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Cerbantez-Bueno VE, Serwatowska J, Rodríguez-Ramos C, Cruz-Valderrama JE, de Folter S. The role of D3-type cyclins is related to cytokinin and the bHLH transcription factor SPATULA in Arabidopsis gynoecium development. PLANTA 2024; 260:48. [PMID: 38980389 PMCID: PMC11233295 DOI: 10.1007/s00425-024-04481-4] [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: 02/21/2024] [Accepted: 07/02/2024] [Indexed: 07/10/2024]
Abstract
MAIN CONCLUSION We studied the D3-type cyclin function during gynoecium development in Arabidopsis and how they are related to the hormone cytokinin and the transcription factor SPATULA. Growth throughout the life of plants is sustained by cell division and differentiation processes in meristematic tissues. In Arabidopsis, gynoecium development implies a multiphasic process where the tissues required for pollination, fertilization, and seed development form. The Carpel Margin Meristem (CMM) is a mass of undifferentiated cells that gives rise to the gynoecium internal tissues, such as septum, ovules, placenta, funiculus, transmitting tract, style, and stigma. Different genetic and hormonal factors, including cytokinin, control the CMM function. Cytokinin regulates the cell cycle transitions through the activation of cell cycle regulators as cyclin genes. D3-type cyclins are expressed in proliferative tissues, favoring the mitotic cell cycle over the endoreduplication. Though the role of cytokinin in CMM and gynoecium development is highly studied, its specific role in regulating the cell cycle in this tissue remains unclear. Additionally, despite extensive research on the relationship between CYCD3 genes and cytokinin, the regulatory mechanism that connects them remains elusive. Here, we found that D3-type cyclins are expressed in proliferative medial and lateral tissues. Conversely, the depletion of the three CYCD3 genes showed that they are not essential for gynoecium development. However, the addition of exogenous cytokinin showed that they could control the division/differentiation balance in gynoecium internal tissues and outgrowths. Finally, we found that SPATULA can be a mechanistic link between cytokinin and the D3-type cyclins. The data suggest that the role of D3-type cyclins in gynoecium development is related to the cytokinin response, and they might be activated by the transcription factor SPATULA.
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Affiliation(s)
- Vincent E Cerbantez-Bueno
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México
- Department of Botany and Plant Sciences, University of California Riverside, Riverside, CA, 92521, USA
| | - Joanna Serwatowska
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México
- Departamento de Ingeniería Genética, Unidad Irapuato, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México
| | - Carolina Rodríguez-Ramos
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México
| | - J Erik Cruz-Valderrama
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México
- Departamento de Biología Molecular de Plantas, Instituto de Biotecnología, Universidad Nacional Autónoma de México, Avenida Universidad 2001, Colonia Chamilpa, 62210, Cuernavaca, Morelos, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional, 36824, Irapuato, México.
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2
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Maio KA, Moubayidin L. 'Organ'ising Floral Organ Development. PLANTS (BASEL, SWITZERLAND) 2024; 13:1595. [PMID: 38931027 PMCID: PMC11207604 DOI: 10.3390/plants13121595] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2024] [Revised: 06/05/2024] [Accepted: 06/06/2024] [Indexed: 06/28/2024]
Abstract
Flowers are plant structures characteristic of the phylum Angiosperms composed of organs thought to have emerged from homologous structures to leaves in order to specialize in a distinctive function: reproduction. Symmetric shapes, colours, and scents all play important functional roles in flower biology. The evolution of flower symmetry and the morphology of individual flower parts (sepals, petals, stamens, and carpels) has significantly contributed to the diversity of reproductive strategies across flowering plant species. This diversity facilitates attractiveness for pollination, protection of gametes, efficient fertilization, and seed production. Symmetry, the establishment of body axes, and fate determination are tightly linked. The complex genetic networks underlying the establishment of organ, tissue, and cellular identity, as well as the growth regulators acting across the body axes, are steadily being elucidated in the field. In this review, we summarise the wealth of research already at our fingertips to begin weaving together how separate processes involved in specifying organ identity within the flower may interact, providing a functional perspective on how identity determination and axial regulation may be coordinated to inform symmetrical floral organ structures.
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Affiliation(s)
| | - Laila Moubayidin
- Department of Cell and Developmental Biology, John Innes Centre, Colney Lane, Norwich NR4 7UH, UK;
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3
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Bernal-Gallardo JJ, González-Aguilera KL, de Folter S. EXPANSIN15 is involved in flower and fruit development in Arabidopsis. PLANT REPRODUCTION 2024; 37:259-270. [PMID: 38285171 PMCID: PMC11180156 DOI: 10.1007/s00497-023-00493-4] [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: 06/04/2023] [Accepted: 12/14/2023] [Indexed: 01/30/2024]
Abstract
KEY MESSAGE EXPANSIN15 is involved in petal cell morphology and size, the fusion of the medial tissues in the gynoecium and expansion of fruit valve cells. It genetically interacts with SPATULA and FRUITFULL. Cell expansion is fundamental for the formation of plant tissues and organs, contributing to their final shape and size during development. To better understand this process in flower and fruit development, we have studied the EXPANSIN15 (EXPA15) gene, which showed expression in petals and in the gynoecium. By analyzing expa15 mutant alleles, we found that EXPA15 is involved in petal shape and size determination, by affecting cell morphology and number. EXPA15 also has a function in fruit size, by affecting cell size and number. Furthermore, EXPA15 promotes fusion of the medial tissues in the gynoecium. In addition, we observed genetic interactions with the transcription factors SPATULA (SPT) and FRUITFULL (FUL) in gynoecium medial tissue fusion, style and stigma development and fruit development in Arabidopsis. These findings contribute to the importance of EXPANSINS in floral and fruit development in Arabidopsis.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), 36824, Irapuato, GTO., Mexico
| | - Karla L González-Aguilera
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), 36824, Irapuato, GTO., Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), 36824, Irapuato, GTO., Mexico.
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4
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Sessa G, Carabelli M, Sassi M. The Ins and Outs of Homeodomain-Leucine Zipper/Hormone Networks in the Regulation of Plant Development. Int J Mol Sci 2024; 25:5657. [PMID: 38891845 PMCID: PMC11171833 DOI: 10.3390/ijms25115657] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2024] [Revised: 05/20/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024] Open
Abstract
The generation of complex plant architectures depends on the interactions among different molecular regulatory networks that control the growth of cells within tissues, ultimately shaping the final morphological features of each structure. The regulatory networks underlying tissue growth and overall plant shapes are composed of intricate webs of transcriptional regulators which synergize or compete to regulate the expression of downstream targets. Transcriptional regulation is intimately linked to phytohormone networks as transcription factors (TFs) might act as effectors or regulators of hormone signaling pathways, further enhancing the capacity and flexibility of molecular networks in shaping plant architectures. Here, we focus on homeodomain-leucine zipper (HD-ZIP) proteins, a class of plant-specific transcriptional regulators, and review their molecular connections with hormonal networks in different developmental contexts. We discuss how HD-ZIP proteins emerge as key regulators of hormone action in plants and further highlight the fundamental role that HD-ZIP/hormone networks play in the control of the body plan and plant growth.
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Affiliation(s)
| | | | - Massimiliano Sassi
- Istituto di Biologia e Patologia Molecolari, Consiglio Nazionale delle Ricerche, 00185 Rome, Italy; (G.S.); (M.C.)
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5
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Wang Q, Wang Y, Zhang F, Han C, Wang Y, Ren M, Qi K, Xie Z, Zhang S, Tao S, Shiratake K. Genome-wide characterisation of HD-Zip transcription factors and functional analysis of PbHB24 during stone cell formation in Chinese white pear (Pyrus bretschneideri). BMC PLANT BIOLOGY 2024; 24:444. [PMID: 38778247 PMCID: PMC11112822 DOI: 10.1186/s12870-024-05138-w] [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: 02/05/2024] [Accepted: 05/13/2024] [Indexed: 05/25/2024]
Abstract
BACKGROUND The homodomain-leucine zipper (HD-Zip) is a conserved transcription factor family unique to plants that regulate multiple developmental processes including lignificaion. Stone cell content is a key determinant negatively affecting pear fruit quality, which causes a grainy texture of fruit flesh, because of the lignified cell walls. RESULTS In this study, a comprehensive bioinformatics analysis of HD-Zip genes in Chinese white pear (Pyrus bretschneideri) (PbHBs) was performed. Genome-wide identification of the PbHB gene family revealed 67 genes encoding PbHB proteins, which could be divided into four subgroups (I, II, III, and IV). For some members, similar intron/exon structural patterns support close evolutionary relationships within the same subgroup. The functions of each subgroup of the PbHB family were predicted through comparative analysis with the HB genes in Arabidopsis and other plants. Cis-element analysis indicated that PbHB genes might be involved in plant hormone signalling and external environmental responses, such as light, stress, and temperature. Furthermore, RNA-sequencing data and quantitative real-time PCR (RT-qPCR) verification revealed the regulatory roles of PbHB genes in pear stone cell formation. Further, co-expression network analysis revealed that the eight PbHB genes could be classified into different clusters of co-expression with lignin-related genes. Besides, the biological function of PbHB24 in promoting stone cell formation has been demonstrated by overexpression in fruitlets. CONCLUSIONS This study provided the comprehensive analysis of PbHBs and highlighted the importance of PbHB24 during stone cell development in pear fruits.
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Affiliation(s)
- Qi Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan
| | - Yueyang Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Fanhang Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Chengyang Han
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Yanling Wang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Mei Ren
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Kaijie Qi
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhihua Xie
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shaoling Zhang
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China
| | - Shutian Tao
- Sanya Institute, College of Horticulture, State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing, 210095, China.
| | - Katsuhiro Shiratake
- Laboratory of Horticultural Science, Graduate School of Bioagricultural Sciences, Nagoya University, Chikusa, Nagoya, 464-8601, Japan.
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6
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Luna-García V, Bernal Gallardo JJ, Rethoret-Pasty M, Pasha A, Provart NJ, de Folter S. A high-resolution gene expression map of the medial and lateral domains of the gynoecium of Arabidopsis. PLANT PHYSIOLOGY 2024; 195:410-429. [PMID: 38088205 DOI: 10.1093/plphys/kiad658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/25/2023] [Accepted: 11/14/2023] [Indexed: 05/02/2024]
Abstract
Angiosperms are characterized by the formation of flowers, and in their inner floral whorl, one or various gynoecia are produced. These female reproductive structures are responsible for fruit and seed production, thus ensuring the reproductive competence of angiosperms. In Arabidopsis (Arabidopsis thaliana), the gynoecium is composed of two fused carpels with different tissues that need to develop and differentiate to form a mature gynoecium and thus the reproductive competence of Arabidopsis. For these reasons, they have become the object of study for floral and fruit development. However, due to the complexity of the gynoecium, specific spatio-temporal tissue expression patterns are still scarce. In this study, we used precise laser-assisted microdissection and high-throughput RNA sequencing to describe the transcriptional profiles of the medial and lateral domain tissues of the Arabidopsis gynoecium. We provide evidence that the method used is reliable and that, in addition to corroborating gene expression patterns of previously reported regulators of these tissues, we found genes whose expression dynamics point to being involved in cytokinin and auxin homeostasis and in cell cycle progression. Furthermore, based on differential gene expression analyses, we functionally characterized several genes and found that they are involved in gynoecium development. This resource is available via the Arabidopsis eFP browser and will serve the community in future studies on developmental and reproductive biology.
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Affiliation(s)
- Valentín Luna-García
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Judith Jazmin Bernal Gallardo
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
| | - Martin Rethoret-Pasty
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
- Polytech Nice Sophia, Université Côte d'Azur, 930 Rte des Colles, 06410 Biot, France
| | - Asher Pasha
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Nicholas J Provart
- Department of Cell & Systems Biology, Centre for the Analysis of Genome Evolution and Function, University of Toronto, 25 Willcocks St., Toronto, ON M5S 3B2, Canada
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato CP 36824, Guanajuato, México
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7
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Jiang Y, Curran-French S, Koh SWH, Jamil I, Gu B, Argirò L, Lopez SG, Martins C, Saalbach G, Moubayidin L. O-glycosylation of the transcription factor SPATULA promotes style development in Arabidopsis. NATURE PLANTS 2024; 10:283-299. [PMID: 38278950 PMCID: PMC10881398 DOI: 10.1038/s41477-023-01617-4] [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: 03/22/2023] [Accepted: 12/21/2023] [Indexed: 01/28/2024]
Abstract
O-linked β-N-acetylglucosamine (O-GlcNAc) and O-fucose are two sugar-based post-translational modifications whose mechanistic role in plant signalling and transcriptional regulation is still largely unknown. Here we investigated how two O-glycosyltransferase enzymes of Arabidopsis thaliana, SPINDLY (SPY) and SECRET AGENT (SEC), promote the activity of the basic helix-loop-helix transcription factor SPATULA (SPT) during morphogenesis of the plant female reproductive organ apex, the style. SPY and SEC modify amino-terminal residues of SPT in vivo and in vitro by attaching O-fucose and O-GlcNAc, respectively. This post-translational regulation does not impact SPT homo- and heterodimerization events, although it enhances the affinity of SPT for the kinase PINOID gene locus and its transcriptional repression. Our findings offer a mechanistic example of the effect of O-GlcNAc and O-fucose on the activity of a plant transcription factor and reveal previously unrecognized roles for SEC and SPY in orchestrating style elongation and shape.
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Affiliation(s)
- Yuxiang Jiang
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | | | - Samuel W H Koh
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Iqra Jamil
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Benguo Gu
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Luca Argirò
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Sergio G Lopez
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK
| | - Carlo Martins
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Gerhard Saalbach
- Department of Molecular Microbiology, John Innes Centre, Norwich, UK
| | - Laila Moubayidin
- Department of Cell and Developmental Biology, John Innes Centre, Norwich, UK.
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8
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Zhao X, Wang Q, Yan C, Sun Q, Wang J, Li C, Yuan C, Mou Y, Shan S. The bHLH transcription factor AhbHLH121 improves salt tolerance in peanut. Int J Biol Macromol 2024; 256:128492. [PMID: 38035960 DOI: 10.1016/j.ijbiomac.2023.128492] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 11/26/2023] [Accepted: 11/27/2023] [Indexed: 12/02/2023]
Abstract
Plants have developed a number of protective mechanisms to respond to salt and other stresses. Previous studies have shown that the basic helix-loop-helix (bHLH) transcription factor AhbHLH121 plays a crucial role in the response to abiotic stresses in peanut, but the mechanisms and functions related to AhbHLH121 remain unclear. In the current research, AhbHLH121 was induced by salt treatment. Overexpression of AhbHLH121 improved salt resistance, whereas silencing AhbHLH121 resulted in the inverse correlation. Our results also demonstrated that overexpression of AhbHLH121 results in greater activity of antioxidant enzymes under stress condition by promoting the expression of the genes for peroxidase, catalase and superoxide dismutase (AhPOD, AhCAT and AhSOD), indicating enhanced scavenging of reactive oxygen species. Further analysis including Yeast one-hybrid (Y1H) assays and electrophoretic mobility shift assays (EMSAs), suggested that AhbHLH121 can bind directly to the G/E-box regions of the AhPOD, AhCAT and AhSOD promoters, thereby promoting their expression and leading to improved antioxidant enzyme activity. Our research improves the understanding of the mechanisms that allow this peanut bHLH transcription factor to improve abiotic tolerance, and provides valuable gene resources for breeding programs to promote salt stress resistance.
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Affiliation(s)
- Xiaobo Zhao
- Shandong Peanut Research Institute, Qingdao 266100, China.
| | - Qi Wang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Caixia Yan
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Quanxi Sun
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Juan Wang
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Chunjuan Li
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Cuiling Yuan
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Yifei Mou
- Shandong Peanut Research Institute, Qingdao 266100, China
| | - Shihua Shan
- Shandong Peanut Research Institute, Qingdao 266100, China.
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9
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Dabravolski SA, Isayenkov SV. The Role of Anthocyanins in Plant Tolerance to Drought and Salt Stresses. PLANTS (BASEL, SWITZERLAND) 2023; 12:2558. [PMID: 37447119 DOI: 10.3390/plants12132558] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/02/2023] [Accepted: 07/04/2023] [Indexed: 07/15/2023]
Abstract
Drought and salinity affect various biochemical and physiological processes in plants, inhibit plant growth, and significantly reduce productivity. The anthocyanin biosynthesis system represents one of the plant stress-tolerance mechanisms, activated by surplus reactive oxygen species. Anthocyanins act as ROS scavengers, protecting plants from oxidative damage and enhancing their sustainability. In this review, we focus on molecular and biochemical mechanisms underlying the role of anthocyanins in acquired tolerance to drought and salt stresses. Also, we discuss the role of abscisic acid and the abscisic-acid-miRNA156 regulatory node in the regulation of drought-induced anthocyanin production. Additionally, we summarise the available knowledge on transcription factors involved in anthocyanin biosynthesis and development of salt and drought tolerance. Finally, we discuss recent progress in the application of modern gene manipulation technologies in the development of anthocyanin-enriched plants with enhanced tolerance to drought and salt stresses.
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Affiliation(s)
- Siarhei A Dabravolski
- Department of Biotechnology Engineering, Braude Academic College of Engineering, Snunit 51, Karmiel 2161002, Israel
| | - Stanislav V Isayenkov
- Department of Plant Food Products and Biofortification, Institute of Food Biotechnology and Genomics, The National Academy of Sciences of Ukraine, Baidi-Vyshneveckogo Str., 2a, 04123 Kyiv, Ukraine
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10
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Hagelthorn L, Monfared MM, Talo A, Harmon FG, Fletcher JC. Unique and overlapping functions for the transcriptional regulators KANADI1 and ULTRAPETALA1 in Arabidopsis gynoecium and stamen gene regulation. PLANT DIRECT 2023; 7:e496. [PMID: 37168319 PMCID: PMC10165739 DOI: 10.1002/pld3.496] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 03/29/2023] [Accepted: 04/18/2023] [Indexed: 05/13/2023]
Abstract
Plants generate their reproductive organs, the stamens and the carpels, de novo within the flowers that form when the plant reaches maturity. The carpels comprise the female reproductive organ, the gynoecium, a complex organ that develops along several axes of polarity and is crucial for plant reproduction, fruit formation, and seed dispersal. The epigenetic trithorax group (trxG) protein ULTRAPETALA1 (ULT1) and the GARP domain transcription factor KANADI1 (KAN1) act cooperatively to regulate Arabidopsis thaliana gynoecium patterning along the apical-basal polarity axis; however, the molecular pathways through which this patterning activity is achieved remain to be explored. In this study, we used transcriptomics to identify genome-wide ULT1 and KAN1 target genes during reproductive development. We discovered 278 genes in developing flowers that are regulated by ULT1, KAN1, or both factors together. Genes involved in developmental and reproductive processes are overrepresented among ULT1 and/or KAN1 target genes, along with genes involved in biotic or abiotic stress responses. Consistent with their function in regulating gynoecium patterning, a number of the downstream target genes are expressed in the developing gynoecium, including a unique subset restricted to the stigmatic tissue. Further, we also uncovered a number of KAN1- and ULT1-induced genes that are transcribed predominantly or exclusively in developing stamens. These findings reveal a potential cooperative role for ULT1 and KAN1 in male as well as female reproductive development that can be investigated with future genetic and molecular experiments.
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Affiliation(s)
- Lynne Hagelthorn
- Plant Gene Expression CenterUnited States Department of Agriculture‐Agricultural Research ServiceAlbanyCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Mona M. Monfared
- Present address:
Department of Molecular and Cellular BiologyUniversity of California, DavisDavisCaliforniaUSA
| | - Anthony Talo
- Biology DepartmentSt. Mary's College of CaliforniaMoragaCaliforniaUSA
| | - Frank G. Harmon
- Plant Gene Expression CenterUnited States Department of Agriculture‐Agricultural Research ServiceAlbanyCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
| | - Jennifer C. Fletcher
- Plant Gene Expression CenterUnited States Department of Agriculture‐Agricultural Research ServiceAlbanyCaliforniaUSA
- Department of Plant and Microbial BiologyUniversity of California, BerkeleyBerkeleyCaliforniaUSA
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11
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Bernal-Gallardo JJ, Zuñiga-Mayo VM, Marsch-Martinez N, de Folter S. Novel Roles of SPATULA in the Control of Stomata and Trichome Number, and Anthocyanin Biosynthesis. PLANTS (BASEL, SWITZERLAND) 2023; 12:596. [PMID: 36771679 PMCID: PMC9919660 DOI: 10.3390/plants12030596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 01/24/2023] [Accepted: 01/24/2023] [Indexed: 06/18/2023]
Abstract
The bHLH transcription factor SPATULA (SPT) has been identified as a regulator during different stages of Arabidopsis development, including the control of leaf size. However, the mechanism via which it performs this function has not been elucidated. To better understand the role of SPT during leaf development, we used a transcriptomic approach to identify putative target genes. We found putative SPT target genes related to leaf development, and to stomata and trichome formation. Furthermore, genes related to anthocyanin biosynthesis. In this work, we demonstrate that SPT is a negative regulator of stomata number and a positive regulator of trichome number. In addition, SPT is required for sucrose-mediated anthocyanin biosynthesis.
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Affiliation(s)
- Judith Jazmin Bernal-Gallardo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
| | - Victor M. Zuñiga-Mayo
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
- CONACYT, Instituto de Fitosanidad, Colegio de Postgraduados, Campus Montecillo, Texcoco 56230, Mexico
| | - Nayelli Marsch-Martinez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Mexico
| | - Stefan de Folter
- Unidad de Genómica Avanzada (UGA-Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Mexico
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12
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Seok HY, Tran HT, Lee SY, Moon YH. AtERF71/ HRE2, an Arabidopsis AP2/ERF Transcription Factor Gene, Contains Both Positive and Negative Cis-Regulatory Elements in Its Promoter Region Involved in Hypoxia and Salt Stress Responses. Int J Mol Sci 2022; 23:ijms23105310. [PMID: 35628120 PMCID: PMC9140466 DOI: 10.3390/ijms23105310] [Citation(s) in RCA: 12] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2022] [Revised: 05/03/2022] [Accepted: 05/09/2022] [Indexed: 02/01/2023] Open
Abstract
In the signal transduction network, from the perception of stress signals to stress-responsive gene expression, various transcription factors and cis-regulatory elements in stress-responsive promoters coordinate plant adaptation to abiotic stresses. Among the AP2/ERF transcription factor family, group VII ERF (ERF-VII) genes, such as RAP2.12, RAP2.2, RAP2.3, AtERF73/HRE1, and AtERF71/HRE2, are known to be involved in the response to hypoxia in Arabidopsis. Notably, HRE2 has been reported to be involved in responses to hypoxia and osmotic stress. In this study, we dissected HRE2 promoter to identify hypoxia- and salt stress-responsive region(s). The analysis of the promoter deletion series of HRE2 using firefly luciferase and GUS as reporter genes indicated that the −116 to −2 region is responsible for both hypoxia and salt stress responses. Using yeast one-hybrid screening, we isolated HAT22/ABIG1, a member of the HD-Zip II subfamily, which binds to the −116 to −2 region of HRE2 promoter. Interestingly, HAT22/ABIG1 repressed the transcription of HRE2 via the EAR motif located in the N-terminal region of HAT22/ABIG1. HAT22/ABIG1 bound to the 5′-AATGATA-3′ sequence, HD-Zip II-binding-like cis-regulatory element, in the −116 to −2 region of HRE2 promoter. Our findings demonstrate that the −116 to −2 region of HRE2 promoter contains both positive and negative cis-regulatory elements, which may regulate the expression of HRE2 in responses to hypoxia and salt stress and that HAT22/ABIG1 negatively regulates HRE2 transcription by binding to the HD-Zip II-binding-like element in the promoter region.
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Affiliation(s)
- Hye-Yeon Seok
- Korea Nanobiotechnology Center, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Huong Thi Tran
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
| | - Sun-Young Lee
- Korea Nanobiotechnology Center, Pusan National University, Busan 46241, Korea; (H.-Y.S.); (S.-Y.L.)
| | - Yong-Hwan Moon
- Department of Integrated Biological Science, Pusan National University, Busan 46241, Korea;
- Department of Molecular Biology, Pusan National University, Busan 46241, Korea
- Institute of Systems Biology, Pusan National University, Busan 46241, Korea
- Correspondence: ; Tel.: +82-51-510-2592
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13
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Ballester P, Martínez-Godoy MA, Ezquerro M, Navarrete-Gómez M, Trigueros M, Rodríguez-Concepción M, Ferrándiz C. A transcriptional complex of NGATHA and bHLH transcription factors directs stigma development in Arabidopsis. THE PLANT CELL 2021; 33:3645-3657. [PMID: 34586419 PMCID: PMC8643694 DOI: 10.1093/plcell/koab236] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/27/2020] [Accepted: 09/17/2021] [Indexed: 05/27/2023]
Abstract
The stigma is an angiosperm-specific tissue that is essential for pollination. In the last two decades, several transcription factors with key roles in stigma development in Arabidopsis thaliana have been identified. However, genetic analyses have thus far been unable to unravel the precise regulatory interactions among these transcription factors or the molecular basis for their selective roles in different spatial and temporal domains. Here, we show that the NGATHA (NGA) and HECATE (HEC) transcription factors, which are involved in different developmental processes but are both essential for stigma development, require each other to perform this function. This relationship is likely mediated by their physical interaction in the apical gynoecium. NGA/HEC transcription factors subsequently upregulate INDEHISCENT (IND) and SPATULA and are indispensable for the binding of IND to some of its targets to allow stigma differentiation. Our findings support a nonhierarchical regulatory scenario in which the combinatorial action of different transcription factors provides exquisite temporal and spatial specificity of their developmental outputs.
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Affiliation(s)
- Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Maria A Martínez-Godoy
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Miguel Ezquerro
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
- Centre for Research in Agricultural Genomics (CRAG) CSIC-IRTA-UAB-UB, 08193 Barcelona, Spain
| | - Marisa Navarrete-Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Marina Trigueros
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Manuel Rodríguez-Concepción
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universitat Politècnica de València, Valencia, Spain
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14
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Coordination of biradial-to-radial symmetry and tissue polarity by HD-ZIP II proteins. Nat Commun 2021; 12:4321. [PMID: 34262040 PMCID: PMC8280177 DOI: 10.1038/s41467-021-24550-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/08/2020] [Accepted: 06/21/2021] [Indexed: 11/15/2022] Open
Abstract
Symmetry establishment is a critical process in the development of multicellular organs and requires careful coordination of polarity axes while cells actively divide within tissues. Formation of the apical style in the Arabidopsis gynoecium involves a bilateral-to-radial symmetry transition, a stepwise process underpinned by the dynamic distribution of the plant morphogen auxin. Here we show that SPATULA (SPT) and the HECATE (HEC) bHLH proteins mediate the final step in the style radialisation process and synergistically control the expression of adaxial-identity genes, HOMEOBOX ARABIDOPSIS THALIANA 3 (HAT3) and ARABIDOPSIS THALIANA HOMEOBOX 4 (ATHB4). HAT3/ATHB4 module drives radialisation of the apical style by promoting basal-to-apical auxin flow and via a negative feedback mechanism that finetune auxin distribution through repression of SPT expression and cytokinin sensitivity. Thus, this work reveals the molecular basis of axes-coordination and hormonal cross-talk during the sequential steps of symmetry transition in the Arabidopsis style. The apical style in Arabidopsis is formed following a bilateral-to-radial symmetry transition in the gynoecium. Here the authors show that the final step in style radialization is coordinated by the adaxial regulators HAT3 and ATHB4, which are induced by the SPT and HEC transcription factors.
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15
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ATHB2 is a negative regulator of germination in Arabidopsis thaliana seeds. Sci Rep 2021; 11:9688. [PMID: 33958633 PMCID: PMC8102570 DOI: 10.1038/s41598-021-88874-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2021] [Accepted: 04/12/2021] [Indexed: 02/03/2023] Open
Abstract
The germination timing of seeds is of the utmost adaptive importance for plant populations. Light is one of the best characterized factors promoting seed germination in several species. The germination is also finely regulated by changes in hormones levels, mainly those of gibberellin (GA) and abscisic acid (ABA). Here, we performed physiological, pharmacological, and molecular analyses to uncover the role of ATHB2, an HD-ZIP II transcription factor, in germination of Arabidopsis seeds. Our study demonstrated that ATHB2 is a negative regulator and sustains the expression of transcription factors to block germination promoted by light. Besides, we found that ATHB2 increases ABA sensitivity. Moreover, ABA and auxin content in athb2-2 mutant is higher than wild-type in dry seeds, but the differences disappeared during the imbibition in darkness and the first hours of exposition to light, respectively. Some ABA and light transcription factors are up-regulated by ATHB2, such as ABI5, ABI3, XERICO, SOMNUS and PIL5/PIF1. In opposition, PIN7, an auxin transport, is down-regulated. The role of ATHB2 as a repressor of germination induced by light affecting the gemination timing, could have differential effects on the establishment of seedlings altering the competitiveness between crops and weeds in the field.
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16
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Tian R, Paul P, Joshi S, Perry SE. Genetic activity during early plant embryogenesis. Biochem J 2020; 477:3743-3767. [PMID: 33045058 PMCID: PMC7557148 DOI: 10.1042/bcj20190161] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2020] [Revised: 09/19/2020] [Accepted: 09/21/2020] [Indexed: 12/13/2022]
Abstract
Seeds are essential for human civilization, so understanding the molecular events underpinning seed development and the zygotic embryo it contains is important. In addition, the approach of somatic embryogenesis is a critical propagation and regeneration strategy to increase desirable genotypes, to develop new genetically modified plants to meet agricultural challenges, and at a basic science level, to test gene function. We briefly review some of the transcription factors (TFs) involved in establishing primary and apical meristems during zygotic embryogenesis, as well as TFs necessary and/or sufficient to drive somatic embryo programs. We focus on the model plant Arabidopsis for which many tools are available, and review as well as speculate about comparisons and contrasts between zygotic and somatic embryo processes.
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Affiliation(s)
- Ran Tian
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Priyanka Paul
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sanjay Joshi
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
| | - Sharyn E. Perry
- Department of Plant and Soil Sciences, University of Kentucky, Lexington, KY 40546-0312, U.S.A
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17
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Andres-Robin A, Reymond MC, Brunoud G, Martin-Magniette ML, Monéger F, Scutt CP. Immediate targets of ETTIN suggest a key role for pectin methylesterase inhibitors in the control of Arabidopsis gynecium development. PLANT SIGNALING & BEHAVIOR 2020; 15:1771937. [PMID: 32498600 PMCID: PMC8570713 DOI: 10.1080/15592324.2020.1771937] [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] [Indexed: 05/02/2023]
Abstract
The control of gynecium development in Arabidopsis thaliana by the auxin response factor ETTIN (ETT) correlates with a reduction in the methylesterification of cell-wall pectins and a decrease in cell-wall stiffness in the valve tissues of the ovary. Here, we determine the list of genes rapidly regulated following the in-vivo activation of an ETT fusion protein, and show these to be significantly enriched in genes encoding cell-wall proteins, including several pectin methylesterases (PMEs) and pectin methylesterase inhibitors (PMEIs). We also perform a genome-wide scan for potential ETT-binding sites, and incorporate the results of this procedure into a comparison of datasets, derived using four distinct methods, to identify genes regulated directly or indirectly by ETT. We conclude from our combined analyses that PMEIs are likely to be key actors that mediate the regulation of gynecium development by ETT, while ETT may simultaneously regulate PMEs to prevent exaggerated developmental effects from the regulation of PMEIs. We also postulate the existence of one or more rapidly-acting intermediate factors in the transcriptional regulation of PMEs and PMEIs by ETT.
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Affiliation(s)
- Amélie Andres-Robin
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Mathieu C. Reymond
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Géraldine Brunoud
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon, France
| | - Marie-Laure Martin-Magniette
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris-Saclay, CNRS, INRAE, University of Evry, Orsay, France
- Institute of Plant Sciences Paris-Saclay (IPS2), Université de Paris, CNRS, INRAE, Orsay, France
- UMR MIA-Paris, AgroParisTech, INRAE, Université Paris-Saclay, Paris, France
| | - Françoise Monéger
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon, France
- CONTACT Françoise Monéger Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, 46 Allée d’Italie, Lyon69364, France
| | - Charles P. Scutt
- Laboratoire de Reproduction et Développement des Plantes, Université de Lyon, ENS de Lyon, UCBL, INRAE, CNRS, Lyon, France
- Charles P. Scutt
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18
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The HD-ZIP II Transcription Factors Regulate Plant Architecture through the Auxin Pathway. Int J Mol Sci 2020; 21:ijms21093250. [PMID: 32375344 PMCID: PMC7246542 DOI: 10.3390/ijms21093250] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 04/29/2020] [Accepted: 05/02/2020] [Indexed: 11/17/2022] Open
Abstract
The homeodomain-leucine zipper (HD-ZIP) family transcription factors play important roles in plant growth and development. However, the underlying mechanisms remain largely unclear. Here we found that ATHB2, encoding a HD-ZIP transcription factor, is an early auxin responsive gene. Phenotypic analyses show that overexpression of ATHB2 impairs plant architecture, including reduced plant height and small leaves, and also reduces auxin response in leaves when grown in soil. Simultaneously, the seedlings with chemical induction of ATHB2 exhibit abnormal root gravitropism, a typical auxin-related phenotype. We further show that the auxin response pattern is altered in roots of the inducible ATHB2 seedlings. Consistently, the transcript levels of some auxin biosynthetic and transport genes are significantly decreased in these transgenic seedlings. Further, protein and promoter sequence analyses in common wheat showed that the HD-ZIP II subfamily transcription factors have highly conserved motifs and most of these encoding gene promoters contain the canonical auxin-responsive elements. Expression analyses confirm that some of these HD-ZIP II genes are indeed regulated by auxin in wheat. Together, our results suggest that the HD-ZIP II subfamily transcription factors regulate plant development possibly through the auxin pathway in plants.
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19
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Goretti D, Silvestre M, Collani S, Langenecker T, Méndez C, Madueño F, Schmid M. TERMINAL FLOWER1 Functions as a Mobile Transcriptional Cofactor in the Shoot Apical Meristem. PLANT PHYSIOLOGY 2020; 182:2081-2095. [PMID: 31996406 PMCID: PMC7140938 DOI: 10.1104/pp.19.00867] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/12/2019] [Accepted: 01/17/2020] [Indexed: 05/26/2023]
Abstract
The floral transition is a critical step in the life cycle of flowering plants, and several mechanisms control this finely orchestrated process. TERMINAL FLOWER1 (TFL1) is a floral repressor and close relative of the florigen, FLOWERING LOCUS T (FT). During the floral transition, TFL1 expression is up-regulated in the inflorescence apex to maintain the indeterminate growth of the shoot apical meristem (SAM). Both TFL1 and FT are mobile proteins, but they move in different ways. FT moves from the leaves to the SAM, while TFL1 appears to move within the SAM. The importance of TFL1 movement for its function in the regulation of flowering time and shoot indeterminacy and its molecular function are still largely unclear. Our results using Arabidopsis (Arabidopsis thaliana) indicate that TFL1 moves from its place of expression in the center of the SAM to the meristem layer L1 and that the movement in the SAM is required for the regulation of the floral transition. Chromatin immunoprecipitation sequencing and RNA sequencing demonstrated that TFL1 functions as a cotranscription factor that associates with and regulates the expression of hundreds of genes. These newly identified direct TFL1 targets provide the possibility to discover new roles for TFL1 in the regulation of floral transition and inflorescence development.
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Affiliation(s)
- Daniela Goretti
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
| | - Marina Silvestre
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), 46022 Valencia, Spain
| | - Silvio Collani
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
| | - Tobias Langenecker
- Max Planck Institute for Developmental Biology, Department of Molecular Biology, 72076 Tuebingen, Germany
| | - Carla Méndez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), 46022 Valencia, Spain
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia (CSIC-UPV), 46022 Valencia, Spain
| | - Markus Schmid
- Umeå Plant Science Centre, Department of Plant Physiology, Umeå University, SE-901 87 Umea, Sweden
- Beijing Advanced Innovation Centre for Tree Breeding by Molecular Design, Beijing Forestry University, Beijing 100083, People's Republic of China
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20
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Li S, Chen N, Li F, Mei F, Wang Z, Cheng X, Kang Z, Mao H. Characterization of wheat homeodomain-leucine zipper family genes and functional analysis of TaHDZ5-6A in drought tolerance in transgenic Arabidopsis. BMC PLANT BIOLOGY 2020; 20:50. [PMID: 32005165 PMCID: PMC6993422 DOI: 10.1186/s12870-020-2252-6] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Accepted: 01/14/2020] [Indexed: 05/20/2023]
Abstract
BACKGROUND Many studies in Arabidopsis and rice have demonstrated that HD-Zip transcription factors play important roles in plant development and responses to abiotic stresses. Although common wheat (Triticum aestivum L.) is one of the most widely cultivated and consumed food crops in the world, the function of the HD-Zip proteins in wheat is still largely unknown. RESULTS To explore the potential biological functions of HD-Zip genes in wheat, we performed a bioinformatics and gene expression analysis of the HD-Zip family. We identified 113 HD-Zip members from wheat and classified them into four subfamilies (I-IV) based on phylogenic analysis against proteins from Arabidopsis, rice, and maize. Most HD-Zip genes are represented by two to three homeoalleles in wheat, which are named as TaHDZX_ZA, TaHDZX_ZB, or TaHDZX_ZD, where X denotes the gene number and Z the wheat chromosome on which it is located. TaHDZs in the same subfamily have similar protein motifs and intron/exon structures. The expression profiles of TaHDZ genes were analysed in different tissues, at different stages of vegetative growth, during seed development, and under drought stress. We found that most TaHDZ genes, especially those in subfamilies I and II, were induced by drought stress, suggesting the potential importance of subfamily I and II TaHDZ members in the responses to abiotic stress. Compared with wild-type (WT) plants, transgenic Arabidopsis plants overexpressing TaHDZ5-6A displayed enhanced drought tolerance, lower water loss rates, higher survival rates, and higher proline content under drought conditions. Additionally, the transcriptome analysis identified a number of differentially expressed genes between 35S::TaHDZ5-6A transgenic and wild-type plants, many of which are involved in stress response. CONCLUSIONS Our results will facilitate further functional analysis of wheat HD-Zip genes, and also indicate that TaHDZ5-6A may participate in regulating the plant response to drought stress. Our experiments show that TaHDZ5-6A holds great potential for genetic improvement of abiotic stress tolerance in crops.
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Affiliation(s)
- Shumin Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Nan Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangfang Li
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Fangming Mei
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhongxue Wang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Xinxiu Cheng
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
| | - Hude Mao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, 712100, Shaanxi, China.
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21
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Chen W, Cheng Z, Liu L, Wang M, You X, Wang J, Zhang F, Zhou C, Zhang Z, Zhang H, You S, Wang Y, Luo S, Zhang J, Wang J, Wang J, Zhao Z, Guo X, Lei C, Zhang X, Lin Q, Ren Y, Zhu S, Wan J. Small Grain and Dwarf 2, encoding an HD-Zip II family transcription factor, regulates plant development by modulating gibberellin biosynthesis in rice. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2019; 288:110208. [PMID: 31521223 DOI: 10.1016/j.plantsci.2019.110208] [Citation(s) in RCA: 29] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2019] [Revised: 07/26/2019] [Accepted: 07/29/2019] [Indexed: 05/23/2023]
Abstract
Homeodomain leucine zipper (HD-Zip) proteins are transcription factors that regulate plant development. Bioactive gibberellin (GA) is a key endogenous hormone that participates in plant growth. However, the relationship between HD-Zip genes and modulation of GA biosynthesis in rice remains elusive. Here, we identified a rice mutant, designated as small grain and dwarf 2 (sgd2), which had reduced height and grain size compared with the wild type. Cytological observations indicated that the defective phenotype was mainly due to decreased cell length. Map-based cloning and complementation tests demonstrated that a 9 bp deletion in a homeodomain leucine zipper (HD-Zip) II family transcription factor was responsible for the sgd2 mutant phenotype. Expression of SGD2 was pronounced in developing panicles, and its protein was localized in nucleus. Luciferase reporter system and transactivation assays in yeast suggested that SGD2 functioned as a transcriptional repressor. High performance liquid chromatography assays showed that the endogenous GA1 level in the sgd2 mutant was dramatically decreased, and exogenous GA3 recovered the second leaf sheath to normal length. Results of qRT-PCR showed that the expression levels of genes positively regulating GA-biosynthesis were mostly down-regulated in the mutant. Our data identified the role of an HD-Zip transcription factor that affects rice plant development by modulating gibberellin biosynthesis.
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Affiliation(s)
- Weiwei Chen
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhijun Cheng
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Linglong Liu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Min Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xiaoman You
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Jian Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Feng Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Chunlei Zhou
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Zhe Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Huan Zhang
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Shimin You
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China
| | - Yupeng Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Sheng Luo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jinhui Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jiulin Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Jie Wang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Zhichao Zhao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xiuping Guo
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Cailin Lei
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Xin Zhang
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Qibing Lin
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Yulong Ren
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China
| | - Shanshan Zhu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China.
| | - Jianmin Wan
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, PR China; State Key Laboratory of Crop Genetics and Germplasm Enhancement, Jiangsu Plant Gene Engineering Research Center, Nanjing Agricultural University, Nanjing, 210095, PR China.
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22
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Millar AJ, Urquiza U, Freeman PL, Hume A, Plotkin GD, Sorokina O, Zardilis A, Zielinski T. Practical steps to digital organism models, from laboratory model species to 'Crops in silico. JOURNAL OF EXPERIMENTAL BOTANY 2019; 70:2403-2418. [PMID: 30615184 DOI: 10.1093/jxb/ery435] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2018] [Accepted: 11/28/2018] [Indexed: 05/20/2023]
Abstract
A recent initiative named 'Crops in silico' proposes that multi-scale models 'have the potential to fill in missing mechanistic details and generate new hypotheses to prioritize directed engineering efforts' in plant science, particularly directed to crop species. To that end, the group called for 'a paradigm shift in plant modelling, from largely isolated efforts to a connected community'. 'Wet' (experimental) research has been especially productive in plant science, since the adoption of Arabidopsis thaliana as a laboratory model species allowed the emergence of an Arabidopsis research community. Parts of this community invested in 'dry' (theoretical) research, under the rubric of Systems Biology. Our past research combined concepts from Systems Biology and crop modelling. Here we outline the approaches that seem most relevant to connected, 'digital organism' initiatives. We illustrate the scale of experimental research required, by collecting the kinetic parameter values that are required for a quantitative, dynamic model of a gene regulatory network. By comparison with the Systems Biology Markup Language (SBML) community, we note computational resources and community structures that will help to realize the potential for plant Systems Biology to connect with a broader crop science community.
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Affiliation(s)
- Andrew J Millar
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Uriel Urquiza
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | | | - Alastair Hume
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
- EPCC, Bayes Centre, University of Edinburgh, Edinburgh, UK
| | - Gordon D Plotkin
- Laboratory for the Foundations of Computer Science, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Oxana Sorokina
- Institute for Adaptive and Neural Computation, School of Informatics, University of Edinburgh, Edinburgh, UK
| | - Argyris Zardilis
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
| | - Tomasz Zielinski
- SynthSys and School of Biological Sciences, University of Edinburgh, Edinburgh, UK
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23
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Damerval C, Citerne H, Conde e Silva N, Deveaux Y, Delannoy E, Joets J, Simonnet F, Staedler Y, Schönenberger J, Yansouni J, Le Guilloux M, Sauquet H, Nadot S. Unraveling the Developmental and Genetic Mechanisms Underpinning Floral Architecture in Proteaceae. FRONTIERS IN PLANT SCIENCE 2019; 10:18. [PMID: 30740117 PMCID: PMC6357683 DOI: 10.3389/fpls.2019.00018] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2018] [Accepted: 01/08/2019] [Indexed: 05/30/2023]
Abstract
Proteaceae are a basal eudicot family with a highly conserved floral groundplan but which displays considerable variation in other aspects of floral and inflorescence morphology. Their morphological diversity and phylogenetic position make them good candidates for understanding the evolution of floral architecture, in particular the question of the homology of the undifferentiated perianth with the differentiated perianth of core eudicots, and the mechanisms underlying the repeated evolution of zygomorphy. In this paper, we combine a morphological approach to explore floral ontogenesis and a transcriptomic approach to access the genes involved in floral organ identity and development, focusing on Grevillea juniperina, a species from subfamily Grevilleoideae. We present developmental data for Grevillea juniperina and three additional species that differ in their floral symmetry using stereomicroscopy, SEM and High Resolution X-Ray Computed Tomography. We find that the adnation of stamens to tepals takes place at early developmental stages, and that the establishment of bilateral symmetry coincides with the asymmetrical growth of the single carpel. To set a framework for understanding the genetic basis of floral development in Proteaceae, we generated and annotated de novo a reference leaf/flower transcriptome from Grevillea juniperina. We found Grevillea homologs of all lineages of MADS-box genes involved in floral organ identity. Using Arabidopsis thaliana gene expression data as a reference, we found homologs of other genes involved in floral development in the transcriptome of G. juniperina. We also found at least 21 class I and class II TCP genes, a gene family involved in the regulation of growth processes, including floral symmetry. The expression patterns of a set of floral genes obtained from the transcriptome were characterized during floral development to assess their organ specificity and asymmetry of expression.
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Affiliation(s)
- Catherine Damerval
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hélène Citerne
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Natalia Conde e Silva
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Yves Deveaux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Etienne Delannoy
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Johann Joets
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Franck Simonnet
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
| | - Yannick Staedler
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jürg Schönenberger
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - Jennifer Yansouni
- Institute of Plant Sciences Paris-Saclay, CNRS, INRA, Universités Paris Diderot, Paris-Sud, Evry, Paris-Saclay, Gif-sur-Yvette, France
| | - Martine Le Guilloux
- GQE-Le Moulon, INRA, Univ. Paris-Sud, CNRS, AgroParisTech, Université Paris-Saclay, Gif-sur-Yvette, France
| | - Hervé Sauquet
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
- National Herbarium of New South Wales (NSW), Royal Botanic Gardens and Domain Trust, Sydney, NSW, Australia
| | - Sophie Nadot
- Ecologie Systématique Evolution, AgroParisTech, CNRS, Univ. Paris-Sud, Université Paris-Saclay, Orsay, France
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24
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Sessa G, Carabelli M, Possenti M, Morelli G, Ruberti I. Multiple Links between HD-Zip Proteins and Hormone Networks. Int J Mol Sci 2018; 19:ijms19124047. [PMID: 30558150 PMCID: PMC6320839 DOI: 10.3390/ijms19124047] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/31/2018] [Revised: 12/06/2018] [Accepted: 12/12/2018] [Indexed: 01/01/2023] Open
Abstract
HD-Zip proteins are unique to plants, and contain a homeodomain closely linked to a leucine zipper motif, which are involved in dimerization and DNA binding. Based on homology in the HD-Zip domain, gene structure and the presence of additional motifs, HD-Zips are divided into four families, HD-Zip I–IV. Phylogenetic analysis of HD-Zip genes using transcriptomic and genomic datasets from a wide range of plant species indicate that the HD-Zip protein class was already present in green algae. Later, HD-Zips experienced multiple duplication events that promoted neo- and sub-functionalizations. HD-Zip proteins are known to control key developmental and environmental responses, and a growing body of evidence indicates a strict link between members of the HD-Zip II and III families and the auxin machineries. Interactions of HD-Zip proteins with other hormones such as brassinolide and cytokinin have also been described. More recent data indicate that members of different HD-Zip families are directly involved in the regulation of abscisic acid (ABA) homeostasis and signaling. Considering the fundamental role of specific HD-Zip proteins in the control of key developmental pathways and in the cross-talk between auxin and cytokinin, a relevant role of these factors in adjusting plant growth and development to changing environment is emerging.
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Affiliation(s)
- Giovanna Sessa
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Monica Carabelli
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
| | - Marco Possenti
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Giorgio Morelli
- Research Centre for Genomics and Bioinformatics, Council for Agricultural Research and Economics (CREA), Via Ardeatina 546, 00178 Rome, Italy.
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, P.le A. Moro 5, 00185 Rome, Italy.
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25
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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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26
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MOTHER-OF-FT-AND-TFL1 represses seed germination under far-red light by modulating phytohormone responses in Arabidopsis thaliana. Proc Natl Acad Sci U S A 2018; 115:8442-8447. [PMID: 30061395 PMCID: PMC6099910 DOI: 10.1073/pnas.1806460115] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Seed germination in many plant species is triggered by sunlight, which is rich in the red (R) wavelength and repressed by under-the-canopy light rich in far red (FR). R:FR ratios are sensed by phytochromes to regulate levels of gibberellins (GAs) and abscisic acid (ABA), which induce and inhibit germination respectively. In this study we have discovered that, under FR light conditions, germination is repressed by MOTHER-OF-FT-AND-TFL1 (MFT) through the regulation of the ABA and GA signaling pathways. We also show that MFT gene expression is tightly regulated by light quality. Previous work has shown that under FR light conditions the transcription factor PHYOCHROME-INTERACTING-FACTOR1 (PIF1) accumulates and promotes expression of SOMNUS (SOM) that, in turn, leads to increased ABA and decreased GA levels. PIF1 also promotes expression of genes encoding ABA-INSENSITIVE5 (ABI5) and DELLA growth-repressor proteins, which act in the ABA and GA signaling pathways, respectively. Here we show that MFT gene expression is promoted by FR light through the PIF1/SOM/ABI5/DELLA pathway and is repressed by R light via the transcription factor SPATULA (SPT). Consistent with this, we also show that SPT gene expression is repressed under FR light in a PIF1-dependent manner. Furthermore, transcriptomic analyses presented in this study indicate that MFT exerts its function by promoting expression of known ABA-induced genes and repressing cell wall expansion-related genes.
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27
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Gaillochet C, Jamge S, van der Wal F, Angenent G, Immink R, Lohmann JU. A molecular network for functional versatility of HECATE transcription factors. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2018; 95:57-70. [PMID: 29667268 DOI: 10.1111/tpj.13930] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/26/2018] [Revised: 03/15/2018] [Accepted: 03/27/2018] [Indexed: 05/16/2023]
Abstract
During the plant life cycle, diverse signaling inputs are continuously integrated and engage specific genetic programs depending on the cellular or developmental context. Consistent with an important role in this process, HECATE (HEC) basic helix-loop-helix transcription factors display diverse functions, from photomorphogenesis to the control of shoot meristem dynamics and gynoecium patterning. However, the molecular mechanisms underlying their functional versatility and the deployment of specific HEC subprograms remain elusive. To address this issue, we systematically identified proteins with the capacity to interact with HEC1, the best-characterized member of the family, and integrated this information with our data set of direct HEC1 target genes. The resulting core genetic modules were consistent with specific developmental functions of HEC1, including its described activities in light signaling, gynoecium development and auxin homeostasis. Importantly, we found that HEC genes also play a role in the modulation of flowering time, and uncovered that their role in gynoecium development may involve the direct transcriptional regulation of NGATHA1 (NGA1) and NGA2 genes. NGA factors were previously shown to contribute to fruit development, but our data now show that they also modulate stem cell homeostasis in the shoot apical meristem. Taken together, our results delineate a molecular network underlying the functional versatility of HEC transcription factors. Our analyses have not only allowed us to identify relevant target genes controlling shoot stem cell activity and a so far undescribed biological function of HEC1, but also provide a rich resource for the mechanistic elucidation of further context-dependent HEC activities.
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Affiliation(s)
- Christophe Gaillochet
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, D-69120, Germany
| | - Suraj Jamge
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Froukje van der Wal
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Gerco Angenent
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Richard Immink
- Wageningen Plant Research, Wageningen University, PO Box 16, Wageningen, 6700AA, The Netherlands
| | - Jan U Lohmann
- Department of Stem Cell Biology, Centre for Organismal Studies, Heidelberg University, Im Neuenheimer Feld 230, Heidelberg, D-69120, Germany
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28
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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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29
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Li Z, Zhang C, Guo Y, Niu W, Wang Y, Xu Y. Evolution and expression analysis reveal the potential role of the HD-Zip gene family in regulation of embryo abortion in grapes (Vitis vinifera L.). BMC Genomics 2017; 18:744. [PMID: 28934927 PMCID: PMC5609062 DOI: 10.1186/s12864-017-4110-y] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2017] [Accepted: 09/01/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The HD-Zip family has a diversity of functions during plant development. In this study, we identify 33 HD-Zip transcription factors in grape and detect their expressions in ovules and somatic embryos, as well as in various vegetative organs. RESULTS A genome-wide survey for HD-Zip transcription factors in Vitis was conducted based on the 12 X grape genome (V. vinifera L.). A total of 33 members were identified and classified into four subfamilies (I-IV) based on phylogeny analysis with Arabidopsis, rice and maize. VvHDZs in the same subfamily have similar protein motifs and intron/exon structures. An evaluation of duplication events suggests several HD-Zip genes arose before the divergence of the grape and Arabidopsis lineages. The 33 members of HD-Zip were differentially expressed in ovules of the stenospermic grape, Thompson Seedless and of the seeded grape, Pinot noir. Most have higher expressions during ovule abortion in Thompson Seedless. In addition, transcripts of the HD-Zip family were also detected in somatic embryogenesis of Thompson Seedless and in different vegetative organs of Thompson Seedless at varying levels. Additionally, VvHDZ28 is located in the nucleus and had transcriptional activity consistent with the typical features of the HD-Zip family. Our results provide a foundation for future grape HD-Zip gene function research. CONCLUSIONS The identification and expression profiles of the HD-Zip transcription factors in grape, reveal their diverse roles during ovule abortion and organ development. Our results lay a foundation for functional analysis of grape HDZ genes.
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Affiliation(s)
- Zhiqian Li
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Chen Zhang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yurui Guo
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Weili Niu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yuejin Wang
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
| | - Yan Xu
- College of Horticulture, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- State Key Laboratory of Crop Stress Biology in Arid Areas, Northwest A&F University, Yangling, Shaanxi People’s Republic of China
- Key Laboratory of Horticultural Plant Biology and Germplasm Innovation in Northwest China, Ministry of Agriculture, Yangling, Shaanxi People’s Republic of China
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30
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Moubayidin L, Østergaard L. Gynoecium formation: an intimate and complicated relationship. Curr Opin Genet Dev 2017; 45:15-21. [DOI: 10.1016/j.gde.2017.02.005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2016] [Revised: 02/07/2017] [Accepted: 02/09/2017] [Indexed: 02/02/2023]
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31
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Reyes-Olalde JI, Zúñiga-Mayo VM, Serwatowska J, Chavez Montes RA, Lozano-Sotomayor P, Herrera-Ubaldo H, Gonzalez-Aguilera KL, Ballester P, Ripoll JJ, Ezquer I, Paolo D, Heyl A, Colombo L, Yanofsky MF, Ferrandiz C, Marsch-Martínez N, de Folter S. The bHLH transcription factor SPATULA enables cytokinin signaling, and both activate auxin biosynthesis and transport genes at the medial domain of the gynoecium. PLoS Genet 2017; 13:e1006726. [PMID: 28388635 PMCID: PMC5400277 DOI: 10.1371/journal.pgen.1006726] [Citation(s) in RCA: 71] [Impact Index Per Article: 10.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2016] [Revised: 04/21/2017] [Accepted: 03/30/2017] [Indexed: 11/18/2022] Open
Abstract
Fruits and seeds are the major food source on earth. Both derive from the gynoecium and, therefore, it is crucial to understand the mechanisms that guide the development of this organ of angiosperm species. In Arabidopsis, the gynoecium is composed of two congenitally fused carpels, where two domains: medial and lateral, can be distinguished. The medial domain includes the carpel margin meristem (CMM) that is key for the production of the internal tissues involved in fertilization, such as septum, ovules, and transmitting tract. Interestingly, the medial domain shows a high cytokinin signaling output, in contrast to the lateral domain, where it is hardly detected. While it is known that cytokinin provides meristematic properties, understanding on the mechanisms that underlie the cytokinin signaling pattern in the young gynoecium is lacking. Moreover, in other tissues, the cytokinin pathway is often connected to the auxin pathway, but we also lack knowledge about these connections in the young gynoecium. Our results reveal that cytokinin signaling, that can provide meristematic properties required for CMM activity and growth, is enabled by the transcription factor SPATULA (SPT) in the medial domain. Meanwhile, cytokinin signaling is confined to the medial domain by the cytokinin response repressor ARABIDOPSIS HISTIDINE PHOSPHOTRANSFERASE 6 (AHP6), and perhaps by ARR16 (a type-A ARR) as well, both present in the lateral domains (presumptive valves) of the developing gynoecia. Moreover, SPT and cytokinin, probably together, promote the expression of the auxin biosynthetic gene TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS 1 (TAA1) and the gene encoding the auxin efflux transporter PIN-FORMED 3 (PIN3), likely creating auxin drainage important for gynoecium growth. This study provides novel insights in the spatiotemporal determination of the cytokinin signaling pattern and its connection to the auxin pathway in the young gynoecium.
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Affiliation(s)
- J. Irepan Reyes-Olalde
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Víctor M. Zúñiga-Mayo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Joanna Serwatowska
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Ricardo A. Chavez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Karla L. Gonzalez-Aguilera
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | - Juan José Ripoll
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Dario Paolo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Alexander Heyl
- Biology Department, Adelphi University, Garden City, New York, United States of America
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Martin F. Yanofsky
- Division of Biological Sciences, University of California San Diego, La Jolla, California, United States of America
| | - Cristina Ferrandiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, Valencia, Spain
| | | | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Guanajuato, México
- * E-mail:
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Zumajo-Cardona C, Ambrose BA, Pabón-Mora N. Evolution of the SPATULA/ALCATRAZ gene lineage and expression analyses in the basal eudicot, Bocconia frutescens L. (Papaveraceae). EvoDevo 2017; 8:5. [PMID: 28331573 PMCID: PMC5353969 DOI: 10.1186/s13227-017-0068-8] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2017] [Accepted: 03/08/2017] [Indexed: 12/19/2022] Open
Abstract
Background SPATULA (SPT) and ALCATRAZ (ALC) are recent paralogs that belong to the large bHLH transcription factor family. Orthologs of these genes have been found in all core eudicots, whereas pre-duplication genes, named paleoSPATULA/ALCATRAZ, have been found in basal eudicots, monocots, basal angiosperms and gymnosperms. Nevertheless, functional studies have only been performed in Arabidopsis thaliana, where SPT and ALC are partially redundant in carpel and valve margin development and ALC has a unique role in the dehiscence zone. Further analyses of pre-duplication genes are necessary to assess the functional evolution of this gene lineage. Results We isolated additional paleoSPT/ALC genes from Aristolochia fimbriata, Bocconia frutescens, Cattleya trianae and Hypoxis decumbens from our transcriptome libraries and performed phylogenetic analyses. We identified the previously described bHLH domain in all analyzed sequences and also new conserved motifs using the MEME suite. Finally, we analyzed the expression of three paleoSPT/ALC genes (BofrSPT1/2/3) from Bocconia frutescens, a basal eudicot in the Papaveraceae. To determine the developmental stages at which these genes were expressed, pre- and post-anthesis carpels and fruits of B. frutescens were collected, sectioned, stained, and examined using light microscopy. Using in situ hybridization we detected that BofrSPT1/2/3 genes are expressed in floral buds, early sepal initiation, stamens and carpel primordia and later during fruit development in the dehiscence zone of the opercular fruit. Conclusions Our expression results, in comparison with those available for core eudicots, suggest conserved roles of members of the SPT/ALC gene lineage across eudicots in the specification of carpel margins and the dehiscence zone of the mature fruits. Although there is some redundancy between ALC and SPT, these gene clades seem to have undergone some degree of sub-functionalization in the core eudicots, likely by changes in cis regulatory regions and to some extent in coding sequences, at least in Brassicaceae. Our results also indicate that in Bocconia frutescens, paleoSPT/ALC genes may play a role in early floral organ specification that was subsequently lost in core eudicot lineages. Electronic supplementary material The online version of this article (doi:10.1186/s13227-017-0068-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Cecilia Zumajo-Cardona
- Instituto de Biología, Universidad de Antioquia, Medellín, 1226, Colombia.,New York Botanical Garden, Bronx, NY 10458 USA.,City University of New York, New York, NY 10016 USA
| | | | - Natalia Pabón-Mora
- Instituto de Biología, Universidad de Antioquia, Medellín, 1226, Colombia
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Song A, Li P, Xin J, Chen S, Zhao K, Wu D, Fan Q, Gao T, Chen F, Guan Z. Transcriptome-Wide Survey and Expression Profile Analysis of Putative Chrysanthemum HD-Zip I and II Genes. Genes (Basel) 2016; 7:genes7050019. [PMID: 27196930 PMCID: PMC4880839 DOI: 10.3390/genes7050019] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2016] [Revised: 04/05/2016] [Accepted: 05/03/2016] [Indexed: 12/30/2022] Open
Abstract
The homeodomain-leucine zipper (HD-Zip) transcription factor family is a key transcription factor family and unique to the plant kingdom. It consists of a homeodomain and a leucine zipper that serve in combination as a dimerization motif. The family can be classified into four subfamilies, and these subfamilies participate in the development of hormones and mediation of hormone action and are involved in plant responses to environmental conditions. However, limited information on this gene family is available for the important chrysanthemum ornamental species (Chrysanthemum morifolium). Here, we characterized 17 chrysanthemum HD-Zip genes based on transcriptome sequences. Phylogenetic analyses revealed that 17 CmHB genes were distributed in the HD-Zip subfamilies I and II and identified two pairs of putative orthologous proteins in Arabidopsis and chrysanthemum and four pairs of paralogous proteins in chrysanthemum. The software MEME was used to identify 7 putative motifs with E values less than 1e-3 in the chrysanthemum HD-Zip factors, and they can be clearly classified into two groups based on the composition of the motifs. A bioinformatics analysis predicted that 8 CmHB genes could be targeted by 10 miRNA families, and the expression of these 17 genes in response to phytohormone treatments and abiotic stresses was characterized. The results presented here will promote research on the various functions of the HD-Zip gene family members in plant hormones and stress responses.
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Affiliation(s)
- Aiping Song
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Peiling Li
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Jingjing Xin
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Sumei Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Kunkun Zhao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dan Wu
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Qingqing Fan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Tianwei Gao
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Fadi Chen
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Zhiyong Guan
- College of Horticulture, Nanjing Agricultural University, Nanjing 210095, China.
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Vialette-Guiraud ACM, Andres-Robin A, Chambrier P, Tavares R, Scutt CP. The analysis of Gene Regulatory Networks in plant evo-devo. JOURNAL OF EXPERIMENTAL BOTANY 2016; 67:2549-63. [PMID: 27006484 DOI: 10.1093/jxb/erw119] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
We provide an overview of methods and workflows that can be used to investigate the topologies of Gene Regulatory Networks (GRNs) in the context of plant evolutionary-developmental (evo-devo) biology. Many of the species that occupy key positions in plant phylogeny are poorly adapted as laboratory models and so we focus here on techniques that can be efficiently applied to both model and non-model species of interest to plant evo-devo. We outline methods that can be used to describe gene expression patterns and also to elucidate the transcriptional, post-transcriptional, and epigenetic regulatory mechanisms underlying these patterns, in any plant species with a sequenced genome. We furthermore describe how the technique of Protein Resurrection can be used to confirm inferences on ancestral GRNs and also to provide otherwise-inaccessible points of reference in evolutionary histories by exploiting paralogues generated in gene and whole genome duplication events. Finally, we argue for the better integration of molecular data with information from paleobotanical, paleoecological, and paleogeographical studies to provide the fullest possible picture of the processes that have shaped the evolution of plant development.
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Affiliation(s)
- Aurélie C M Vialette-Guiraud
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Amélie Andres-Robin
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Pierre Chambrier
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Raquel Tavares
- Laboratoire de Biométrie et Biologie Évolutive (UMR 5558 - CNRS/université Lyon 1/université de Lyon), Bâtiment Gregor Mendel, 43 bd du 11 novembre 1918, 69622 Villeurbanne Cedex, France
| | - Charles P Scutt
- Laboratoire de Reproduction et Développement des Plantes (UMR 5667 - CNRS/INRA/ENS-Lyon/université Lyon 1/université de Lyon), Ecole Normale Supérieure de Lyon, 46 allée d'Italie, 69364 Lyon Cedex 07, France
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Ji X, Nie X, Liu Y, Zheng L, Zhao H, Zhang B, Huo L, Wang Y. A bHLH gene from Tamarix hispida improves abiotic stress tolerance by enhancing osmotic potential and decreasing reactive oxygen species accumulation. TREE PHYSIOLOGY 2016; 36:193-207. [PMID: 26786541 DOI: 10.1093/treephys/tpv139] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/23/2015] [Accepted: 12/03/2015] [Indexed: 05/20/2023]
Abstract
Basic helix-loop-helix (bHLH) leucine-zipper transcription factors play important roles in abiotic stress responses. However, their specific roles in abiotic stress tolerance are not fully known. Here, we functionally characterized a bHLH gene, ThbHLH1, from Tamarix hispida in abiotic stress tolerance. ThbHLH1 specifically binds to G-box motif with the sequence of 'CACGTG'. Transiently transfected T. hispida plantlets with transiently overexpressed ThbHLH1 and RNAi-silenced ThbHLH1 were generated for gain- and loss-of-function analysis. Transgenic Arabidopsis thaliana lines overexpressing ThbHLH1 were generated to confirm the gain- and loss-of-function analysis. Overexpression of ThbHLH1 significantly elevates glycine betaine and proline levels, increases Ca(2+) concentration and enhances peroxidase (POD) and superoxide dismutase (SOD) activities to decrease reactive oxygen species (ROS) accumulation. Additionally, ThbHLH1 regulates the expression of the genes including P5CS, BADH, CaM, POD and SOD, to activate the above physiological changes, and also induces the expression of stress tolerance-related genes LEAs and HSPs. These data suggest that ThbHLH1 induces the expression of stress tolerance-related genes to improve abiotic stress tolerance by increasing osmotic potential, improving ROS scavenging capability and enhancing second messenger in stress signaling cascades.
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Affiliation(s)
- Xiaoyu Ji
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011 Urumqi, Xinjiang, China
| | - Xianguang Nie
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040 Harbin, China
| | - Yujia Liu
- College of Food Engineering, Harbin University of Commerce, 1 Xuehai Street, 150028 Harbin, China
| | - Lei Zheng
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040 Harbin, China
| | - Huimin Zhao
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040 Harbin, China
| | - Bing Zhang
- State Key Laboratory of Tree Genetics and Breeding (Northeast Forestry University), 26 Hexing Road, 150040 Harbin, China
| | - Lin Huo
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011 Urumqi, Xinjiang, China
| | - Yucheng Wang
- Key Laboratory of Biogeography and Bioresource in Arid Land, Xinjiang Institute of Ecology and Geography, Chinese Academy of Sciences, 830011 Urumqi, Xinjiang, China
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Vialette-Guiraud ACM, Chauvet A, Gutierrez-Mazariegos J, Eschstruth A, Ratet P, Scutt CP. A Conserved Role for the NAM/miR164 Developmental Module Reveals a Common Mechanism Underlying Carpel Margin Fusion in Monocarpous and Syncarpous Eurosids. FRONTIERS IN PLANT SCIENCE 2016; 6:1239. [PMID: 26793217 PMCID: PMC4710747 DOI: 10.3389/fpls.2015.01239] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/03/2015] [Accepted: 12/20/2015] [Indexed: 05/05/2023]
Abstract
The majority of angiosperms are syncarpous- their gynoecium is composed of two or more fused carpels. In Arabidopsis thaliana, this fusion is regulated through the balance of expression between CUP SHAPED COTYLEDON (CUC) genes, which are orthologs of the Petunia hybrida transcription factor NO APICAL MERISTEM (NAM), and their post-transcriptional regulator miR164. Accordingly, the expression of a miR164-insensitive form of A. thaliana CUC2 causes a radical breakdown of carpel fusion. Here, we investigate the role of the NAM/miR164 genetic module in carpel closure in monocarpous plants. We show that the disruption of this module in monocarpous flowers of A. thaliana aux1-22 mutants causes a failure of carpel closure, similar to the failure of carpel fusion observed in the wild-type genetic background. This observation suggested that closely related mechanisms may bring about carpel closure and carpel fusion, at least in A. thaliana. We therefore tested whether these mechanisms were conserved in a eurosid species that is monocarpous in its wild-type form. We observed that expression of MtNAM, the NAM ortholog in the monocarpous eurosid Medicago truncatula, decreases during carpel margin fusion, suggesting a role for the NAM/miR164 module in this process. We transformed M. truncatula with a miR164-resistant form of MtNAM and observed, among other phenotypes, incomplete carpel closure in the resulting transformants. These data confirm the underlying mechanistic similarity between carpel closure and carpel fusion which we observed in A. thaliana. Our observations suggest that the role of the NAM/miR164 module in the fusion of carpel margins has been conserved at least since the most recent common ancestor of the eurosid clade, and open the possibility that a similar mechanism may have been responsible for carpel closure at much earlier stages of angiosperm evolution. We combine our results with studies of early diverging angiosperms to speculate on the role of the NAM/miR164 module in the origin and further evolution of the angiosperm carpel.
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Affiliation(s)
- Aurélie C. M. Vialette-Guiraud
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Lyon, Ecole Normale Supérieure de LyonLyon, France
| | - Aurélie Chauvet
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Lyon, Ecole Normale Supérieure de LyonLyon, France
| | - Juliana Gutierrez-Mazariegos
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Lyon, Ecole Normale Supérieure de LyonLyon, France
| | - Alexis Eschstruth
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Paris SudOrsay, France
| | - Pascal Ratet
- Institute of Plant Sciences Paris-Saclay, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Paris SudOrsay, France
| | - Charles P. Scutt
- Laboratoire de Reproduction et Développement des Plantes, UMR 5667, Centre National de la Recherche Scientifique – Institut National de la Recherche Agronomique – Université de Lyon, Ecole Normale Supérieure de LyonLyon, France
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Roig-Villanova I, Martínez-García JF. Plant Responses to Vegetation Proximity: A Whole Life Avoiding Shade. FRONTIERS IN PLANT SCIENCE 2016; 7:236. [PMID: 26973679 PMCID: PMC4770057 DOI: 10.3389/fpls.2016.00236] [Citation(s) in RCA: 68] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2015] [Accepted: 02/12/2016] [Indexed: 05/20/2023]
Abstract
In high density of vegetation, plants detect neighbors by perceiving changes in light quality through phytochrome photoreceptors. Close vegetation proximity might result in competition for resources, such as light. To face this challenge, plants have evolved two alternative strategies: to either tolerate or avoid shade. Shade-avoiding species generally adapt their development by inducing hypocotyl, stem, and petiole elongation, apical dominance and flowering, and decreasing leaf expansion and yield, a set of responses collectively known as the shade avoidance syndrome (SAS). The SAS responses have been mostly studied at the seedling stage, centered on the increase of hypocotyl elongation. After compiling the main findings about SAS responses in seedlings, this review is focused on the response to shade at adult stages of development, such as petioles of adult leaves, and the little information available on the SAS responses in reproductive tissues. We discuss these responses based on the knowledge about the molecular mechanisms and components with a role in regulating the SAS response of the hypocotyls of Arabidopsis thaliana. The transcriptional networks involved in this process, as well as the communication among the tissues that perceive the shade and the ones that respond to this stimulus will also be briefly commented.
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Affiliation(s)
- Irma Roig-Villanova
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas – Institut Recerca i Tecnologia Agroalimentaries – Universitat Autònoma de Barcelona – Universitat de BarcelonaBarcelona, Spain
- *Correspondence: Irma Roig-Villanova, ; Jaime F. Martínez-García,
| | - Jaime F. Martínez-García
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas – Institut Recerca i Tecnologia Agroalimentaries – Universitat Autònoma de Barcelona – Universitat de BarcelonaBarcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA)Barcelona, Spain
- *Correspondence: Irma Roig-Villanova, ; Jaime F. Martínez-García,
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Turchi L, Baima S, Morelli G, Ruberti I. Interplay of HD-Zip II and III transcription factors in auxin-regulated plant development. JOURNAL OF EXPERIMENTAL BOTANY 2015; 66:5043-53. [PMID: 25911742 DOI: 10.1093/jxb/erv174] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
The homeodomain-leucine zipper (HD-Zip) class of transcription factors is unique to plants. HD-Zip proteins bind to DNA exclusively as dimers recognizing dyad symmetric sequences and act as positive or negative regulators of gene expression. On the basis of sequence homology in the HD-Zip DNA-binding domain, HD-Zip proteins have been grouped into four families (HD-Zip I-IV). Each HD-Zip family can be further divided into subfamilies containing paralogous genes that have arisen through genome duplication. Remarkably, all the members of the HD-Zip IIγ and -δ clades are regulated by light quality changes that induce in the majority of the angiosperms the shade-avoidance response, a process regulated at multiple levels by auxin. Intriguingly, it has recently emerged that, apart from their function in shade avoidance, the HD-Zip IIγ and -δ transcription factors control several auxin-regulated developmental processes, including apical embryo patterning, lateral organ polarity, and gynoecium development, in a white-light environment. This review presents recent advances in our understanding of HD-Zip II protein function in plant development, with particular emphasis on the impact of loss-of-function HD-Zip II mutations on auxin distribution and response. The review also describes evidence demonstrating that HD-Zip IIγ and -δ genes are directly and positively regulated by HD-Zip III transcription factors, primary determinants of apical shoot development, known to control the expression of several auxin biosynthesis, transport, and response genes. Finally, the interplay between HD-Zip II and III transcription factors in embryo apical patterning and organ polarity is discussed.
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Affiliation(s)
- L Turchi
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
| | - S Baima
- Food and Nutrition Research Centre, Agricultural Research Council, Via Ardeatina 546, 00178 Rome, Italy
| | - G Morelli
- Food and Nutrition Research Centre, Agricultural Research Council, Via Ardeatina 546, 00178 Rome, Italy
| | - I Ruberti
- Institute of Molecular Biology and Pathology, National Research Council, Piazzale Aldo Moro 5, 00185 Rome, Italy
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Nozue K, Tat AV, Kumar Devisetty U, Robinson M, Mumbach MR, Ichihashi Y, Lekkala S, Maloof JN. Shade avoidance components and pathways in adult plants revealed by phenotypic profiling. PLoS Genet 2015; 11:e1004953. [PMID: 25874869 PMCID: PMC4398415 DOI: 10.1371/journal.pgen.1004953] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Accepted: 12/11/2014] [Indexed: 01/01/2023] Open
Abstract
Shade from neighboring plants limits light for photosynthesis; as a consequence, plants have a variety of strategies to avoid canopy shade and compete with their neighbors for light. Collectively the response to foliar shade is called the shade avoidance syndrome (SAS). The SAS includes elongation of a variety of organs, acceleration of flowering time, and additional physiological responses, which are seen throughout the plant life cycle. However, current mechanistic knowledge is mainly limited to shade-induced elongation of seedlings. Here we use phenotypic profiling of seedling, leaf, and flowering time traits to untangle complex SAS networks. We used over-representation analysis (ORA) of shade-responsive genes, combined with previous annotation, to logically select 59 known and candidate novel mutants for phenotyping. Our analysis reveals shared and separate pathways for each shade avoidance response. In particular, auxin pathway components were required for shade avoidance responses in hypocotyl, petiole, and flowering time, whereas jasmonic acid pathway components were only required for petiole and flowering time responses. Our phenotypic profiling allowed discovery of seventeen novel shade avoidance mutants. Our results demonstrate that logical selection of mutants increased success of phenotypic profiling to dissect complex traits and discover novel components.
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Affiliation(s)
- Kazunari Nozue
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - An V. Tat
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Upendra Kumar Devisetty
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Matthew Robinson
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Maxwell R. Mumbach
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Yasunori Ichihashi
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Saradadevi Lekkala
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
| | - Julin N. Maloof
- Department of Plant Biology, University of California, Davis, Davis, California, United States of America
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ten Hove CA, Lu KJ, Weijers D. Building a plant: cell fate specification in the early Arabidopsis embryo. Development 2015; 142:420-30. [DOI: 10.1242/dev.111500] [Citation(s) in RCA: 150] [Impact Index Per Article: 16.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Embryogenesis is the beginning of plant development, yet the cell fate decisions and patterning steps that occur during this time are reiterated during development to build the post-embryonic architecture. In Arabidopsis, embryogenesis follows a simple and predictable pattern, making it an ideal model with which to understand how cellular and tissue developmental processes are controlled. Here, we review the early stages of Arabidopsis embryogenesis, focusing on the globular stage, during which time stem cells are first specified and all major tissues obtain their identities. We discuss four different aspects of development: the formation of outer versus inner layers; the specification of vascular and ground tissues; the determination of shoot and root domains; and the establishment of the first stem cells.
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Affiliation(s)
- Colette A. ten Hove
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Kuan-Ju Lu
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
| | - Dolf Weijers
- Wageningen University, Laboratory of Biochemistry, Dreijenlaan 3, 6703 HA Wageningen, The Netherlands
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Liu W, Tai H, Li S, Gao W, Zhao M, Xie C, Li WX. bHLH122 is important for drought and osmotic stress resistance in Arabidopsis and in the repression of ABA catabolism. THE NEW PHYTOLOGIST 2014; 201:1192-1204. [PMID: 24261563 DOI: 10.1111/nph.12607] [Citation(s) in RCA: 162] [Impact Index Per Article: 16.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/08/2013] [Accepted: 10/15/2013] [Indexed: 05/17/2023]
Abstract
• Although proteins in the basic helix-loop-helix (bHLH) family are universal transcription factors in eukaryotes, the biological roles of most bHLH family members are not well understood in plants. • The Arabidopsis thaliana bHLH122 transcripts were strongly induced by drought, NaCl and osmotic stresses, but not by ABA treatment. Promoter::GUS analysis showed that bHLH122 was highly expressed in vascular tissues and guard cells. Compared with wild-type (WT) plants, transgenic plants overexpressing bHLH122 displayed greater resistance to drought, NaCl and osmotic stresses. In contrast, the bhlh122 loss-of-function mutant was more sensitive to NaCl and osmotic stresses than were WT plants. • Microarray analysis indicated that bHLH122 was important for the expression of a number of abiotic stress-responsive genes. In electrophoretic mobility shift assay and chromatin immunoprecipitation assays, bHLH122 could bind directly to the G-box/E-box cis-elements in the CYP707A3 promoter, and repress its expression. Further, up-regulation of bHLH122 substantially increased cellular ABA levels. • These results suggest that bHLH122 functions as a positive regulator of drought, NaCl and osmotic signaling.
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Affiliation(s)
- Wenwen Liu
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Huanhuan Tai
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Songsong Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wei Gao
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Meng Zhao
- Key Laboratory of Plant and Soil Interactions, College of Resources and Environmental Sciences, China Agricultural University, Beijing, 100193, China
| | - Chuanxiao Xie
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Wen-Xue Li
- National Key Facility for Crop Gene Resources and Genetic Improvement, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
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Leivar P, Monte E. PIFs: systems integrators in plant development. THE PLANT CELL 2014; 26:56-78. [PMID: 24481072 PMCID: PMC3963594 DOI: 10.1105/tpc.113.120857] [Citation(s) in RCA: 377] [Impact Index Per Article: 37.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2013] [Revised: 01/03/2014] [Accepted: 01/14/2014] [Indexed: 05/17/2023]
Abstract
Phytochrome-interacting factors (PIFs) are members of the Arabidopsis thaliana basic helix-loop-helix family of transcriptional regulators that interact specifically with the active Pfr conformer of phytochrome (phy) photoreceptors. PIFs are central regulators of photomorphogenic development that act to promote stem growth, and this activity is reversed upon interaction with phy in response to light. Recently, significant progress has been made in defining the transcriptional networks directly regulated by PIFs, as well as the convergence of other signaling pathways on the PIFs to modulate growth. Here, we summarize and highlight these findings in the context of PIFs acting as integrators of light and other signals. We discuss progress in our understanding of the transcriptional and posttranslational regulation of PIFs that illustrates the integration of light with hormonal pathways and the circadian clock, and we review seedling hypocotyl growth as a paradigm of PIFs acting at the interface of these signals. Based on these advances, PIFs are emerging as required factors for growth, acting as central components of a regulatory node that integrates multiple internal and external signals to optimize plant development.
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Pabón-Mora N, Wong GKS, Ambrose BA. Evolution of fruit development genes in flowering plants. FRONTIERS IN PLANT SCIENCE 2014; 5:300. [PMID: 25018763 PMCID: PMC4071287 DOI: 10.3389/fpls.2014.00300] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 06/07/2014] [Indexed: 05/18/2023]
Abstract
The genetic mechanisms regulating dry fruit development and opercular dehiscence have been identified in Arabidopsis thaliana. In the bicarpellate silique, valve elongation and differentiation is controlled by FRUITFULL (FUL) that antagonizes SHATTERPROOF1-2 (SHP1/SHP2) and INDEHISCENT (IND) at the dehiscence zone where they control normal lignification. SHP1/2 are also repressed by REPLUMLESS (RPL), responsible for replum formation. Similarly, FUL indirectly controls two other factors ALCATRAZ (ALC) and SPATULA (SPT) that function in the proper formation of the separation layer. FUL and SHP1/2 belong to the MADS-box family, IND and ALC belong to the bHLH family and RPL belongs to the homeodomain family, all of which are large transcription factor families. These families have undergone numerous duplications and losses in plants, likely accompanied by functional changes. Functional analyses of homologous genes suggest that this network is fairly conserved in Brassicaceae and less conserved in other core eudicots. Only the MADS box genes have been functionally characterized in basal eudicots and suggest partial conservation of the functions recorded for Brassicaceae. Here we do a comprehensive search of SHP, IND, ALC, SPT, and RPL homologs across core-eudicots, basal eudicots, monocots and basal angiosperms. Based on gene-tree analyses we hypothesize what parts of the network for fruit development in Brassicaceae, in particular regarding direct and indirect targets of FUL, might be conserved across angiosperms.
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Affiliation(s)
- Natalia Pabón-Mora
- Instituto de Biología, Universidad de AntioquiaMedellín, Colombia
- The New York Botanical GardenBronx, NY, USA
- *Correspondence: Natalia Pabón-Mora, Instituto de Biología, Universidad de Antioquia, Calle 70 No 52-21, AA 1226 Medellín, Colombia e-mail:
| | - Gane Ka-Shu Wong
- Department of Biological Sciences, University of AlbertaEdmonton, AB, Canada
- Department of Medicine, University of AlbertaEdmonton, AB, Canada
- BGI-Shenzhen, Beishan Industrial ZoneShenzhen, China
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Reyes-Olalde JI, Zuñiga-Mayo VM, Chávez Montes RA, Marsch-Martínez N, de Folter S. Inside the gynoecium: at the carpel margin. TRENDS IN PLANT SCIENCE 2013; 18:644-55. [PMID: 24008116 DOI: 10.1016/j.tplants.2013.08.002] [Citation(s) in RCA: 78] [Impact Index Per Article: 7.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/06/2013] [Revised: 07/09/2013] [Accepted: 08/07/2013] [Indexed: 05/05/2023]
Abstract
The gynoecium, which is produced at the center of most flowers, is the female reproductive organ and consists of one or more carpels. The Arabidopsis gynoecium consists of two fused carpels. Its inner tissues possess meristematic characteristics and are called the carpel margin meristem (CMM), because they are located at the margins of the carpels and generate the 'marginal' tissues of the gynoecium (placenta, ovules, septum, transmitting tract, style, and stigma). A key question is which factors are guiding the correct development of all these tissues, many of which are essential for reproduction. Besides regulatory genes, hormones play an important part in the development of the marginal tissues, and recent reports have highlighted the role of cytokinins, as discussed in this review.
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Affiliation(s)
- J Irepan Reyes-Olalde
- Laboratorio Nacional de Genómica para la Biodiversidad (Langebio), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, CP 36821 Irapuato, Gto., México
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Stewart Lilley JL, Gan Y, Graham IA, Nemhauser JL. The effects of DELLAs on growth change with developmental stage and brassinosteroid levels. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 76:165-73. [PMID: 23834248 DOI: 10.1111/tpj.12280] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/21/2013] [Revised: 06/26/2013] [Accepted: 07/02/2013] [Indexed: 05/03/2023]
Abstract
There are two stages in photomorphogenesis. First, seedlings detect light and open their cotyledons. Second, seedlings optimize their light environment by controlled elongation of the seedling stem or hypocotyl. In this study, we used time-lapse imaging to investigate the relationship between the brassinosteroid (BR) and gibberellin (GA) hormones across both stages of photomorphogenesis. During the transition between one stage and the other, growth promotion by BRs and GAs switched from an additive to a synergistic relationship. Molecular genetic analysis revealed unexpected roles for known participants in the GA pathway during this period. Members of the DELLA family could either repress or enhance BR growth responses, depending on developmental stage. At the transition point for seedling growth dynamics, the BR and GA pathways had opposite effects on DELLA protein levels. In contrast to GA-induced DELLA degradation, BR treatments increased the levels of REPRESSOR of ga1-3 (RGA) and mimicked the molecular effects of stabilizing DELLAs. In addition, DELLAs showed complex regulation of genes involved in BR biosynthesis, implicating them in BR homeostasis. Growth promotion by GA alone depended on the PHYTOCHROME INTERACTING FACTOR (PIF) family of master growth regulators. The effects of BR, including the synergistic effects with GA, were largely independent of PIFs. These results point to a multi-level, dynamic relationship between the BR and GA pathways.
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Cifuentes-Esquivel N, Bou-Torrent J, Galstyan A, Gallemí M, Sessa G, Salla Martret M, Roig-Villanova I, Ruberti I, Martínez-García JF. The bHLH proteins BEE and BIM positively modulate the shade avoidance syndrome in Arabidopsis seedlings. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 75:989-1002. [PMID: 23763263 DOI: 10.1111/tpj.12264] [Citation(s) in RCA: 46] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2012] [Revised: 05/29/2013] [Accepted: 06/03/2013] [Indexed: 05/25/2023]
Abstract
The shade avoidance syndrome (SAS) refers to a set of plant responses initiated after perception by the phytochromes of light with a reduced red to far-red ratio, indicative of vegetation proximity or shade. These responses, including elongation growth, anticipate eventual shading from potential competitor vegetation by overgrowing neighboring plants or flowering to ensure production of viable seeds for the next generation. In Arabidopsis thaliana seedlings, the SAS includes dramatic changes in gene expression, such as induction of PHYTOCHROME RAPIDLY REGULATED 1 (PAR1), encoding an atypical basic helix-loop-helix (bHLH) protein that acts as a transcriptional co-factor to repress hypocotyl elongation. Indeed, PAR1 has been proposed to act fundamentally as a dominant negative antagonist of conventional bHLH transcription factors by forming heterodimers with them to prevent their binding to DNA or other transcription factors. Here we report the identification of PAR1-interacting factors, including the brassinosteroid signaling components BR-ENHANCED EXPRESSION (BEE) and BES1-INTERACTING MYC-LIKE (BIM), and characterize their role as networked positive regulators of SAS hypocotyl responses. We provide genetic evidence that these bHLH transcriptional regulators not only control plant growth and development under shade and non-shade conditions, but are also redundant in the control of plant viability. Our results suggest that SAS responses are initiated as a consequence of a new balance of transcriptional regulators within the pre-existing bHLH network triggered by plant proximity, eventually causing hypocotyls to elongate.
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Affiliation(s)
- Nicolás Cifuentes-Esquivel
- Centre for Research in Agricultural Genomics (CRAG), Consejo Superior de Investigaciones Científicas (CSIC) - Institut de Recerca i Tecnologia Agroalimentàries (IRTA) - Universitat Autòmona de Barcelona (UAB) - Universitat de Barcelona (UB), Campus UAB Bellaterra, Barcelona 08193, Spain
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Carabelli M, Turchi L, Ruzza V, Morelli G, Ruberti I. Homeodomain-Leucine Zipper II family of transcription factors to the limelight: central regulators of plant development. PLANT SIGNALING & BEHAVIOR 2013; 8:25447. [PMID: 23838958 PMCID: PMC4002598 DOI: 10.4161/psb.25447] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/13/2013] [Accepted: 06/18/2013] [Indexed: 05/20/2023]
Abstract
The Arabidopsis genome encodes 10 Homeodomain-Leucine Zipper (HD-Zip) II transcription factors that can be subdivided into 4 clades (α-δ). All the γ (ARABIDOPSIS THALIANA HOMEOBOX 2 [ATHB2], HOMEOBOX ARABIDOPSIS THALIANA 1 [HAT1], HAT2) and δ (HAT3, ATHB4) genes are regulated by light quality changes (Low Red [R]/Far-Red [FR]) that induce the shade avoidance response in most of the angiosperms. HD-Zip IIγ and HD-Zip IIδ transcription factors function as positive regulators of shade avoidance, and there is evidence that at least ATHB2 is directly positively regulated by the basic Helix-Loop-Helix (bHLH) proteins PHYTOCHROME INTERACTING FACTOR 4 (PIF4) and PIF5. Recent evidence demonstrate that, in addition to their function in shade avoidance, HD-Zip IIγ and HD-Zip IIδ proteins play an essential role in plant development from embryogenesis onwards in a white light environment.
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Affiliation(s)
- Monica Carabelli
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Luana Turchi
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Valentino Ruzza
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
| | - Giorgio Morelli
- Food and Nutrition Research Centre; Agricultural Research Council (CRA); Rome, Italy
| | - Ida Ruberti
- Institute of Molecular Biology and Pathology; National Research Council; Rome, Italy
- Correspondence to: Ida Ruberti,
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Differential control of seed primary dormancy in Arabidopsis ecotypes by the transcription factor SPATULA. Proc Natl Acad Sci U S A 2013; 110:10866-71. [PMID: 23754415 DOI: 10.1073/pnas.1301647110] [Citation(s) in RCA: 80] [Impact Index Per Article: 7.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022] Open
Abstract
Freshly matured seeds exhibit primary dormancy, which prevents germination until environmental conditions are favorable. The establishment of dormancy occurs during seed development and involves both genetic and environmental factors that impact on the ratio of two antagonistic phytohormones: abscisic acid (ABA), which promotes dormancy, and gibberellic acid, which promotes germination. Although our understanding of dormancy breakage in mature seeds is well advanced, relatively little is known about the mechanisms involved in establishing dormancy during seed maturation. We previously showed that the SPATULA (SPT) transcription factor plays a key role in regulating seed germination. Here we investigate its role during seed development and find that, surprisingly, it has opposite roles in setting dormancy in Landsberg erecta and Columbia Arabidopsis ecotypes. We also find that SPT regulates expression of five transcription factor encoding genes: ABA-INSENSITIVE4 (ABI4) and ABI5, which mediate ABA signaling; REPRESSOR-OF-GA (RGA) and RGA-LIKE3 involved in gibberellic acid signaling; and MOTHER-OF-FT-AND-TFL1 (MFT) that we show here promotes Arabidopsis seed dormancy. Although ABI4, RGA, and MFT are repressed by SPT, ABI5 and RGL3 are induced. Furthermore, we show that RGA, MFT, and ABI5 are direct targets of SPT in vivo. We present a model in which SPT drives two antagonistic "dormancy-repressing" and "dormancy-promoting" routes that operate simultaneously in freshly matured seeds. Each of these routes has different impacts and this in turn explains the opposite effect of SPT on seed dormancy of the two ecotypes analyzed here.
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Tran F, Penniket C, Patel RV, Provart NJ, Laroche A, Rowland O, Robert LS. Developmental transcriptional profiling reveals key insights into Triticeae reproductive development. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2013; 74:971-88. [PMID: 23581995 DOI: 10.1111/tpj.12206] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/03/2013] [Revised: 03/15/2013] [Accepted: 03/22/2013] [Indexed: 05/25/2023]
Abstract
Despite their importance, there remains a paucity of large-scale gene expression-based studies of reproductive development in species belonging to the Triticeae. As a first step to address this deficiency, a gene expression atlas of triticale reproductive development was generated using the 55K Affymetrix GeneChip(®) wheat genome array. The global transcriptional profiles of the anther/pollen, ovary and stigma were analyzed at concurrent developmental stages, and co-expressed as well as preferentially expressed genes were identified. Data analysis revealed both novel and conserved regulatory factors underlying Triticeae floral development and function. This comprehensive resource rests upon detailed gene annotations, and the expression profiles are readily accessible via a web browser.
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Affiliation(s)
- Frances Tran
- Agriculture and Agri-Food Canada, Eastern Cereal and Oilseed Research Centre, 960 Carling Avenue, Ottawa, ON K1A 0C6, Canada
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50
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Makkena S, Lamb RS. The bHLH transcription factor SPATULA is a key regulator of organ size in Arabidopsis thaliana. PLANT SIGNALING & BEHAVIOR 2013; 8:e24140. [PMID: 23470719 PMCID: PMC3897497 DOI: 10.4161/psb.24140] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/08/2023]
Abstract
Plant organ size and thus plant size is determined by both cell proliferation and cell expansion. The bHLH transcription factor SPATULA (SPT) was originally identified as a regulator of carpel patterning. It has subsequently been found to control growth of the organs of the shoot. It does this at least in part by controlling the size of meristematic regions of organs in parallel to gibberellic acid (GA). It also acts downstream of several environmental signals, influencing growth in response to light and temperature. We have recently demonstrated that SPT functions to repress the size of the root meristem and thus root growth and size. It appears to do this using a similar mechanism to its control of leaf size. Based on the recent work on SPT, we propose that it is a growth repressor that acts to limit the size of meristems in response to environmental signals, perhaps by regulating auxin transport.
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Affiliation(s)
- Srilakshmi Makkena
- Plant Cellular and Molecular Biology Graduate Program; Ohio State University; Columbus, OH USA
| | - Rebecca S. Lamb
- Plant Cellular and Molecular Biology Graduate Program; Ohio State University; Columbus, OH USA
- Department of Molecular Genetics; Ohio State University; Columbus, OH USA
- Correspondence to: Rebecca S. Lamb,
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