li
- State Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Tai'an, China
| | - Xiaochun Qin
- School of Biological Science and Technology, University of Jinan, Jinan, China
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27
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Wang F, Gao Y, Liu Y, Zhang X, Gu X, Ma D, Zhao Z, Yuan Z, Xue H, Liu H. BES1-regulated BEE1 controls photoperiodic flowering downstream of blue light signaling pathway in Arabidopsis. THE NEW PHYTOLOGIST 2019; 223:1407-1419. [PMID: 31009078 DOI: 10.1111/nph.15866] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/27/2018] [Accepted: 04/14/2019] [Indexed: 05/23/2023]
Abstract
BRI1-EMS-SUPPRESSOR 1 (BES1) functions as a key regulator in the brassinosteroid (BR) pathway that promotes plant growth. However, whether BES1 is involved in photoperiodic flowering is unknown. Here we report that BES1 acts as a positive regulator of photoperiodic flowering, but it cannot directly bind FLOWERING LOCUS T (FT) promoter. BR ENHANCED EXPRESSION 1 (BEE1) is the direct target of BES1 and acts downstream of BES1. BEE1 is also a positive regulator of photoperiodic flowering. BEE1 binds directly to the FT chromatin to activate the transcription of FT and promote flowering initiation. More importantly, BEE1 promotes flowering in a blue light photoreceptor CRYPTOCHROME 2 (CRY2) partially dependent manner, as it physically interacts with CRY2 under the blue light. Furthermore, BEE1 is regulated by both BRs and blue light. The transcription of BEE1 is induced by BRs, and the BEE1 protein is stabilized under the blue light. Our findings indicate that BEE1 is the integrator of BES1 and CRY2 mediating flowering, and BES1-BEE1-FT is a new signaling pathway in regulating photoperiodic flowering.
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Affiliation(s)
- Fei Wang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Yongshun Gao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-bioresources/Key Laboratory of Biology and Germplasm Enhancement of Horticultural Crops in South China, Ministry of Agriculture/College of Horticulture, South China Agricultural University, Guangzhou, 510642, China
| | - Yawen Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Xin Zhang
- College of Life and Environmental Sciences, Shanghai Normal University, Shanghai, 200234, China
| | - Xingxing Gu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Dingbang Ma
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhiwei Zhao
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Zhenjiang Yuan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hongwei Xue
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, 200032, China
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28
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Mao TY, Liu YY, Zhu HH, Zhang J, Yang JX, Fu Q, Wang N, Wang Z. Genome-wide analyses of the bHLH gene family reveals structural and functional characteristics in the aquatic plant Nelumbo nucifera. PeerJ 2019; 7:e7153. [PMID: 31231599 PMCID: PMC6573809 DOI: 10.7717/peerj.7153] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2019] [Accepted: 05/17/2019] [Indexed: 12/20/2022] Open
Abstract
Lotus (Nelumbo nucifera Gaertn.) is an economically important aquatic plant with multiple applications, but water salinity and cold stress seriously affect lotus yield and distribution. The basic helix-loop-helix (bHLH) transcription factors (TFs) play a vital role in plant growth and development, metabolic regulation processes and responses to environmental changes. However, systematic analyses of the bHLH TF family in lotus has not yet been reported. Here, we report the identification and description of bHLH genes in lotus (NnbHLHs) with a focus on functional prediction, particularly for those involved in stress resistance. In all, 115 NnbHLHs were identified in the lotus genome and classified into 19 subfamilies. The chromosomal distribution, physicochemical properties, bHLH domain, conserved motif compositions and evolution of these 115 NnbHLHs were further analyzed. To better understand the functions of the lotus bHLH family, gene ontology, cis-element, and phylogenetic analyses were conducted. NnbHLHs were predicted to be involved in plant development, metabolic regulation and responses to stress, in accordance with previous findings. Overall, 15 NnbHLHs were further investigated with functional prediction via quantitative real-time PCR analyses. Meanwhile, expression profiles of NnbHLHs in four tissues indicated that many NnbHLHs showed tissue preference in their expression. This study is supposed to provide a good foundation for further research into the functions and evolution of NnbHLHs, and identifies candidate genes for stress resistance in lotus.
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Affiliation(s)
- Tian-Yu Mao
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Yao-Yao Liu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Huan-Huan Zhu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Jie Zhang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ju-Xiang Yang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Qiang Fu
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Nian Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
| | - Ze Wang
- Key Laboratory of Horticultural Plant Biology, College of Horticulture and Forestry Sciences, Huazhong Agriculture University, Wuhan, China.,Key Laboratory of Urban Agriculture in Central China, Ministry of Agriculture and Rural Affairs, Wuhan, China
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29
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Sakaguchi J, Matsushita T, Watanabe Y. DWARF4 accumulation in root tips is enhanced via blue light perception by cryptochromes. PLANT, CELL & ENVIRONMENT 2019; 42:1615-1629. [PMID: 30620085 DOI: 10.1111/pce.13510] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2017] [Revised: 09/20/2018] [Accepted: 12/12/2018] [Indexed: 05/20/2023]
Abstract
Brassinosteroid (BR) signalling is known to be coordinated with light signalling in above ground tissue. Many studies focusing on the shade avoidance response in above ground tissue or hypocotyl elongation in darkness have revealed the contribution of the BR signalling pathway to these processes. We previously analysed the expression of DWARF 4 (DWF4), a key BR biosynthesis enzyme, and revealed that light perception in above ground tissues triggered DWF4 accumulation in root tips. To determine the required wavelength of light and photoreceptors responsible for this regulation, we studied DWF4-GUS marker plants grown in several monochromatic light conditions. We revealed that monochromatic blue LED light could induce DWF4 accumulation in primary root tips and root growth as much as white light, whereas monochromatic red LED could not. Consistent with this, a cryptochrome1/2 double mutant showed retarded root growth under white light whereas a phytochromeA/B double mutant did not. Taken together, our data strongly indicated that blue light signalling was important for DWF4 accumulation in root tips and root growth. Furthermore, DWF4 accumulation patterns in primary root tips were not altered by auxin or sugar treatment. Therefore, we hypothesize that blue light signalling from the shoot tissue is different from auxin and sugar signalling.
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Affiliation(s)
- Jun Sakaguchi
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
| | | | - Yuichiro Watanabe
- Department of Life Sciences, Graduate School of Arts and Sciences, The University of Tokyo, Tokyo, 153-8902, Japan
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30
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Carlson KD, Bhogale S, Anderson D, Tomanek L, Madlung A. Phytochrome A Regulates Carbon Flux in Dark Grown Tomato Seedlings. FRONTIERS IN PLANT SCIENCE 2019; 10:152. [PMID: 30873186 PMCID: PMC6400891 DOI: 10.3389/fpls.2019.00152] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/05/2018] [Accepted: 01/29/2019] [Indexed: 06/09/2023]
Abstract
Phytochromes comprise a small family of photoreceptors with which plants gather environmental information that they use to make developmental decisions, from germination to photomorphogenesis to fruit development. Most phytochromes are activated by red light and de-activated by far-red light, but phytochrome A (phyA) is responsive to both and plays an important role during the well-studied transition of seedlings from dark to light growth. The role of phytochromes during skotomorphogenesis (dark development) prior to reaching light, however, has received considerably less attention although previous studies have suggested that phytochrome must play a role even in the dark. We profiled proteomic and transcriptomic seedling responses in tomato during the transition from dark to light growth and found that phyA participates in the regulation of carbon flux through major primary metabolic pathways, such as glycolysis, beta-oxidation, and the tricarboxylic acid (TCA) cycle. Additionally, phyA is involved in the attenuation of root growth soon after reaching light, possibly via control of sucrose allocation throughout the seedling by fine-tuning the expression levels of several sucrose transporters of the SWEET gene family even before the seedling reaches the light. Presumably, by participating in the control of major metabolic pathways, phyA sets the stage for photomorphogenesis for the dark grown seedling in anticipation of light.
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Affiliation(s)
- Keisha D. Carlson
- Department of Biology, University of Puget Sound, Tacoma, WA, United States
| | - Sneha Bhogale
- Department of Biology, University of Puget Sound, Tacoma, WA, United States
| | - Drew Anderson
- Department of Biology, University of Puget Sound, Tacoma, WA, United States
| | - Lars Tomanek
- Department of Biology, California Polytechnic State University, San Luis Obispo, CA, United States
| | - Andreas Madlung
- Department of Biology, University of Puget Sound, Tacoma, WA, United States
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31
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Pathways in the Control of the Shade Avoidance Response. PLANTS 2018; 7:plants7040102. [PMID: 30453622 PMCID: PMC6313891 DOI: 10.3390/plants7040102] [Citation(s) in RCA: 30] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/19/2018] [Revised: 11/13/2018] [Accepted: 11/14/2018] [Indexed: 01/09/2023]
Abstract
To detect the presence of neighboring vegetation, shade-avoiding plants have evolved the ability to perceive and integrate multiple signals. Among them, changes in light quality and quantity are central to elicit and regulate the shade avoidance response. Here, we describe recent progresses in the comprehension of the signaling mechanisms underlying the shade avoidance response, focusing on Arabidopsis, because most of our knowledge derives from studies conducted on this model plant. Shade avoidance is an adaptive response that results in phenotypes with a high relative fitness in individual plants growing within dense vegetation. However, it affects the growth, development, and yield of crops, and the design of new strategies aimed at attenuating shade avoidance at defined developmental stages and/or in specific organs in high-density crop plantings is a major challenge for the future. For this reason, in this review, we also report on recent advances in the molecular description of the shade avoidance response in crops, such as maize and tomato, and discuss their similarities and differences with Arabidopsis.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, 00185 Rome, Italy.
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32
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Gommers CMM, Buti S, Tarkowská D, Pěnčík A, Banda JP, Arricastres V, Pierik R. Organ-specific phytohormone synthesis in two Geranium species with antithetical responses to far-red light enrichment. PLANT DIRECT 2018; 2:e00066. [PMID: 31245741 PMCID: PMC6508794 DOI: 10.1002/pld3.66] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2017] [Revised: 05/24/2018] [Accepted: 06/09/2018] [Indexed: 05/23/2023]
Abstract
Plants growing in high densities experience a reduced red (R) to far-red (FR) light ratio and shade-intolerant species respond with accelerated elongation growth to reach the top of the canopy: the shade avoidance syndrome (SAS). FR-enriched light inactivates phytochrome photoreceptors, which results in subsequent action of several plant hormones regulating growth. SAS is adaptive for shade-intolerant plants, but is suppressed in shade-tolerant plant species. Inspired by a previously published transcriptome analysis, we use two species of the genus Geranium here to study the involvement of auxin, brassinosteroids (BRs), and gibberellins (GAs) in supplemental FR-induced elongation growth. G. pyrenaicum, a shade-avoiding species, strongly induces auxin and gibberellin levels, but not BR, in elongating petioles. We show that, in this species, FR light perception, hormone synthesis, and growth are local and restricted to the petiole, and not the leaf lamina. Using chemical hormone inhibitors, we confirm the essential role of auxin and GAs in supplemental FR-induced elongation growth. Shade-tolerant G. robertianum does not display the change in hormone levels upon FR light enrichment, resulting in the lack of a shade avoidance response.
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Affiliation(s)
- Charlotte M. M. Gommers
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
- Plant Development and Signal Transduction ProgramCenter for Research in Agricultural Genomics (CRAG)BarcelonaSpain
| | - Sara Buti
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Danuše Tarkowská
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCRFaculty of SciencePalacký UniversityOlomoucCzechia
| | - Aleš Pěnčík
- Laboratory of Growth RegulatorsCentre of the Region Haná for Biotechnological and Agricultural ResearchInstitute of Experimental Botany ASCRFaculty of SciencePalacký UniversityOlomoucCzechia
| | - Jason P. Banda
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
- Present address:
Centre for Plant Integrative BiologySchool of BiosciencesUniversity of NottinghamSutton BoningtonUK
| | - Vincent Arricastres
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
| | - Ronald Pierik
- Plant EcophysiologyInstitute of Environmental BiologyUtrecht UniversityUtrechtThe Netherlands
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33
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Liu K, Li Y, Chen X, Li L, Liu K, Zhao H, Wang Y, Han S. ERF72 interacts with ARF6 and BZR1 to regulate hypocotyl elongation in Arabidopsis. JOURNAL OF EXPERIMENTAL BOTANY 2018; 69:3933-3947. [PMID: 29897568 PMCID: PMC6054149 DOI: 10.1093/jxb/ery220] [Citation(s) in RCA: 49] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 06/18/2018] [Indexed: 05/21/2023]
Abstract
The phytohormones brassinosteroid (BR), auxin, and gibberellin (GA) regulate photomorphogenesis-related hypocotyl elongation in Arabidopsis via the co-operative interaction of BZR-ARF-PIF/DELLA (BAP/D) transcription factors/regulators. In addition, ethylene activates the PIF3 or ERF1 pathway through EIN3/EIL1 to balance hypocotyl elongation in Arabidopsis seedlings. However, the mechanism by which ethylene is co-ordinated with other phytohormones to produce light-regulated hypocotyl growth remains elusive. In this study, we found that hypocotyl cell elongation is regulated by a network involving ethylene, auxin, and BR signalling, which is mediated by interactions among ERF72, ARF6, and BZR1. ERF72 interacted directly with ARF6 and BZR1 in vitro and in vivo, and it antagonised regulation by ARF6 and BZR1 of the transcription of BEE3 and XTH7. In addition, light modulated the subcellular localisation of ERF72 and transcription of ERF72 through the EIN2-EIN3/EIL1 pathway, facilitating the function of ERF72 in photomorphogenesis. The expression of BEE3 and XTH7 was also regulated by the EIN2-EIN3/EIL1 pathway. Our findings indicate that a revised BZR-ARF-PIF/DELLA-ERF (BAP/DE) module integrates light and hormone signals to regulate hypocotyl elongation in Arabidopsis.
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Affiliation(s)
- Kun Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yihao Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Xuena Chen
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Lijuan Li
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Kai Liu
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Heping Zhao
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
| | - Yingdian Wang
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- Correspondence: or
| | - Shengcheng Han
- Beijing Key Laboratory of Gene Resource and Molecular Development, College of Life Sciences, Beijing Normal University, Beijing, China
- Correspondence: or
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Moreno JE, Moreno-Piovano G, Chan RL. The antagonistic basic helix-loop-helix partners BEE and IBH1 contribute to control plant tolerance to abiotic stress. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2018; 271:143-150. [PMID: 29650152 DOI: 10.1016/j.plantsci.2018.03.024] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/15/2017] [Revised: 03/17/2018] [Accepted: 03/22/2018] [Indexed: 06/08/2023]
Abstract
The bHLH family is composed by canonical and non-canonical transcription factors (TFs) that differ in the presence or absence of their DNA-binding domain, respectively. Since both types of bHLH proteins are able to dimerize, their relative abundance impacts their biological activity. Among this TF family BEE and IBH are canonical and non-canonical bHLHs, respectively and previous reports indicated that BEE2 and IBH1 dimerize. Wondering whether BEE TFs participate in the abiotic stress response and how the dimerization with IBH1 could regulate their role in Arabidopsis, double bee1/bee2 and triple bee1/bee2/bee3 mutants were tested under salinity and drought stresses. The bee1/bee2/bee3 mutant showed an enhanced tolerance whereas the double mutant behaved similar to wild type plants. These results indicated that BEE genes play a role in the stress response and also put in evidence the redundancy within the BEE family. Moreover, ectopic expression of IBH1 on different mutant backgrounds improved plant tolerance to abiotic stress, independently of the background. However, the yield of these transgenic plants was penalized with abortive seeds. Our results suggest that BEE genes are negative regulators of physiological responses to abiotic stress whereas IBH1 is a positive modulator via different pathways, one of them involving BEE TFs.
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Affiliation(s)
- Javier E Moreno
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Guillermo Moreno-Piovano
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina
| | - Raquel L Chan
- Instituto de Agrobiotecnología del Litoral, Universidad Nacional del Litoral - CONICET, Facultad de Bioquímica y Ciencias Biológicas, Colectora Ruta Nacional 168 km 0, Santa Fe, Argentina.
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35
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Hawkins AK, Garza ER, Dietz VA, Hernandez OJ, Hawkins WD, Burrell AM, Pepper AE. Transcriptome Signatures of Selection, Drift, Introgression, and Gene Duplication in the Evolution of an Extremophile Endemic Plant. Genome Biol Evol 2017; 9:3478-3494. [PMID: 29220486 PMCID: PMC5751042 DOI: 10.1093/gbe/evx259] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/04/2017] [Indexed: 12/26/2022] Open
Abstract
Plants on serpentine soils provide extreme examples of adaptation to environment, and thus offer excellent models for the study of evolution at the molecular and genomic level. Serpentine outcrops are derived from ultramafic rock and have extremely low levels of essential plant nutrients (e.g., N, P, K, and Ca), as well as toxic levels of heavy metals (e.g., Ni, Cr, and Co) and low moisture availability. These outcrops provide habitat to a number of endemic plant species, including the annual mustard Caulanthus amplexicaulis var. barbarae (Cab) (Brassicaceae). Its sister taxon, C. amplexicaulis var. amplexicaulis (Caa), is intolerant to serpentine soils. Here, we assembled and annotated comprehensive reference transcriptomes of both Caa and Cab for use in protein coding sequence comparisons. A set of 29,443 reciprocal best Blast hit (RBH) orthologs between Caa and Cab was compared with identify coding sequence variants, revealing a high genome-wide dN/dS ratio between the two taxa (mean = 0.346). We show that elevated dN/dS likely results from the composite effects of genetic drift, positive selection, and the relaxation of negative selection. Further, analysis of paralogs within each taxon revealed the signature of a period of elevated gene duplication (∼10 Ma) that is shared with other species of the tribe Thelypodieae, and may have played a role in the striking morphological and ecological diversity of this tribe. In addition, distribution of the synonymous substitution rate, dS, is strongly bimodal, indicating a history of reticulate evolution that may have contributed to serpentine adaptation.
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36
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Singh M, Gupta A, Singh D, Khurana JP, Laxmi A. Arabidopsis RSS1 Mediates Cross-Talk Between Glucose and Light Signaling During Hypocotyl Elongation Growth. Sci Rep 2017; 7:16101. [PMID: 29170398 PMCID: PMC5701026 DOI: 10.1038/s41598-017-16239-y] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 11/09/2017] [Indexed: 11/11/2022] Open
Abstract
Plants possess exuberant plasticity that facilitates its ability to adapt and survive under challenging environmental conditions. The developmental plasticity largely depends upon cellular elongation which is governed by a complex network of environmental and phytohormonal signals. Here, we report role of glucose (Glc) and Glc-regulated factors in controlling elongation growth and shade response in Arabidopsis. Glc controls shade induced hypocotyl elongation in a dose dependent manner. We have identified a Glc repressed factor REGULATED BY SUGAR AND SHADE1 (RSS1) encoding for an atypical basic helix-loop-helix (bHLH) protein of unknown biological function that is required for normal Glc actions. Phenotype analysis of mutant and overexpression lines suggested RSS1 to be a negative regulator of elongation growth. RSS1 affects overall auxin homeostasis. RSS1 interacts with the elongation growth-promoting proteins HOMOLOG OF BEE2 INTERACTING WITH IBH 1 (HBI1) and BR ENHANCED EXPRESSION2 (BEE2) and negatively affects the transcription of their downstream targets such as YUCs, INDOLE-3-ACETIC ACID INDUCIBLE (IAAs), LONG HYPOCOTYL IN FAR-RED1 (HFR1), HOMEOBOX PROTEIN 2 (ATHB2), XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASES (XTHs) and EXPANSINS. We propose, Glc signals might maintain optimal hypocotyl elongation under multiple signals such as light, shade and phytohormones through the central growth regulatory bHLH/HLH module.
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Affiliation(s)
- Manjul Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India.,Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Aditi Gupta
- National Institute of Plant Genome Research, New Delhi, 110067, India.,Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Dhriti Singh
- National Institute of Plant Genome Research, New Delhi, 110067, India
| | - Jitendra P Khurana
- Interdisciplinary center for Plant Genomics and Department of Plant Molecular biology, University of Delhi South Campus, New Delhi, 110021, India
| | - Ashverya Laxmi
- National Institute of Plant Genome Research, New Delhi, 110067, India.
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Gallemí M, Molina-Contreras MJ, Paulišić S, Salla-Martret M, Sorin C, Godoy M, Franco-Zorrilla JM, Solano R, Martínez-García JF. A non-DNA-binding activity for the ATHB4 transcription factor in the control of vegetation proximity. THE NEW PHYTOLOGIST 2017; 216:798-813. [PMID: 28805249 DOI: 10.1111/nph.14727] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2016] [Accepted: 06/29/2017] [Indexed: 05/20/2023]
Abstract
In plants, perception of vegetation proximity by phytochrome photoreceptors activates a transcriptional network that implements a set of responses to adapt to plant competition, including elongation of stems or hypocotyls. In Arabidopsis thaliana, the homeodomain-leucine zipper (HD-Zip) transcription factor ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4) regulates this and other responses, such as leaf polarity. To better understand the shade regulatory transcriptional network, we have carried out structure-function analyses of ATHB4 by overexpressing a series of truncated and mutated forms and analyzing three different responses: hypocotyl response to shade, transcriptional activity and leaf polarity. Our results indicated that ATHB4 has two physically separated molecular activities: that performed by HD-Zip, which is involved in binding to DNA-regulatory elements, and that performed by the ETHYLENE-RESPONSIVE ELEMENT BINDING FACTOR-associated amphiphilic repression (EAR)-containing N-terminal region, which is involved in protein-protein interaction. Whereas both activities are required to regulate leaf polarity, DNA-binding activity is not required for the regulation of the seedling responses to plant proximity, which indicates that ATHB4 works as a transcriptional cofactor in the regulation of this response. These findings suggest that transcription factors might employ alternative mechanisms of action to regulate different developmental processes.
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Affiliation(s)
- Marçal Gallemí
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Maria Jose Molina-Contreras
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Mercè Salla-Martret
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Céline Sorin
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
| | - Marta Godoy
- National Centre for Biotechnology (CNB), CSIC, Campus University Autónoma, Madrid, 28049, Spain
| | | | - Roberto Solano
- National Centre for Biotechnology (CNB), CSIC, Campus University Autónoma, Madrid, 28049, Spain
| | - Jaime F Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, Bellaterra, Barcelona, 08193, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, 08010, Spain
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38
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Ballaré CL, Pierik R. The shade-avoidance syndrome: multiple signals and ecological consequences. PLANT, CELL & ENVIRONMENT 2017; 40:2530-2543. [PMID: 28102548 DOI: 10.1111/pce.12914] [Citation(s) in RCA: 203] [Impact Index Per Article: 29.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Revised: 01/10/2017] [Accepted: 01/13/2017] [Indexed: 05/18/2023]
Abstract
Plants use photoreceptor proteins to detect the proximity of other plants and to activate adaptive responses. Of these photoreceptors, phytochrome B (phyB), which is sensitive to changes in the red (R) to far-red (FR) ratio of sunlight, is the one that has been studied in greatest detail. The molecular connections between the proximity signal (low R:FR) and a model physiological response (increased elongation growth) have now been mapped in considerable detail in Arabidopsis seedlings. We briefly review our current understanding of these connections and discuss recent progress in establishing the roles of other photoreceptors in regulating growth-related pathways in response to competition cues. We also consider processes other than elongation that are controlled by photoreceptors and contribute to plant fitness under variable light conditions, including photoresponses that optimize the utilization of soil resources. In examining recent advances in the field, we highlight emerging roles of phyB as a major modulator of hormones related to plant immunity, in particular salicylic acid and jasmonic acid (JA). Recent attempts to manipulate connections between light signals and defence in Arabidopsis suggest that it might be possible to improve crop health at high planting densities by targeting links between phyB and JA signalling.
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Affiliation(s)
- Carlos L Ballaré
- IFEVA, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad de Buenos Aires, Ave. San Martín 4453, C1417DSE, Buenos Aires, Argentina
- IIB-INTECH, Consejo Nacional de Investigaciones Científicas y Técnicas, Universidad Nacional de San Martín, B1650HMP, Buenos Aires, Argentina
| | - Ronald Pierik
- Plant Ecophysiology, Institute of Environmental Biology, Utrecht University, Padualaan 8, 3584 CH, Utrecht, The Netherlands
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39
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Pham GM, Newton L, Wiegert-Rininger K, Vaillancourt B, Douches DS, Buell CR. Extensive genome heterogeneity leads to preferential allele expression and copy number-dependent expression in cultivated potato. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2017; 92:624-637. [PMID: 28869794 DOI: 10.1111/tpj.13706] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/08/2017] [Revised: 08/23/2017] [Accepted: 08/31/2017] [Indexed: 06/07/2023]
Abstract
Relative to homozygous diploids, the presence of multiple homologs or homeologs in polyploids affords greater tolerance to mutations that can impact genome evolution. In this study, we describe sequence and structural variation in the genomes of six accessions of cultivated potato (Solanum tuberosum L.), a vegetatively propagated autotetraploid and their impact on the transcriptome. Sequence diversity was high with a mean single nucleotide polymorphisms (SNP) rate of approximately 1 per 50 bases suggestive of high levels of allelic diversity. Additive gene expression was observed in leaves (3605 genes) and tubers (6156 genes) that contrasted the preferential allele expression of between 2180 and 3502 and 3367 and 5270 genes in the leaf and tuber transcriptome, respectively. Preferential allele expression was significantly associated with evolutionarily conserved genes suggesting selection of specific alleles of genes responsible for biological processes common to angiosperms during the breeding selection process. Copy number variation was rampant with between 16 098 and 18 921 genes in each cultivar exhibiting duplication or deletion. Copy number variable genes tended to be evolutionarily recent, lowly expressed, and enriched in genes that show increased expression in response to biotic and abiotic stress treatments suggestive of a role in adaptation. Gene copy number impacts on gene expression were detected with 528 genes having correlations between copy number and gene expression. Collectively, these data suggest that in addition to allelic variation of coding sequence, the heterogenous nature of the tetraploid potato genome contributes to a highly dynamic transcriptome impacted by allele preferential and copy number-dependent expression effects.
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Affiliation(s)
- Gina M Pham
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-1312, USA
| | - Linsey Newton
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-1312, USA
| | | | - Brieanne Vaillancourt
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-1312, USA
| | - David S Douches
- Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, Michigan, 48824-1312, USA
| | - C Robin Buell
- Department of Plant Biology, Michigan State University, East Lansing, Michigan, 48824-1312, USA
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Creighton MT, Kolton A, Kataya ARA, Maple-Grødem J, Averkina IO, Heidari B, Lillo C. Methylation of protein phosphatase 2A-Influence of regulators and environmental stress factors. PLANT, CELL & ENVIRONMENT 2017; 40:2347-2358. [PMID: 28741704 DOI: 10.1111/pce.13038] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/28/2017] [Revised: 07/08/2017] [Accepted: 07/11/2017] [Indexed: 05/13/2023]
Abstract
Protein phosphatase 2A catalytic subunit (PP2A-C) has a terminal leucine subjected to methylation, a regulatory mechanism conserved from yeast to mammals and plants. Two enzymes, LCMT1 and PME1, methylate and demethylate PP2A-C, respectively. The physiological importance of these posttranslational modifications is still enigmatic. We investigated these processes in Arabidopsis thaliana by mutant phenotyping, by global expression analysis, and by monitoring methylation status of PP2A-C under different environmental conditions. The lcmt1 mutant, possessing essentially only unmethylated PP2A-C, had less dense rosettes, and earlier flowering than wild type (WT). The pme1 mutant, with 30% reduction in unmethylated PP2A-C, was phenotypically comparable with WT. Approximately 200 overlapping genes were twofold upregulated, and 200 overlapping genes were twofold downregulated in both lcmt1 and pme1 relative to WT. Differences between the 2 mutants were also striking; 97 genes were twofold upregulated in pme1 compared with lcmt1, indicating that PME1 acts as a negative regulator for these genes. Analysis of enriched GO terms revealed categories of both abiotic and biotic stress genes. Furthermore, methylation status of PP2A-C was influenced by environmental stress, especially by hypoxia and salt stress, which led to increased levels of unmethylated PP2A-C, and highlights the importance of PP2A-C methylation/demethylation in environmental responses.
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Affiliation(s)
- Maria T Creighton
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Anna Kolton
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
- Faculty of Biotechnology and Horticulture, University of Agriculture in Krakow, Kraków, 31-425 Kraków, Poland
| | - Amr R A Kataya
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Jodi Maple-Grødem
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Irina O Averkina
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Behzad Heidari
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
| | - Cathrine Lillo
- Centre for Organelle Research, Faculty of Science and Technology, University of Stavanger, Stavanger, N-4036, Norway
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Chen E, Wang X, Gong Q, Butt HI, Chen Y, Zhang C, Yang Z, Wu Z, Ge X, Zhang X, Li F, Zhang X. A novel GhBEE1-Like gene of cotton causes anther indehiscence in transgenic Arabidopsis under uncontrolled transcription level. Gene 2017; 627:49-56. [PMID: 28600178 DOI: 10.1016/j.gene.2017.06.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2017] [Revised: 05/12/2017] [Accepted: 06/05/2017] [Indexed: 11/18/2022]
Abstract
Male-sterile lines are very important for selective breeding, and anther dehiscence defect is an effective way to generate male-sterile lines. Although several bHLH-family proteins in Arabidopsis have been characterized, little is known about the role of bHLH-family proteins in cotton. Here, we isolated a novel bHLH protein from cotton (Gossypium hirsutum), named GhBEE1-Like. Protein domain analysis showed that GhBEE1-Like contained a basic domain and an HLH domain. Subcellular localization analysis revealed that GhBEE1-Like was a nuclear-localized protein. Expression pattern analysis showed GhBEE1-Like was highly expressed in floral organs, and its expression was induced by the active brassinosteroid (BR) substance 24-epi-BL. GhBEE1-Like overexpression in Arabidopsis resulted in two types of transgenic lines, one with normal anther dehiscence and the other with defective anther dehiscence. Semi-qRT-PCR and qRT-PCR analyses revealed that GhBEE1-Like transcript levels acted as a check-point determining how anther dehiscence proceeds in these transgenic lines; regulated transcript levels result in normal anther dehiscence, whereas uncontrolled transcript levels lead to anther indehiscence. These results suggest that GhBEE1-Like plays an important role via its accumulation in regulating anther dehiscence. Therefore, controlling the level of GhBEE1-Like expression in cotton could be a convenient tool for generating male-sterile lines to use in selective breeding.
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Affiliation(s)
- Eryong Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China; Huazhong Agricultural University, Wuhan 430070, China
| | - Xiaoqian Wang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Qian Gong
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Hamama Islam Butt
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Yanli Chen
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Chaojun Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zuoren Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Zhixia Wu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xiaoyang Ge
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | | | - Fuguang Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China
| | - Xueyan Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang 455000, China.
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Niu X, Guan Y, Chen S, Li H. Genome-wide analysis of basic helix-loop-helix (bHLH) transcription factors in Brachypodium distachyon. BMC Genomics 2017; 18:619. [PMID: 28810832 PMCID: PMC5558667 DOI: 10.1186/s12864-017-4044-4] [Citation(s) in RCA: 57] [Impact Index Per Article: 8.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2017] [Accepted: 08/09/2017] [Indexed: 01/21/2023] Open
Abstract
BACKGROUND As a superfamily of transcription factors (TFs), the basic helix-loop-helix (bHLH) proteins have been characterized functionally in many plants with a vital role in the regulation of diverse biological processes including growth, development, response to various stresses, and so on. However, no systemic analysis of the bHLH TFs has been reported in Brachypodium distachyon, an emerging model plant in Poaceae. RESULTS A total of 146 bHLH TFs were identified in the Brachypodium distachyon genome and classified into 24 subfamilies. BdbHLHs in the same subfamily share similar protein motifs and gene structures. Gene duplication events showed a close relationship to rice, maize and sorghum, and segment duplications might play a key role in the expansion of this gene family. The amino acid sequence of the bHLH domains were quite conservative, especially Leu-27 and Leu-54. Based on the predicted binding activities, the BdbHLHs were divided into DNA binding and non-DNA binding types. According to the gene ontology (GO) analysis, BdbHLHs were speculated to function in homodimer or heterodimer manner. By integrating the available high throughput data in public database and results of quantitative RT-PCR, we found the expression profiles of BdbHLHs were different, implying their differentiated functions. CONCLUSION One hundred fourty-six BdbHLHs were identified and their conserved domains, sequence features, phylogenetic relationship, chromosomal distribution, GO annotations, gene structures, gene duplication and expression profiles were investigated. Our findings lay a foundation for further evolutionary and functional elucidation of BdbHLH genes.
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Affiliation(s)
- Xin Niu
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Yuxiang Guan
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Shoukun Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
| | - Haifeng Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Agronomy, Northwest A&F University, Yangling, China
- Xinjiang Agricultural Vocational Technical College, Changji, China
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Filiz E, Vatansever R, Ozyigit II. Dissecting a co-expression network of basic helix-loop-helix ( bHLH ) genes from phosphate (Pi)-starved soybean ( Glycine max ). ACTA ACUST UNITED AC 2017. [DOI: 10.1016/j.plgene.2016.12.001] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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44
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Kim Y, Song JH, Park SU, Jeong YS, Kim SH. Brassinosteroid-Induced Transcriptional Repression and Dephosphorylation-Dependent Protein Degradation Negatively Regulate BIN2-Interacting AIF2 (a BR Signaling-Negative Regulator) bHLH Transcription Factor. PLANT & CELL PHYSIOLOGY 2017; 58:227-239. [PMID: 28069895 DOI: 10.1093/pcp/pcw223] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2016] [Accepted: 12/12/2016] [Indexed: 05/19/2023]
Abstract
Brassinosteroids (BRs) are plant polyhydroxy-steroids that play important roles in plant growth and development via extensive signal integration through direct interactions between regulatory components of different signaling pathways. Recent studies have shown that diverse helix-loop-helix/basic helix-loop-helix (HLH/bHLH) family proteins are actively involved in control of BR signaling pathways and interact with other signaling pathways. In this study, we show that ATBS1-INTERACTING FACTOR 2 (AIF2), a nuclear-localized atypical bHLH transcription factor, specifically interacts with BRASSINOSTEROID-INSENSITIVE 2 (BIN2) among other BR signaling molecules. Overexpression of AIF2 down-regulated transcript expression of growth-promoting genes, thus resulting in retardation of growth. AIF2 renders plants hyposensitive to BR-induced root growth inhibition, but shows little effects on BR-promoted hypocotyl elongation. Notably, AIF2 was dephosphorylated by BR, and the dephosphorylated AIF2 was subject to proteasome-mediated degradation. AIF2 degradation was greatly induced by BR and ABA, but relatively slightly by other hormones such as auxin, gibberellin, cytokinin and ethylene. Moreover, AIF2 transcription was significantly suppressed by a BRI1/BZR1-mediated BR signaling pathway through a direct binding of BRASSINAZOLE RESISTANT 1 (BZR1) to the BR response element (BRRE) region of the AIF2 promoter. In conclusion, our study suggests that BIN2-driven AIF2 phosphorylation could augment the BIN2/AIF2-mediated negative circuit of BR signaling pathways, and the BR-induced transcriptional repression and protein degradation negatively regulate AIF2 transcription factor, reinforcing the BZR1/BES1-mediated positive BR signaling pathway.
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Affiliation(s)
- Yoon Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, Korea
| | - Ji-Hye Song
- Division of Biological Science and Technology, Yonsei University, Wonju, Korea
| | - Seon-U Park
- Division of Biological Science and Technology, Yonsei University, Wonju, Korea
| | - You-Seung Jeong
- Division of Biological Science and Technology, Yonsei University, Wonju, Korea
| | - Soo-Hwan Kim
- Division of Biological Science and Technology, Yonsei University, Wonju, Korea
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Yang C, Li L. Hormonal Regulation in Shade Avoidance. FRONTIERS IN PLANT SCIENCE 2017; 8:1527. [PMID: 28928761 PMCID: PMC5591575 DOI: 10.3389/fpls.2017.01527] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2017] [Accepted: 08/21/2017] [Indexed: 05/10/2023]
Abstract
At high vegetation density, shade-intolerant plants sense a reduction in the red (660 nm) to far-red (730 nm) light ratio (R/FR) in addition to a general reduction in light intensity. These light signals trigger a spectrum of morphological changes manifested by growth of stem-like tissue (hypocotyl, petiole, etc.) instead of harvestable organs (leaves, fruits, seeds, etc.)-namely, shade avoidance syndrome (SAS). Common phenotypical changes related to SAS are changes in leaf hyponasty, an increase in hypocotyl and internode elongation and extended petioles. Prolonged shade exposure leads to early flowering, less branching, increased susceptibility to insect herbivory, and decreased seed yield. Thus, shade avoidance significantly impacts on agronomic traits. Many genetic and molecular studies have revealed that phytochromes, cryptochromes and UVR8 (UV-B photoreceptor protein) monitor the changes in light intensity under shade and regulate the stability or activity of phytochrome-interacting factors (PIFs). PIF-governed modulation of the expression of auxin biosynthesis, transporter and signaling genes is the major driver for shade-induced hypocotyl elongation. Besides auxin, gibberellins, brassinosteroids, and ethylene are also required for shade-induced hypocotyl or petiole elongation growth. In leaves, accumulated auxin stimulates cytokinin oxidase expression to break down cytokinins and inhibit leaf growth. In the young buds, shade light promotes the accumulation of abscisic acid to repress branching. Shade light also represses jasmonate- and salicylic acid-induced defense responses to balance resource allocation between growth and defense. Here we will summarize recent findings relating to such hormonal regulation in SAS in Arabidopsis thaliana, Brassica rapa, and certain crops.
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Kebrom TH, McKinley B, Mullet JE. Dynamics of gene expression during development and expansion of vegetative stem internodes of bioenergy sorghum. BIOTECHNOLOGY FOR BIOFUELS 2017; 10:159. [PMID: 28649278 PMCID: PMC5480195 DOI: 10.1186/s13068-017-0848-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/21/2016] [Accepted: 06/14/2017] [Indexed: 05/18/2023]
Abstract
BACKGROUND Bioenergy sorghum accumulates 75% of shoot biomass in stem internodes. Grass stem internodes are formed during vegetative growth and elongate in response to developmental and environmental signals. To identify genes and molecular mechanisms that modulate the extent of internode growth, we conducted microscopic and transcriptomic analyses of four successive sub-apical vegetative internodes representing different stages of internode development of the bioenergy sorghum genotype R.07020. RESULTS Stem internodes of sorghum genotype R.07020 are formed during the vegetative phase and their length is enhanced by environmental signals such as shade and floral induction in short days. During vegetative growth, the first visible and youngest sub-apical internode was ~0.7 cm in length, whereas the fourth fully expanded internode was ~5 cm in length. Microscopic analyses revealed that all internode tissue types including pith parenchyma and vascular bundles are present in the four successive internodes. Growth in the first two sub-apical internodes occurred primarily through an increase in cell number consistent with expression of genes involved in the cell cycle and DNA replication. Growth of the 3rd internode was associated with an increase in cell length and growth cessation in the 4th internode was associated with up-regulation of genes involved in secondary cell wall deposition. The expression of genes involved in hormone metabolism and signaling indicates that GA, BR, and CK activity decreased while ethylene, ABA, and JA increased in the 3rd/4th internodes. While the level of auxin appears to be increasing as indicated by the up-regulation of ARFs, down-regulation of TIR during development indicates that auxin signaling is also modified. The expression patterns of transcription factors are closely associated with their role during the development of the vegetative internodes. CONCLUSIONS Microscopic and transcriptome analyses of four successive sub-apical internodes characterized the developmental progression of vegetative stem internodes from initiation through full elongation in the sorghum genotype R.07020. Transcriptome profiling indicates that dynamic variation in the levels and action of GA, CK, IAA, BR, ethylene, ABA, and JA modulate gene expression and growth during internode growth and development. This study provides detailed microscopic and transcriptomic data useful for identifying genes and molecular pathways regulating internode elongation in response to various developmental and environmental signals.
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Affiliation(s)
- Tesfamichael H. Kebrom
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
| | - Brian McKinley
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
| | - John E. Mullet
- Department of Biochemistry and Biophysics, Texas A&M University, College Station, TX 77843 USA
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Mao K, Dong Q, Li C, Liu C, Ma F. Genome Wide Identification and Characterization of Apple bHLH Transcription Factors and Expression Analysis in Response to Drought and Salt Stress. FRONTIERS IN PLANT SCIENCE 2017; 8:480. [PMID: 28443104 PMCID: PMC5387082 DOI: 10.3389/fpls.2017.00480] [Citation(s) in RCA: 105] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2016] [Accepted: 03/20/2017] [Indexed: 05/19/2023]
Abstract
The bHLH (basic helix-loop-helix) transcription factor family is the second largest in plants. It occurs in all three eukaryotic kingdoms, and plays important roles in regulating growth and development. However, family members have not previously been studied in apple. Here, we identified 188 MdbHLH proteins in apple "Golden Delicious" (Malus × domestica Borkh.), which could be classified into 18 groups. We also investigated the gene structures and 12 conserved motifs in these MdbHLHs. Coupled with expression analysis and protein interaction network prediction, we identified several genes that might be responsible for abiotic stress responses. This study provides insight and rich resources for subsequent investigations of such proteins in apple.
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Shwartz I, Levy M, Ori N, Bar M. Hormones in tomato leaf development. Dev Biol 2016; 419:132-142. [PMID: 27339291 DOI: 10.1016/j.ydbio.2016.06.023] [Citation(s) in RCA: 37] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2016] [Revised: 05/16/2016] [Accepted: 06/17/2016] [Indexed: 11/19/2022]
Abstract
Leaf development serves as a model for plant developmental flexibility. Flexible balancing of morphogenesis and differentiation during leaf development results in a large diversity of leaf forms, both between different species and within the same species. This diversity is particularly evident in compound leaves. Hormones are prominent regulators of leaf development. Here we discuss some of the roles of plant hormones and the cross-talk between different hormones in tomato compound-leaf development.
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Affiliation(s)
- Ido Shwartz
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Matan Levy
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel
| | - Naomi Ori
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel.
| | - Maya Bar
- The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture and The Otto Warburg Minerva Center for Agricultural Biotechnology, Hebrew University, P.O. Box 12, Rehovot 76100, Israel.
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Pearce S, Kippes N, Chen A, Debernardi JM, Dubcovsky J. RNA-seq studies using wheat PHYTOCHROME B and PHYTOCHROME C mutants reveal shared and specific functions in the regulation of flowering and shade-avoidance pathways. BMC PLANT BIOLOGY 2016; 16:141. [PMID: 27329140 PMCID: PMC4915087 DOI: 10.1186/s12870-016-0831-3] [Citation(s) in RCA: 43] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2016] [Accepted: 06/15/2016] [Indexed: 05/21/2023]
Abstract
BACKGROUND In cereal crops such as wheat, an optimal timing of developmental transitions is required to maximize grain yield. Many of these developmental changes are precisely regulated by changes in the duration, intensity or quality of light. Phytochromes are dimeric photoreceptors that absorb light maximally in the red and far-red wavelengths and induce large-scale transcriptional changes in response to variation in light quality. In wheat, PHYC is required for early flowering under long days. However, it is currently unknown whether this function requires the presence of PHYB. In this study, we characterized the role of PHYB in wheat development and used RNA-seq to analyze and compare the transcriptomes of phyB-null and phyC-null TILLING mutants. RESULTS Under long-day photoperiods, phyB-null plants exhibit a severe delay in flowering comparable to the delay observed in phyC-null plants. These results demonstrate that both genes are required for the induction of wheat flowering under long days. Using replicated RNA-seq studies we identified 82 genes that are significantly up or down regulated in both the phyB-null and phyC-null mutant relative to their respective wild-type controls. Among these genes are several well-characterized positive regulators of flowering, including PPD1, FT1 and VRN1. Eight-fold more genes were differentially regulated only in the phyB-null mutant (2202) than only in the phyC-null mutant (261). The PHYB-regulated genes were enriched in components of the auxin, gibberellin and brassinosteroid biosynthesis and signaling pathways, and in transcription factors with putative roles in regulating vegetative development and shade-avoidance responses. Several genes involved in abiotic stress tolerance pathways were also found to be regulated by PHYB. CONCLUSIONS PHYB and PHYC are both required for the photoperiodic induction of wheat flowering, whereas PHYB alone regulates a large number of genes involved in hormone biosynthesis and signaling, shade-avoidance response, and abiotic stress tolerance. Our analysis provides a comprehensive overview of the PHYB- and PHYC-mediated transcriptional changes during light signaling, and an initial step towards the dissection of this regulatory gene network in wheat. This further dissection will be required to explore the individual phytochrome-mediated developmental responses and to evaluate their potential to improve wheat adaptation to changing environments.
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Affiliation(s)
- Stephen Pearce
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
- />Present Address: Department of Soil and Crop Sciences, Colorado State University, Fort Collins, CO 80523 USA
| | - Nestor Kippes
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | - Andrew Chen
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
| | | | - Jorge Dubcovsky
- />Department of Plant Sciences, University of California, Davis, CA 95616 USA
- />Howard Hughes Medical Institute, Chevy Chase, MD 20815 USA
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Gallemí M, Galstyan A, Paulišić S, Then C, Ferrández-Ayela A, Lorenzo-Orts L, Roig-Villanova I, Wang X, Micol JL, Ponce MR, Devlin PF, Martínez-García JF. DRACULA2 is a dynamic nucleoporin with a role in regulating the shade avoidance syndrome in Arabidopsis. Development 2016; 143:1623-31. [PMID: 26989173 DOI: 10.1242/dev.130211] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2015] [Accepted: 03/03/2016] [Indexed: 12/28/2022]
Abstract
When plants grow in close proximity basic resources such as light can become limiting. Under such conditions plants respond to anticipate and/or adapt to the light shortage, a process known as the shade avoidance syndrome (SAS). Following genetic screening using a shade-responsive luciferase reporter line (PHYB:LUC), we identified DRACULA2 (DRA2), which encodes an Arabidopsis homolog of mammalian nucleoporin 98, a component of the nuclear pore complex (NPC). DRA2, together with other nucleoporins, participates positively in the control of the hypocotyl elongation response to plant proximity, a role that can be considered dependent on the nucleocytoplasmic transport of macromolecules (i.e. is transport dependent). In addition, our results reveal a specific role for DRA2 in controlling shade-induced gene expression. We suggest that this novel regulatory role of DRA2 is transport independent and that it might rely on its dynamic localization within and outside of the NPC. These results provide mechanistic insights in to how SAS responses are rapidly established by light conditions. They also indicate that nucleoporins have an active role in plant signaling.
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Affiliation(s)
- Marçal Gallemí
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Anahit Galstyan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Sandi Paulišić
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Christiane Then
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | | | - Laura Lorenzo-Orts
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Irma Roig-Villanova
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain
| | - Xuewen Wang
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jose Luis Micol
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Maria Rosa Ponce
- Instituto de Bioingeniería, Universidad Miguel Hernández, Campus de Elche, 03202 Elche, Spain
| | - Paul F Devlin
- School of Biological Sciences, Royal Holloway University of London, Egham TW20 0EX, UK
| | - Jaime F Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus UAB, 08193 Barcelona, Spain Institució Catalana de Recerca i Estudis Avançats (ICREA), Ps. Lluís Companys 10, 08010 Barcelona, Spain
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