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Omelyanchuk NA, Lavrekha VV, Bogomolov AG, Dolgikh VA, Sidorenko AD, Zemlyanskaya EV. Computational Reconstruction of the Transcription Factor Regulatory Network Induced by Auxin in Arabidopsis thaliana L. PLANTS (BASEL, SWITZERLAND) 2024; 13:1905. [PMID: 39065433 PMCID: PMC11280061 DOI: 10.3390/plants13141905] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/01/2024] [Revised: 07/05/2024] [Accepted: 07/06/2024] [Indexed: 07/28/2024]
Abstract
In plant hormone signaling, transcription factor regulatory networks (TFRNs), which link the master transcription factors to the biological processes under their control, remain insufficiently characterized despite their crucial function. Here, we identify a TFRN involved in the response to the key plant hormone auxin and define its impact on auxin-driven biological processes. To reconstruct the TFRN, we developed a three-step procedure, which is based on the integrated analysis of differentially expressed gene lists and a representative collection of transcription factor binding profiles. Its implementation is available as a part of the CisCross web server. With the new method, we distinguished two transcription factor subnetworks. The first operates before auxin treatment and is switched off upon hormone application, the second is switched on by the hormone. Moreover, we characterized the functioning of the auxin-regulated TFRN in control of chlorophyll and lignin biosynthesis, abscisic acid signaling, and ribosome biogenesis.
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Affiliation(s)
- Nadya A. Omelyanchuk
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Viktoriya V. Lavrekha
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Anton G. Bogomolov
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
| | - Vladislav A. Dolgikh
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Aleksandra D. Sidorenko
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
| | - Elena V. Zemlyanskaya
- Department of Systems Biology, Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia; (N.A.O.); (V.V.L.); (A.G.B.); (V.A.D.); (A.D.S.)
- Department of Natural Sciences, Novosibirsk State University, 630090 Novosibirsk, Russia
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Zhuo M, Sakuraba Y, Yanagisawa S. Dof1.7 and NIGT1 transcription factors mediate multilayered transcriptional regulation for different expression patterns of NITRATE TRANSPORTER2 genes under nitrogen deficiency stress. THE NEW PHYTOLOGIST 2024; 242:2132-2147. [PMID: 38523242 DOI: 10.1111/nph.19695] [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: 10/31/2023] [Accepted: 03/01/2024] [Indexed: 03/26/2024]
Abstract
Elucidating the mechanisms regulating nitrogen (N) deficiency responses in plants is of great agricultural importance. Previous studies revealed that decreased expression of NITRATE-INDUCIBLE GARP-TYPE TRANSCRIPTIONAL REPRESSOR1 (NIGT1) transcriptional repressor genes upon N deficiency is involved in N deficiency-inducible gene expression in Arabidopsis thaliana. However, our knowledge of the mechanisms controlling N deficiency-induced changes in gene expression is still limited. Through the identification of Dof1.7 as a direct target of NIGT1 repressors and a novel N deficiency response-related transcriptional activator gene, we here show that NIGT1 and Dof1.7 transcription factors (TFs) differentially regulate N deficiency-inducible expression of three high-affinity nitrate transporter genes, NRT2.1, NRT2.4, and NRT2.5, which are responsible for most of the soil nitrate uptake activity of Arabidopsis plants under N-deficient conditions. Unlike NIGT1 repressors, which directly suppress NRT2.1, NRT2.4, and NRT2.5 under N-sufficient conditions, Dof1.7 directly activated only NRT2.5 but indirectly and moderately activated NRT2.1 and NRT2.4 under N-deficient conditions, probably by indirectly decreasing NIGT1 expression. Thus, Dof1.7 converted passive transcriptional activation into active and potent transcriptional activation, further differentially enhancing the expression of NRT2 genes. These findings clarify the mechanism underlying different expression patterns of NRT2 genes upon N deficiency, suggesting that time-dependent multilayered transcriptional regulation generates complicated expression patterns of N deficiency-inducible genes.
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Affiliation(s)
- Mengna Zhuo
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Yasuhito Sakuraba
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
| | - Shuichi Yanagisawa
- Agro-Biotechnology Research Center, Graduate School of Agricultural and Life Sciences, The University of Tokyo, Yayoi 1-1-1, Bunkyo-ku, Tokyo, 113-8657, Japan
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Yu J, Gao B, Li D, Li S, Chiang VL, Li W, Zhou C. Ectopic Expression of PtrLBD39 Retarded Primary and Secondary Growth in Populus trichocarpa. Int J Mol Sci 2024; 25:2205. [PMID: 38396881 PMCID: PMC10889148 DOI: 10.3390/ijms25042205] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2023] [Revised: 02/07/2024] [Accepted: 02/08/2024] [Indexed: 02/25/2024] Open
Abstract
Primary and secondary growth of trees are needed for increments in plant height and stem diameter, respectively, affecting the production of woody biomass for applications in timber, pulp/paper, and related biomaterials. These two types of growth are believed to be both regulated by distinct transcription factor (TF)-mediated regulatory pathways. Notably, we identified PtrLBD39, a highly stem phloem-specific TF in Populus trichocarpa and found that the ectopic expression of PtrLBD39 in P. trichocarpa markedly retarded both primary and secondary growth. In these overexpressing plants, the RNA-seq, ChIP-seq, and weighted gene co-expression network analysis (WGCNA) revealed that PtrLBD39 directly or indirectly regulates TFs governing vascular tissue development, wood formation, hormonal signaling pathways, and enzymes responsible for wood components. This regulation led to growth inhibition, decreased fibrocyte secondary cell wall thickness, and reduced wood production. Therefore, our study indicates that, following ectopic expression in P. trichocarpa, PtrLBD39 functions as a repressor influencing both primary and secondary growth.
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Affiliation(s)
- Jing Yu
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Boyuan Gao
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Danning Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Shuang Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Vincent L. Chiang
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
- Forest Biotechnology Group, Department of Forestry and Environmental Resources, North Carolina State University, Raleigh, NC 27695, USA
| | - Wei Li
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
| | - Chenguang Zhou
- State Key Laboratory of Tree Genetics and Breeding, Northeast Forestry University, Harbin 150040, China; (J.Y.); (B.G.); (D.L.); (S.L.); (V.L.C.); (W.L.)
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Liu Z, Cheng J. C 4 rice engineering, beyond installing a C 4 cycle. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108256. [PMID: 38091938 DOI: 10.1016/j.plaphy.2023.108256] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/06/2023] [Revised: 11/28/2023] [Accepted: 11/30/2023] [Indexed: 02/15/2024]
Abstract
C4 photosynthesis in higher plants is carried out by two distinct cell types: mesophyll cells and bundle sheath cells, as a result highly concentrated carbon dioxide is released surrounding RuBisCo in chloroplasts of bundle sheath cells and the photosynthetic efficiency is significantly higher than that of C3 plants. The evolution of the dual-cell C4 cycle involved complex modifications to leaf anatomy and cell ultra-structures. These include an increase in leaf venation, the formation of Kranz anatomy, changes in chloroplast morphology in bundle sheath cells, and increases in the density of plasmodesmata at interfaces between the bundle sheath and mesophyll cells. It is predicted that cereals will be in severe worldwide shortage at the mid-term of this century. Rice is a staple food that feeds more than half of the world's population. If rice can be engineered to perform C4 photosynthesis, it is estimated that rice yield will be increased by at least 50% due to enhanced photosynthesis. Thus, the Second Green Revolution has been launched on this principle by genetically installing C4 photosynthesis into C3 crops. The studies on molecular mechanisms underlying the changes in leaf morphoanatomy involved in C4 photosynthesis have made great progress in recent years. As there are plenty of reviews discussing the installment of the C4 cycle, we focus on the current progress and challenges posed to the research regarding leaf anatomy and cell ultra-structure modifications made towards the development of C4 rice.
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Affiliation(s)
- Zheng Liu
- State Key Laboratory of North China Crop Improvement and Regulation, College of Agronomy, Hebei Agricultural University, Baoding, 071001, China.
| | - Jinjin Cheng
- College of Agronomy, Shanxi Agricultural University, Jinzhong, 030801, China
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Singh T, Bisht N, Ansari MM, Chauhan PS. The hidden harmony: Exploring ROS-phytohormone nexus for shaping plant root architecture in response to environmental cues. PLANT PHYSIOLOGY AND BIOCHEMISTRY : PPB 2024; 206:108273. [PMID: 38103339 DOI: 10.1016/j.plaphy.2023.108273] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/28/2023] [Accepted: 12/07/2023] [Indexed: 12/19/2023]
Abstract
Root system architecture, encompassing lateral roots and root hairs, plays a vital in overall plant growth and stress tolerance. Reactive oxygen species (ROS) and plant hormones intricately regulate root growth and development, serving as signaling molecules that govern processes such as cell proliferation and differentiation. Manipulating the interplay between ROS and hormones has the potential to enhance nutrient absorption, stress tolerance, and agricultural productivity. In this review, we delve into how studying these processes provides insights into how plants respond to environmental changes and optimize growth patterns to better control cellular processes and stress responses in crops. We discuss various factors and complex signaling networks that may exist among ROS and phytohormones during root development. Additionally, the review highlights possible role of reactive nitrogen species (RNS) in ROS-phytohormone interactions and in shaping root system architecture according to environmental cues.
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Affiliation(s)
- Tanya Singh
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Nikita Bisht
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India
| | - Mohd Mogees Ansari
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India
| | - Puneet Singh Chauhan
- CSIR-National Botanical Research Institute (CSIR-NBRI), Rana Pratap Marg, Lucknow, India; Academy of Scientific and Innovative Research (AcSIR), Ghaziabad, India.
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Wójcikowska B, Belaidi S, Robert HS. Game of thrones among AUXIN RESPONSE FACTORs-over 30 years of MONOPTEROS research. JOURNAL OF EXPERIMENTAL BOTANY 2023; 74:6904-6921. [PMID: 37450945 PMCID: PMC10690734 DOI: 10.1093/jxb/erad272] [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: 02/28/2023] [Accepted: 07/11/2023] [Indexed: 07/18/2023]
Abstract
For many years, research has been carried out with the aim of understanding the mechanism of auxin action, its biosynthesis, catabolism, perception, and transport. One central interest is the auxin-dependent gene expression regulation mechanism involving AUXIN RESPONSE FACTOR (ARF) transcription factors and their repressors, the AUXIN/INDOLE-3-ACETIC ACID (Aux/IAA) proteins. Numerous studies have been focused on MONOPTEROS (MP)/ARF5, an activator of auxin-dependent gene expression with a crucial impact on plant development. This review summarizes over 30 years of research on MP/ARF5. We indicate the available analytical tools to study MP/ARF5 and point out the known mechanism of MP/ARF5-dependent regulation of gene expression during various developmental processes, namely embryogenesis, leaf formation, vascularization, and shoot and root meristem formation. However, many questions remain about the auxin dose-dependent regulation of gene transcription by MP/ARF5 and its isoforms in plant cells, the composition of the MP/ARF5 protein complex, and, finally, all the genes under its direct control. In addition, information on post-translational modifications of MP/ARF5 protein is marginal, and knowledge about their consequences on MP/ARF5 function is limited. Moreover, the epigenetic factors and other regulators that act upstream of MP/ARF5 are poorly understood. Their identification will be a challenge in the coming years.
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Affiliation(s)
- Barbara Wójcikowska
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- Institute of Biology, Biotechnology, and Environmental Protection, Faculty of Natural Sciences, University of Silesia in Katowice, Katowice, Poland
| | - Samia Belaidi
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
- National Centre for Biomolecular Research, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Hélène S Robert
- Mendel Centre for Genomics and Proteomics of Plants Systems, CEITEC MU - Central European Institute of Technology, Masaryk University, Brno, Czech Republic
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Zhang T, Ge Y, Cai G, Pan X, Xu L. WOX-ARF modules initiate different types of roots. Cell Rep 2023; 42:112966. [PMID: 37556327 DOI: 10.1016/j.celrep.2023.112966] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Revised: 06/25/2023] [Accepted: 07/26/2023] [Indexed: 08/11/2023] Open
Abstract
Seed plants have evolved a complex root system consisting of at least three root types, i.e., adventitious roots, lateral roots, and the primary root. Auxin is the key hormone that controls the initiation of different root types. Here, we show that protein complexes with different combinations of intermediate-clade WUSCHEL-RELATED HOMEOBOXs (IC-WOXs) and class-A AUXIN RESPONSE FACTORs (A-ARFs) initiate the three root types in Arabidopsis thaliana. In adventitious root founder cells from detached leaves, the WOX11-ARF6/8 complex activates RGF1 INSENSITIVEs (RGIs) and LATERAL ORGAN BOUNDARIES DOMAIN 16 (LBD16) to initiate the adventitious root primordium. In lateral root founder cells, ARF7/19 activate RGIs and LBD16 without IC-WOX to initiate the lateral root primordium. In the primary root founder cell (i.e., hypophysis of an embryo), the WOX9-ARF5 complex initiates the primary root by activation of RGIs. Overall, the WOX-ARF modules show a division of labor to initiate different type of roots.
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Affiliation(s)
- Teng Zhang
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Yachao Ge
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Gui Cai
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Xuan Pan
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China; University of Chinese Academy of Sciences, 19A Yuquan Road, Beijing 100049, China
| | - Lin Xu
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 300 Fenglin Road, Shanghai 200032, China.
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Zou X, Sun H. DOF transcription factors: Specific regulators of plant biological processes. FRONTIERS IN PLANT SCIENCE 2023; 14:1044918. [PMID: 36743498 PMCID: PMC9897228 DOI: 10.3389/fpls.2023.1044918] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2022] [Accepted: 01/03/2023] [Indexed: 06/12/2023]
Abstract
Plant biological processes, such as growth and metabolism, hormone signal transduction, and stress responses, are affected by gene transcriptional regulation. As gene expression regulators, transcription factors activate or inhibit target gene transcription by directly binding to downstream promoter elements. DOF (DNA binding with One Finger) is a classic transcription factor family exclusive to plants that is characterized by its single zinc finger structure. With breakthroughs in taxonomic studies of different species in recent years, many DOF members have been reported to play vital roles throughout the plant life cycle. They are not only involved in regulating hormone signals and various biotic or abiotic stress responses but are also reported to regulate many plant biological processes, such as dormancy, tissue differentiation, carbon and nitrogen assimilation, and carbohydrate metabolism. Nevertheless, some outstanding issues remain. This article mainly reviews the origin and evolution, protein structure, and functions of DOF members reported in studies published in many fields to clarify the direction for future research on DOF transcription factors.
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Affiliation(s)
- Xiaoman Zou
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
| | - Hongmei Sun
- Key Laboratory of Protected Horticulture of Education Ministry, College of Horticulture, Shenyang Agricultural University, Shenyang, China
- National and Local Joint Engineering Research Center of Northern Horticultural Facilities Design and Application Technology, Shenyang, China
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Genome-Wide Identification and Analysis of DOF Gene Family in Eugenia uniflora L. (Myrtaceae). Genes (Basel) 2022; 13:genes13122235. [PMID: 36553502 PMCID: PMC9778057 DOI: 10.3390/genes13122235] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2022] [Revised: 11/16/2022] [Accepted: 11/19/2022] [Indexed: 11/29/2022] Open
Abstract
Eugenia uniflora is a Brazilian native plant species with great ecological and economic importance. It is distributed throughout the Atlantic forest, where two distinct populations show local adaptation to the contrasting conditions of restinga and riparian forest. Among various TFs described in plants, the DOF TF family has been reported to affect flowering and vascular development, making them promising candidates for characterization in E. uniflora. In this study, 28 DOF genes were identified by a genome-wide analysis, of which 20 were grouped into 11 MCOGs by Bayesian phylogeny, suggesting a shared functionallity between members. Based on RNA-seq experiments, we have detected eight drought responsive genes, and SNPs identification revealed population unique polymorphisms, implying a role in local adapatation mechanisms. Finally, analysis of conserved motifs through MEME revealed 15 different protein motifs, and a promoter region analysis returned 40 enriched TF binding motifs, both reporting novel biological functions circa the DOF gene family. In general, the DOF family is found to be conserved both in sequence and expression. Furthermore, this study contributes to both DOF literature and the genetic exploration of native species, elucidating their genetic potential and bringing to light new research topics, paving the way to future studies.
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Zhang F, Fan R, Yan L, Hu L, Su F, Yang D, Li J. Genome-wide identification of black pepper (Piper nigrum L.) Dof gene family and the differential gene screening in resistance to Phytophthora capsici. Biologia (Bratisl) 2022. [DOI: 10.1007/s11756-022-01232-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/02/2022]
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11
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Transcriptional reprogramming during floral fate acquisition. iScience 2022; 25:104683. [PMID: 35856019 PMCID: PMC9287482 DOI: 10.1016/j.isci.2022.104683] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2022] [Revised: 06/13/2022] [Accepted: 06/23/2022] [Indexed: 11/20/2022] Open
Abstract
Coordinating growth and patterning is essential for eukaryote morphogenesis. In plants, auxin is a key regulator of morphogenesis implicated throughout development. Despite this central role, our understanding of how auxin coordinates cell fate and growth changes is still limited. Here, we addressed this question using a combination of genomic screens to delve into the transcriptional network induced by auxin at the earliest stage of flower development, prior to morphological changes. We identify a shoot-specific network suggesting that auxin initiates growth through an antagonistic regulation of growth-promoting and growth-repressive hormones, quasi-synchronously to floral fate specification. We further identify two DNA-binding One Zinc Finger (DOF) transcription factors acting in an auxin-dependent network that could interface growth and cell fate from the early stages of flower development onward. Pharmacological approach to probe transcriptional responses in shoot meristems Analysis of a shoot-specific network regulated by auxin during flower initiation Two DOF transcription factors are induced in flower primordia The DOF genes potentially link growth to organ identity acquisition
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Hu G, Wang K, Huang B, Mila I, Frasse P, Maza E, Djari A, Hernould M, Zouine M, Li Z, Bouzayen M. The auxin-responsive transcription factor SlDOF9 regulates inflorescence and flower development in tomato. NATURE PLANTS 2022; 8:419-433. [PMID: 35422080 DOI: 10.1038/s41477-022-01121-1] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/10/2021] [Accepted: 03/03/2022] [Indexed: 05/04/2023]
Abstract
Understanding the mechanisms underlying differentiation of inflorescence and flower meristems is essential towards enlarging our knowledge of reproductive organ formation and to open new prospects for improving yield traits. Here, we show that SlDOF9 is a new modulator of floral differentiation in tomato. CRISPR/Cas9 knockout strategy uncovered the role of SlDOF9 in controlling inflorescence meristem and floral meristem differentiation via the regulation of cell division genes and inflorescence architecture regulator LIN. Tomato dof9-KO lines have more flowers in both determinate and indeterminate cultivars and produce more fruit upon vibration-assisted fertilization. SlDOF9 regulates inflorescence development through an auxin-dependent ARF5-DOF9 module that seems to operate, at least in part, differently in Arabidopsis and tomato. Our findings add a new actor to the complex mechanisms underlying reproductive organ differentiation in flowering plants and provide leads towards addressing the diversity of factors controlling the transition to reproductive organs.
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Affiliation(s)
- Guojian Hu
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Keke Wang
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Baowen Huang
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Isabelle Mila
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
| | - Pierre Frasse
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Elie Maza
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Anis Djari
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Michel Hernould
- Biologie du Fruit et Pathologie-UMR 1332, Université Bordeaux, INRAE, Villenave d'Ornon, France
| | - Mohamed Zouine
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France
| | - Zhengguo Li
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China
| | - Mondher Bouzayen
- Université de Toulouse, INRAe/INP Toulouse, Génomique et Biotechnologie des Fruits-UMR990, Castanet-Tolosan, France.
- Laboratoire de Recherche en Sciences Végétales-UMR5546, Université de Toulouse, CNRS, UPS, Toulouse-INP, Toulouse, France.
- Key Laboratory of Plant Hormones and Development Regulation of Chongqing, School of Life Sciences, Chongqing University, Chongqing, China.
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13
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Zheng J, Zhang Z, Gong Z, Liang Y, Sang Z, Xu Y, Li X, Wang J. Genome-Wide Association Analysis of Salt-Tolerant Traits in Terrestrial Cotton at Seedling Stage. PLANTS (BASEL, SWITZERLAND) 2021; 11:plants11010097. [PMID: 35009100 PMCID: PMC8747425 DOI: 10.3390/plants11010097] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2021] [Revised: 12/01/2021] [Accepted: 12/11/2021] [Indexed: 06/01/2023]
Abstract
Soil salinization is the main abiotic stress factor affecting agricultural production worldwide, and salt stress has a significant impact on plant growth and development. Cotton is one of the most salt-tolerant crops. Therefore, the selection and utilization of salt-tolerant germplasm resources and the excavation of salt resistance genes play important roles in improving cotton production in saline-alkali soils. In this study, we analysed the population structure and genetic diversity of a total 149 cotton plant materials including 137 elite Gossypium hirsutum cultivar accessions collected from China and 12 elite Gossypium hirsutum cultivar accessions collected from around the world. Illumina Cotton SNP 70 K was used to obtain genome-wide single-nucleotide polymorphism (SNP) data for 149 elite Gossypium hirsutum cultivar accessions, and 18,430 highly consistent SNP loci were obtained by filtering. It was assessed by using PCA principal component analysis so that the 149 elite Gossypium hirsutum cultivar accessions could be divided into two subgroups, including subgroup 1 with 78 materials and subgroup 2 with 71 materials. Using the obtained SNP and other marker genotype test results, under salt stress, the salt tolerance traits 3d Germination potential, 3d Radicle length drop rate, 7d Germination rate, 7d Radicle length drop rate, 7d Germination weight, 3d Radicle length, 7d Radicle length, Relative Germination potential, Relative Germination rate, 7d Radicle weight drop rate, Salt tolerance index 3d Germination potential index, 3d Radicle length index, 7d Radicle length index, 7d Radicle weight index and 7d Germination rate index were evaluated by GWAS (genome-wide association analysis). A total of 27 SNP markers closely related to the salt tolerance traits and 15 SNP markers closely related to the salt tolerance index were detected. At the SNP locus associated with phenotyping, Gh_D01G0943, Gh_D01G0945, Gh_A01G0906, Gh_A01G0908, Gh_D08G1308 and Gh_D08G1309 related to plant salt tolerance were detected, and they were found to be involved in intracellular transport, sucrose synthesis, osmotic pressure balance, transmembrane transport, N-glycosylation, auxin response and cell amplification. This study provides a theoretical basis for the selection and breeding of salt-tolerant upland cotton varieties.
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Affiliation(s)
- Juyun Zheng
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zeliang Zhang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Zhaolong Gong
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Yajun Liang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Zhiwei Sang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
- Engineering Research Centre of Cotton, Ministry of Education, College of Agriculture, Xinjiang Agricultural University, 311 Nongda East Road, Urumqi 830052, China
| | - Yanchao Xu
- State Key Laboratory of Cotton Biology (China), Institute of Cotton Research, Chinese Academy of Agricultural Science (ICR-CAAS), Anyang 455000, China;
| | - Xueyuan Li
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
| | - Junduo Wang
- Economic Crops Research Institute, Xinjiang Academy of Agricultural Science (XAAS), Urumqi 830001, China; (J.Z.); (Z.Z.); (Z.G.); (Y.L.); (Z.S.)
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14
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Zluhan-Martínez E, López-Ruíz BA, García-Gómez ML, García-Ponce B, de la Paz Sánchez M, Álvarez-Buylla ER, Garay-Arroyo A. Integrative Roles of Phytohormones on Cell Proliferation, Elongation and Differentiation in the Arabidopsis thaliana Primary Root. FRONTIERS IN PLANT SCIENCE 2021; 12:659155. [PMID: 33981325 PMCID: PMC8107238 DOI: 10.3389/fpls.2021.659155] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2021] [Accepted: 03/24/2021] [Indexed: 05/17/2023]
Abstract
The growth of multicellular organisms relies on cell proliferation, elongation and differentiation that are tightly regulated throughout development by internal and external stimuli. The plasticity of a growth response largely depends on the capacity of the organism to adjust the ratio between cell proliferation and cell differentiation. The primary root of Arabidopsis thaliana offers many advantages toward understanding growth homeostasis as root cells are continuously produced and move from cell proliferation to elongation and differentiation that are processes spatially separated and could be studied along the longitudinal axis. Hormones fine tune plant growth responses and a huge amount of information has been recently generated on the role of these compounds in Arabidopsis primary root development. In this review, we summarized the participation of nine hormones in the regulation of the different zones and domains of the Arabidopsis primary root. In some cases, we found synergism between hormones that function either positively or negatively in proliferation, elongation or differentiation. Intriguingly, there are other cases where the interaction between hormones exhibits unexpected results. Future analysis on the molecular mechanisms underlying crosstalk hormone action in specific zones and domains will unravel their coordination over PR development.
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Affiliation(s)
- Estephania Zluhan-Martínez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Brenda Anabel López-Ruíz
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Mónica L. García-Gómez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Berenice García-Ponce
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - María de la Paz Sánchez
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Elena R. Álvarez-Buylla
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
| | - Adriana Garay-Arroyo
- Laboratorio de Genética Molecular, Desarrollo y Evolución de Plantas, Departamento de Ecología Funcional, Instituto de Ecología, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- Centro de Ciencias de la Complejidad, Universidad Nacional Autónoma de México, Ciudad de México, Mexico
- *Correspondence: Adriana Garay-Arroyo,
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15
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Ramachandran V, Tobimatsu Y, Masaomi Y, Sano R, Umezawa T, Demura T, Ohtani M. Plant-specific Dof transcription factors VASCULAR-RELATED DOF1 and VASCULAR-RELATED DOF2 regulate vascular cell differentiation and lignin biosynthesis in Arabidopsis. PLANT MOLECULAR BIOLOGY 2020; 104:263-281. [PMID: 32740898 DOI: 10.1007/s11103-020-01040-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/03/2019] [Accepted: 07/23/2020] [Indexed: 05/28/2023]
Abstract
Plant-specific Dof transcription factors VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime in Arabidopsis, with shifting their transcriptional target genes. Vascular system is one of critical tissues for vascular plants to transport low-molecular compounds, such as water, minerals, and the photosynthetic product, sucrose. Here, we report the involvement of two Dof transcription factors, named VASCULAR-RELATED DOF1 (VDOF1)/VDOF4.6 and VDOF2/VDOF1.8, in vascular cell differentiation and lignin biosynthesis in Arabidopsis. VDOF genes were expressed in vascular tissues, but the detailed expression sites were partly different between VDOF1 and VDOF2. Vein patterning and lignin analysis of VDOF overexpressors and double mutant vdof1 vdof2 suggested that VDOF1 and VDOF2 would function as negative regulators of vein formation in seedlings, and lignin deposition in inflorescence stems. Interestingly, effects of VDOF overexpression in lignin deposition were different by developmental stages of inflorescence stems, and total lignin contents were increased and decreased in VDOF1 and VDOF2 overexpressors, respectively. RNA-seq analysis of inducible VDOF overexpressors demonstrated that the genes for cell wall biosynthesis, including lignin biosynthetic genes, and the transcription factor genes related to stress response and brassinosteroid signaling were commonly affected by VDOF1 and VDOF2 overexpression. Taken together, we concluded that VDOF1 and VDOF2 are novel regulators of vascular cell differentiation through the course of a lifetime, with shifting their transcriptional target genes: in seedlings, the VDOF genes negatively regulate vein formation, while at reproductive stages, the VDOF proteins target lignin biosynthesis.
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Affiliation(s)
- Vasagi Ramachandran
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Yuki Tobimatsu
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Yamamura Masaomi
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
| | - Ryosuke Sano
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan
| | - Toshiaki Umezawa
- Research Institute for Sustainable Humanosphere, Kyoto University, Uji, Kyoto, 611-0011, Japan
- Research Unit for Development of Global Sustainability, Kyoto University, Uji, Gokasho, Kyoto, 611-0011, Japan
| | - Taku Demura
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
| | - Misato Ohtani
- Graduate School of Science and Technology, Nara Institute of Science and Technology, Ikoma, Nara, 630-0192, Japan.
- Department of Integrated Biosciences, Graduate School of Frontier Sciences, The University of Tokyo, Kashiwa, 277-8562, Japan.
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16
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Architecture of DNA elements mediating ARF transcription factor binding and auxin-responsive gene expression in Arabidopsis. Proc Natl Acad Sci U S A 2020; 117:24557-24566. [PMID: 32929017 PMCID: PMC7533888 DOI: 10.1073/pnas.2009554117] [Citation(s) in RCA: 28] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023] Open
Abstract
The hormone auxin controls many aspects of the plant life cycle by regulating the expression of thousands of genes. The transcriptional output of the nuclear auxin signaling pathway is determined by the activity of AUXIN RESPONSE transcription FACTORs (ARFs), through their binding to cis-regulatory elements in auxin-responsive genes. Crystal structures, in vitro, and heterologous studies have fueled a model in which ARF dimers bind with high affinity to distinctly spaced repeats of canonical AuxRE motifs. However, the relevance of this "caliper" model, and the mechanisms underlying the binding affinities in vivo, have remained elusive. Here we biochemically and functionally interrogate modes of ARF-DNA interaction. We show that a single additional hydrogen bond in Arabidopsis ARF1 confers high-affinity binding to individual DNA sites. We demonstrate the importance of AuxRE cooperativity within repeats in the Arabidopsis TMO5 and IAA11 promoters in vivo. Meta-analysis of transcriptomes further reveals strong genome-wide association of auxin response with both inverted (IR) and direct (DR) AuxRE repeats, which we experimentally validated. The association of these elements with auxin-induced up-regulation (DR and IR) or down-regulation (IR) was correlated with differential binding affinities of A-class and B-class ARFs, respectively, suggesting a mechanistic basis for the distinct activity of these repeats. Our results support the relevance of high-affinity binding of ARF transcription factors to uniquely spaced DNA elements in vivo, and suggest that differential binding affinities of ARF subfamilies underlie diversity in cis-element function.
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17
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Guerriero G, Piasecki E, Berni R, Xu X, Legay S, Hausman JF. Identification of Callose Synthases in Stinging Nettle and Analysis of Their Expression in Different Tissues. Int J Mol Sci 2020; 21:ijms21113853. [PMID: 32481765 PMCID: PMC7313033 DOI: 10.3390/ijms21113853] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 05/27/2020] [Accepted: 05/27/2020] [Indexed: 11/29/2022] Open
Abstract
Callose is an important biopolymer of β-1,3-linked glucose units involved in different phases of plant development, reproduction and response to external stimuli. It is synthesized by glycosyltransferases (GTs) known as callose synthases (CalS) belonging to family 48 in the Carbohydrate-Active enZymes (CAZymes) database. These GTs are anchored to the plasma membrane via transmembrane domains. Several genes encoding CalS have been characterized in higher plants with 12 reported in the model organism Arabidopsis thaliana. Recently, the de novo transcriptome of a fibre-producing clone of stinging nettle (Urtica dioica L.) was published and here it is mined for CalS genes with the aim of identifying members differentially expressed in the core and cortical tissues of the stem. The goal is to understand whether specific CalS genes are associated with distinct developmental stages of the stem internodes (elongation, thickening). Nine genes, eight of which encoding full-length CalS, are identified in stinging nettle. The phylogenetic analysis with CalS proteins from other fibre crops, namely textile hemp and flax, reveals grouping into 6 clades. The expression profiles in nettle tissues (roots, leaves, stem internodes sampled at different heights) reveal differences that are most noteworthy in roots vs. leaves. Two CalS are differentially expressed in the internodes sampled at the top and middle of the stem. Implications of their role in nettle stem tissue development are discussed.
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Affiliation(s)
- Gea Guerriero
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, Z.A.E. Robert Steichen, L-4940 Hautcharage, Luxembourg; (E.P.); (X.X.); (S.L.); (J.-F.H.)
- Correspondence: ; Tel.: +352-275-888-5096; Fax: +352-275-8885
| | - Emilie Piasecki
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, Z.A.E. Robert Steichen, L-4940 Hautcharage, Luxembourg; (E.P.); (X.X.); (S.L.); (J.-F.H.)
| | - Roberto Berni
- Department of Life Sciences, University of Siena, via P.A. Mattioli 4, I-53100 Siena, Italy;
| | - Xuan Xu
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, Z.A.E. Robert Steichen, L-4940 Hautcharage, Luxembourg; (E.P.); (X.X.); (S.L.); (J.-F.H.)
| | - Sylvain Legay
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, Z.A.E. Robert Steichen, L-4940 Hautcharage, Luxembourg; (E.P.); (X.X.); (S.L.); (J.-F.H.)
| | - Jean-Francois Hausman
- Environmental Research and Innovation (ERIN) Department, Luxembourg Institute of Science and Technology, 5, rue Bommel, Z.A.E. Robert Steichen, L-4940 Hautcharage, Luxembourg; (E.P.); (X.X.); (S.L.); (J.-F.H.)
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18
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Smit ME, McGregor SR, Sun H, Gough C, Bågman AM, Soyars CL, Kroon JT, Gaudinier A, Williams CJ, Yang X, Nimchuk ZL, Weijers D, Turner SR, Brady SM, Etchells JP. A PXY-Mediated Transcriptional Network Integrates Signaling Mechanisms to Control Vascular Development in Arabidopsis. THE PLANT CELL 2020; 32:319-335. [PMID: 31806676 PMCID: PMC7008486 DOI: 10.1105/tpc.19.00562] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 11/12/2019] [Accepted: 12/05/2019] [Indexed: 05/18/2023]
Abstract
The cambium and procambium generate the majority of biomass in vascular plants. These meristems constitute a bifacial stem cell population from which xylem and phloem are specified on opposing sides by positional signals. The PHLOEM INTERCALATED WITH XYLEM (PXY) receptor kinase promotes vascular cell division and organization. However, how these functions are specified and integrated is unknown. Here, we mapped a putative PXY-mediated transcriptional regulatory network comprising 690 transcription factor-promoter interactions in Arabidopsis (Arabidopsis thaliana). Among these interactions was a feedforward loop containing transcription factors WUSCHEL HOMEOBOX RELATED14 (WOX14) and TARGET OF MONOPTEROS6 (TMO6), each of which regulates the expression of the gene encoding a third transcription factor, LATERAL ORGAN BOUNDARIES DOMAIN4 (LBD4). PXY signaling in turn regulates the WOX14, TMO6, and LBD4 feedforward loop to control vascular proliferation. Genetic interaction between LBD4 and PXY suggests that LBD4 marks the phloem-procambium boundary, thus defining the shape of the vascular bundle. These data collectively support a mechanism that influences the recruitment of cells into the phloem lineage, and they define the role of PXY signaling in this context in determining the arrangement of vascular tissue.
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Affiliation(s)
- Margot E Smit
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Shauni R McGregor
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Heng Sun
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Catherine Gough
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Anne-Maarit Bågman
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Cara L Soyars
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Johannes T Kroon
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
| | - Allison Gaudinier
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Clara J Williams
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - Xiyan Yang
- National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan, Hubei 430070, China
| | - Zachary L Nimchuk
- Department of Biology, University of North Carolina, Chapel Hill, North Carolina 27599
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6708 WE, Wageningen, The Netherlands
| | - Simon R Turner
- School of Biological Science, University of Manchester, Manchester, M13 9PT, United Kingdom
| | - Siobhán M Brady
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
| | - J Peter Etchells
- Department of Plant Biology and Genome Center, University of California, Davis, California 95616
- Department of Biosciences, Durham University, Durham DH1 3LE, United Kingdom
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19
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Guo W, Zhang X, Peng Q, Luo D, Jiao K, Su S. Love on wings, a Dof family protein regulates floral vasculature in Vigna radiata. BMC PLANT BIOLOGY 2019; 19:495. [PMID: 31726995 PMCID: PMC6854777 DOI: 10.1186/s12870-019-2099-x] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/17/2019] [Accepted: 10/24/2019] [Indexed: 05/30/2023]
Abstract
BACKGROUND The interaction among plants and their pollinators has been a major factor which enriched floral traits known as pollination syndromes and promoted the diversification of flowering plants. One of the bee-pollination syndromes in Faboideae with keel blossoms is the formation of a landing platform by wing and keel petals. However, the molecular mechanisms of elaborating a keel blossom remain unclear. RESULTS By performing large scale mutagenesis, we isolated and characterized a mutant in Vigna radiata, love on wings (low), which shows developmental defects in petal asymmetry and vasculature, leading to a failure in landing platform formation. We cloned the locus through map-based cloning together with RNA-sequencing (RNA-seq) analysis. We found that LOW encoded a nucleus-localized Dof-like protein and was expressed in the flower provascular and vascular tissues. A single copy of LOW was detected in legumes, in contrast with other taxa where there seems to be at least 2 copies. Thirty one Dof proteins have been identified from the V. radiata's genome, which can be further divided into four Major Cluster of Orthologous Groups (MCOGs). We also showed that ectopic expression of LOW in Arabidopsis driven by its native promoter caused changes in petal vasculature pattern. CONCLUSIONS To summarize, our study isolated a legume Dof-like factor LOW from V. radiata, which affects vasculature development in this species and this change can, in turn, impact petal development and overall morphology of keel blossom.
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Affiliation(s)
- Wuxiu Guo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Xue Zhang
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Qincheng Peng
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Da Luo
- State Key Laboratory of Biocontrol and Guangdong Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, Haizhu district, Guangzhou, 510275 Guangdong China
| | - Keyuan Jiao
- Institute of Traditional Chinese Medicine and Natural Products, College of Pharmacy, Jinan University, Guangzhou, 510632 Guangdong China
| | - Shihao Su
- Institute of Transformative Bio-Molecules (WPI-ITbM), Nagoya University, Furo-cho, Chikusa-ku, Nagoya, Aichi 464-8601 Japan
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20
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Biedroń M, Banasiak A. Auxin-mediated regulation of vascular patterning in Arabidopsis thaliana leaves. PLANT CELL REPORTS 2018; 37:1215-1229. [PMID: 29992374 PMCID: PMC6096608 DOI: 10.1007/s00299-018-2319-0] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/24/2018] [Accepted: 07/04/2018] [Indexed: 05/02/2023]
Abstract
The vascular system develops in response to auxin flow as continuous strands of conducting tissues arranged in regular spatial patterns. However, a mechanism governing their regular and repetitive formation remains to be fully elucidated. A model system for studying the vascular pattern formation is the process of leaf vascularization in Arabidopsis. In this paper, we present current knowledge of important factors and their interactions in this process. Additionally, we propose the sequence of events leading to the emergence of continuous vascular strands and point to significant problems that need to be resolved in the future to gain a better understanding of the regulation of the vascular pattern development.
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Affiliation(s)
- Magdalena Biedroń
- Department of Plant Developmental Biology, Institute of Experimental Biology, University of Wrocław, ul. Kanonia 6/8, 50-328, Wrocław, Poland
| | - Alicja Banasiak
- Department of Plant Developmental Biology, Institute of Experimental Biology, University of Wrocław, ul. Kanonia 6/8, 50-328, Wrocław, Poland.
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21
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Guan C, Wu B, Yu T, Wang Q, Krogan NT, Liu X, Jiao Y. Spatial Auxin Signaling Controls Leaf Flattening in Arabidopsis. Curr Biol 2017; 27:2940-2950.e4. [PMID: 28943086 DOI: 10.1016/j.cub.2017.08.042] [Citation(s) in RCA: 90] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2017] [Revised: 07/18/2017] [Accepted: 08/17/2017] [Indexed: 11/18/2022]
Abstract
The flattening of leaves to form broad blades is an important adaptation that maximizes photosynthesis. However, the molecular mechanism underlying this process remains unclear. The WUSCHEL-RELATED HOMEOBOX (WOX) genes WOX1 and PRS are expressed in the leaf marginal domain to enable leaf flattening, but the nature of WOX expression establishment remains elusive. Here, we report that adaxial-expressed MONOPTEROS (MP) and abaxial-enriched auxin together act as positional cues for patterning the WOX domain. MP directly binds to the WOX1 and PRS promoters and activates their expression. Furthermore, redundant abaxial-enriched ARF repressors suppress WOX1 and PRS expression, also through direct binding. In particular, we show that ARF2 is redundantly required with ARF3 and ARF4 to maintain the abaxial identity. Taken together, these findings explain how adaxial-abaxial polarity patterns the mediolateral axis and subsequent lateral expansion of leaves.
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Affiliation(s)
- Chunmei Guan
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China
| | - Binbin Wu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ting Yu
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China; College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qingqing Wang
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Naden T Krogan
- Department of Biology, American University, Washington, DC 20016, USA
| | - Xigang Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Center for Agricultural Resources Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Shijiazhuang 050021, China
| | - Yuling Jiao
- State Key Laboratory of Plant Genomics, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, and National Center for Plant Gene Research, Beijing 100101, China; College of Life Sciences, University of Chinese Academy of Sciences, Beijing 100049, China.
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Molina-Hidalgo FJ, Medina-Puche L, Cañete-Gómez C, Franco-Zorrilla JM, López-Vidriero I, Solano R, Caballero JL, Rodríguez-Franco A, Blanco-Portales R, Muñoz-Blanco J, Moyano E. The fruit-specific transcription factor FaDOF2 regulates the production of eugenol in ripe fruit receptacles. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:4529-4543. [PMID: 28981772 DOI: 10.1093/jxb/erx257] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/18/2023]
Abstract
Only a few transcription factors have been described in the regulation of the strawberry (Fragaria x ananassa) fruit ripening process. Using a transcriptomic approach, we identified and functionally characterized FaDOF2, a DOF-type ripening-related transcription factor, which is hormonally regulated and specific to the receptacle, though high expression levels were also found in petals. The expression pattern of FaDOF2 correlated with eugenol content, a phenylpropanoid volatile, in both fruit receptacles and petals. When FaDOF2 expression was silenced in ripe strawberry receptacles, the expression of FaEOBII and FaEGS2, two key genes involved in eugenol production, were down-regulated. These fruits showed a concomitant decrease in eugenol content, which confirmed that FaDOF2 is a transcription factor that is involved in eugenol production in ripe fruit receptacles. By using the yeast two-hybrid system and bimolecular fluorescence complementation, we demonstrated that FaDOF2 interacts with FaEOBII, a previously reported regulator of eugenol production, which determines fine-tuning of the expression of key genes that are involved in eugenol production. These results provide evidence that FaDOF2 plays a subsidiary regulatory role with FaEOBII in the expression of genes encoding enzymes that control eugenol production. Taken together, our results provide new insights into the regulation of the volatile phenylpropanoid pathway in ripe strawberry receptacles.
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Affiliation(s)
- Francisco Javier Molina-Hidalgo
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | - Laura Medina-Puche
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba, Spain
- Shanghai Center for Plant Stress Biology, Shanghai Institutes of Biological Sciences, University of Chinese Academy of Sciences, Shanghai 200031, China
| | - Carlos Cañete-Gómez
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | | | | | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología-CSIC, Darwin 3, 28049-Madrid, Spain
| | - José Luis Caballero
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | - Antonio Rodríguez-Franco
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | - Rosario Blanco-Portales
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | - Juan Muñoz-Blanco
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
| | - Enriqueta Moyano
- Departamento de Bioquímica y Biología Molecular, Edificio Severo Ochoa, Campus Universitario de Rabanales y Campus de Excelencia Internacional Agroalimentario CEIA3, Universidad de Córdoba, 14071 Córdoba,Spain
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23
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Auxin response cell-autonomously controls ground tissue initiation in the early Arabidopsis embryo. Proc Natl Acad Sci U S A 2017; 114:E2533-E2539. [PMID: 28265057 DOI: 10.1073/pnas.1616493114] [Citation(s) in RCA: 62] [Impact Index Per Article: 8.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/12/2023] Open
Abstract
Plant organs are typically organized into three main tissue layers. The middle ground tissue layer comprises the majority of the plant body and serves a wide range of functions, including photosynthesis, selective nutrient uptake and storage, and gravity sensing. Ground tissue patterning and maintenance in Arabidopsis are controlled by a well-established gene network revolving around the key regulator SHORT-ROOT (SHR). In contrast, it is completely unknown how ground tissue identity is first specified from totipotent precursor cells in the embryo. The plant signaling molecule auxin, acting through AUXIN RESPONSE FACTOR (ARF) transcription factors, is critical for embryo patterning. The auxin effector ARF5/MONOPTEROS (MP) acts both cell-autonomously and noncell-autonomously to control embryonic vascular tissue formation and root initiation, respectively. Here we show that auxin response and ARF activity cell-autonomously control the asymmetric division of the first ground tissue cells. By identifying embryonic target genes, we show that MP transcriptionally initiates the ground tissue lineage and acts upstream of the regulatory network that controls ground tissue patterning and maintenance. Strikingly, whereas the SHR network depends on MP, this MP function is, at least in part, SHR independent. Our study therefore identifies auxin response as a regulator of ground tissue specification in the embryonic root, and reveals that ground tissue initiation and maintenance use different regulators and mechanisms. Moreover, our data provide a framework for the simultaneous formation of multiple cell types by the same transcriptional regulator.
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Chandler JW. Auxin response factors. PLANT, CELL & ENVIRONMENT 2016; 39:1014-28. [PMID: 26487015 DOI: 10.1111/pce.12662] [Citation(s) in RCA: 148] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/29/2015] [Revised: 09/22/2015] [Accepted: 10/05/2015] [Indexed: 05/03/2023]
Abstract
Auxin signalling involves the activation or repression of gene expression by a class of auxin response factor (ARF) proteins that bind to auxin response elements in auxin-responsive gene promoters. The release of ARF repression in the presence of auxin by the degradation of their cognate auxin/indole-3-acetic acid repressors forms a paradigm of transcriptional response to auxin. However, this mechanism only applies to activating ARFs, and further layers of complexity of ARF function and regulation are being revealed, which partly reflect their highly modular domain structure. This review summarizes our knowledge concerning ARF binding site specificity, homodimer and heterodimer multimeric ARF association and cooperative function and how activator ARFs activate target genes via chromatin remodelling and evolutionary information derived from phylogenetic comparisons from ARFs from diverse species. ARFs are regulated in diverse ways, and their importance in non-auxin-regulated pathways is becoming evident. They are also embedded within higher-order transcription factor complexes that integrate signalling pathways from other hormones and in response to the environment. The ways in which new information concerning ARFs on many levels is causing a revision of existing paradigms of auxin response are discussed.
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Affiliation(s)
- John William Chandler
- Institute of Developmental Biology, University of Cologne, Cologne Biocenter, Zuelpicher Strasse 47b, Cologne, D-50674, Germany
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25
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Abstract
Auxin is arguably the most important signaling molecule in plants, and the last few decades have seen remarkable breakthroughs in understanding its production, transport, and perception. Recent investigations have focused on transcriptional responses to auxin, providing novel insight into the functions of the domains of key transcription regulators in responses to the hormonal cue and prominently implicating chromatin regulation in these responses. In addition, studies are beginning to identify direct targets of the auxin-responsive transcription factors that underlie auxin modulation of development. Mechanisms to tune the response to different auxin levels are emerging, as are first insights into how this single hormone can trigger diverse responses. Key unanswered questions center on the mechanism for auxin-directed transcriptional repression and the identity of additional determinants of auxin response specificity. Much of what has been learned in model plants holds true in other species, including the earliest land plants.
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Affiliation(s)
- Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, 6703 HA Wageningen, The Netherlands;
| | - Doris Wagner
- Department of Biology, University of Pennsylvania, Philadelphia, Pennsylvania 19104;
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26
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Smit ME, Weijers D. The role of auxin signaling in early embryo pattern formation. CURRENT OPINION IN PLANT BIOLOGY 2015; 28:99-105. [PMID: 26495766 DOI: 10.1016/j.pbi.2015.10.001] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/03/2015] [Revised: 09/28/2015] [Accepted: 10/02/2015] [Indexed: 05/09/2023]
Abstract
Pattern formation of the early Arabidopsis embryo generates precursors to all major cell types, and is profoundly controlled by the signaling molecule auxin. Here we discuss recent milestones in our understanding of auxin-dependent embryo patterning. Auxin biosynthesis, transport and response mechanisms interact to generate local auxin accumulation in the early embryo. New auxin-dependent reporters help identifying these sites, while atomic structures of transcriptional response mediators help explain the diverse outputs of auxin signaling. Key auxin outputs are control of cell identity and cell division orientation, and progress has been made towards understanding the cellular basis of each. Importantly, a number of studies have combined computational modeling and experiments to analyze the developmental role, genetic circuitry and molecular mechanisms of auxin-dependent cell division control.
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Affiliation(s)
- Margot E Smit
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Wageningen, The Netherlands.
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27
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Konishi M, Yanagisawa S. Transcriptional repression caused by Dof5.8 is involved in proper vein network formation in Arabidopsis thaliana leaves. JOURNAL OF PLANT RESEARCH 2015; 128:643-652. [PMID: 25794540 DOI: 10.1007/s10265-015-0712-0] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/01/2014] [Accepted: 02/09/2015] [Indexed: 06/04/2023]
Abstract
Vascular plants have a network of vasculature in their leaves, which supplies water and nutrients and exports photoassimilates to other tissues. The vascular network is patterned during the development of leaf primordia through the induction of provascular differentiation by auxin. Arabidopsis thaliana Dof5.8, encoding a Dof-type transcription factor, is expressed early in provascular cells under the control of the MONOPTEROS transcription factor, also known as auxin response factor 5 (ARF5). Here, we report the effect of overexpressing Dof5.8 in provascular cells on the formation of the vascular network. Overexpression of Dof5.8 inhibited the formation of higher-order veins in cotyledons and leaves, probably through transcriptional repression by Dof5.8. The expression of auxin-associated transcription factor genes, DORNRöSCHEN and SHI-RELATED SEQUENCE 5, was downregulated in the Dof5.8 overexpressors, and overexpression of these genes partially rescued the impaired formation of higher-order veins in Dof5.8-overexpressing lines, suggesting that the overexpression of Dof5.8 modulates the auxin response and leads to impaired vein formation in A. thaliana.
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Affiliation(s)
- Mineko Konishi
- Biotechnology Research Center, The University of Tokyo, Yayoi 1-1-1, Bunkyo-Ku, Tokyo, 113-8657, Japan
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