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Shi B, Felipo-Benavent A, Cerutti G, Galvan-Ampudia C, Jilli L, Brunoud G, Mutterer J, Vallet E, Sakvarelidze-Achard L, Davière JM, Navarro-Galiano A, Walia A, Lazary S, Legrand J, Weinstain R, Jones AM, Prat S, Achard P, Vernoux T. A quantitative gibberellin signaling biosensor reveals a role for gibberellins in internode specification at the shoot apical meristem. Nat Commun 2024; 15:3895. [PMID: 38719832 PMCID: PMC11079023 DOI: 10.1038/s41467-024-48116-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2022] [Accepted: 04/17/2024] [Indexed: 05/12/2024] Open
Abstract
Growth at the shoot apical meristem (SAM) is essential for shoot architecture construction. The phytohormones gibberellins (GA) play a pivotal role in coordinating plant growth, but their role in the SAM remains mostly unknown. Here, we developed a ratiometric GA signaling biosensor by engineering one of the DELLA proteins, to suppress its master regulatory function in GA transcriptional responses while preserving its degradation upon GA sensing. We demonstrate that this degradation-based biosensor accurately reports on cellular changes in GA levels and perception during development. We used this biosensor to map GA signaling activity in the SAM. We show that high GA signaling is found primarily in cells located between organ primordia that are the precursors of internodes. By gain- and loss-of-function approaches, we further demonstrate that GAs regulate cell division plane orientation to establish the typical cellular organization of internodes, thus contributing to internode specification in the SAM.
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Affiliation(s)
- Bihai Shi
- College of Agriculture, South China Agricultural University, Guangdong Laboratory for Lingnan Modern Agriculture, 510642, Guangzhou, China
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Amelia Felipo-Benavent
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Guillaume Cerutti
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Carlos Galvan-Ampudia
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Lucas Jilli
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Geraldine Brunoud
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Jérome Mutterer
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Elody Vallet
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Lali Sakvarelidze-Achard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | - Jean-Michel Davière
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France
| | | | - Ankit Walia
- Sainsbury Laboratory, Cambridge University, Cambridge, CB2 1LR, UK
| | - Shani Lazary
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, 69978, Israel
| | - Jonathan Legrand
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France
| | - Roy Weinstain
- Department of Molecular Biology and Ecology of Plants, Tel Aviv University, Tel Aviv, 69978, Israel
| | | | - Salomé Prat
- Centre for Research in Agricultural Genomics, 08193 Cerdanyola, Barcelona, Spain
| | - Patrick Achard
- Institut de biologie moléculaire des plantes, CNRS, Université de Strasbourg, 67084, Strasbourg, France.
| | - Teva Vernoux
- Laboratoire Reproduction et Développement des Plantes, Univ Lyon, ENS de Lyon, CNRS, INRAE, INRIA, 69342, Lyon, France.
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2
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Evans KV, Ransom E, Nayakoti S, Wilding B, Mohd Salleh F, Gržina I, Erber L, Tse C, Hill C, Polanski K, Holland A, Bukhat S, Herbert RJ, de Graaf BHJ, Denby K, Buchanan-Wollaston V, Rogers HJ. Expression of the Arabidopsis redox-related LEA protein, SAG21 is regulated by ERF, NAC and WRKY transcription factors. Sci Rep 2024; 14:7756. [PMID: 38565965 PMCID: PMC10987515 DOI: 10.1038/s41598-024-58161-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2023] [Accepted: 03/26/2024] [Indexed: 04/04/2024] Open
Abstract
SAG21/LEA5 is an unusual late embryogenesis abundant protein in Arabidopsis thaliana, that is primarily mitochondrially located and may be important in regulating translation in both chloroplasts and mitochondria. SAG21 expression is regulated by a plethora of abiotic and biotic stresses and plant growth regulators indicating a complex regulatory network. To identify key transcription factors regulating SAG21 expression, yeast-1-hybrid screens were used to identify transcription factors that bind the 1685 bp upstream of the SAG21 translational start site. Thirty-three transcription factors from nine different families bound to the SAG21 promoter, including members of the ERF, WRKY and NAC families. Key binding sites for both NAC and WRKY transcription factors were tested through site directed mutagenesis indicating the presence of cryptic binding sites for both these transcription factor families. Co-expression in protoplasts confirmed the activation of SAG21 by WRKY63/ABO3, and SAG21 upregulation elicited by oligogalacturonide elicitors was partially dependent on WRKY63, indicating its role in SAG21 pathogen responses. SAG21 upregulation by ethylene was abolished in the erf1 mutant, while wound-induced SAG21 expression was abolished in anac71 mutants, indicating SAG21 expression can be regulated by several distinct transcription factors depending on the stress condition.
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Affiliation(s)
- Kelly V Evans
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Elspeth Ransom
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Swapna Nayakoti
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Ben Wilding
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Faezah Mohd Salleh
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
- Investigative and Forensic Sciences Research Group, Universiti Teknologi Malaysia, 81310, Johor Bahru, Johor, Malaysia
| | - Irena Gržina
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Lieselotte Erber
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Carmen Tse
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Claire Hill
- School of Life Sciences, University of Warwick, Coventry, CV4 7AL, UK
| | | | - Alistair Holland
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Sherien Bukhat
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Robert J Herbert
- School of Science and the Environment, University of Worcester, Henwick Grove, Worcester, WR2 6AJ, UK
| | - Barend H J de Graaf
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK
| | - Katherine Denby
- Department of Biology, Centre for Novel Agricultural Products (CNAP), University of York, Heslington, York, YO10 5DD, UK
| | | | - Hilary J Rogers
- School of Biosciences, Cardiff University, Sir Martin Evans Building, Museum Avenue, Cardiff, CF10 3AT, UK.
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3
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Duan L, Wang F, Shen H, Xie S, Chen X, Xie Q, Li R, Cao A, Li H. Identification, evolution, and expression of GDSL-type Esterase/Lipase (GELP) gene family in three cotton species: a bioinformatic analysis. BMC Genomics 2023; 24:795. [PMID: 38129780 PMCID: PMC10734139 DOI: 10.1186/s12864-023-09717-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2023] [Accepted: 10/04/2023] [Indexed: 12/23/2023] Open
Abstract
BACKGROUND GDSL esterase/lipases (GELPs) play important roles in plant growth, development, and response to biotic and abiotic stresses. Presently, an extensive and in-depth analysis of GELP family genes in cotton is still not clear enough, which greatly limits the further understanding of cotton GELP function and regulatory mechanism. RESULTS A total of 389 GELP family genes were identified in three cotton species of Gossypium hirsutum (193), G. arboreum (97), and G. raimondii (99). These GELPs could be classified into three groups and eight subgroups, with the GELPs in same group to have similar gene structures and conserved motifs. Evolutionary event analysis showed that the GELP family genes tend to be diversified at the spatial dimension and certain conservative at the time dimension, with a trend of potential continuous expansion in the future. The orthologous or paralogous GELPs among different genomes/subgenomes indicated the inheritance from genome-wide duplication during polyploidization, and the paralogous GELPs were derived from chromosomal segment duplication or tandem replication. GELP genes in the A/D subgenome underwent at least three large-scale replication events in the evolutionary process during the period of 0.6-3.2 MYA, with two large-scale evolutionary events between 0.6-1.8 MYA that were associated with tetraploidization, and the large-scale duplication between 2.6-9.1 MYA that occurred during diploidization. The cotton GELPs indicated diverse expression patterns in tissue development, ovule and fiber growth, and in response to biotic and abiotic stresses, combining the existing cis-elements in the promoter regions, suggesting the GELPs involvements of functions to be diversification and of the mechanisms to be a hormone-mediated manner. CONCLUSIONS Our results provide a systematic and comprehensive understanding the function and regulatory mechanism of cotton GELP family, and offer an effective reference for in-depth genetic improvement utilization of cotton GELPs.
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Affiliation(s)
- Lisheng Duan
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Fei Wang
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
| | - Haitao Shen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Shuangquan Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Xifeng Chen
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Quanliang Xie
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Rong Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Aiping Cao
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China
| | - Hongbin Li
- Key Laboratory of Xinjiang Phytomedicine Resource and Utilization of Ministry of Education, Key Laboratory of Oasis Town and Mountain-Basin System Ecology of Xinjiang Production and Construction Corps, College of Life Sciences, Shihezi University, Shihezi, 832003, China.
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4
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Lu H, Wang F, Wang Y, Lin R, Wang Z, Mao C. Molecular mechanisms and genetic improvement of low-phosphorus tolerance in rice. PLANT, CELL & ENVIRONMENT 2023; 46:1104-1119. [PMID: 36208118 DOI: 10.1111/pce.14457] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/20/2022] [Revised: 09/01/2022] [Accepted: 10/03/2022] [Indexed: 06/16/2023]
Abstract
Phosphorus (P) is a macronutrient required for plant growth and reproduction. Orthophosphate (Pi), the preferred P form for plant uptake, is easily fixed in the soil, making it unavailable to plants. Limited phosphate rock resources, low phosphate fertilizer use efficiency and high demands for green agriculture production make it important to clarify the molecular mechanisms underlying plant responses to P deficiency and to improve plant phosphate efficiency in crops. Over the past 20 years, tremendous progress has been made in understanding the regulatory mechanisms of the plant P starvation response. Here, we systematically review current research on the mechanisms of Pi acquisition, transport and distribution from the rhizosphere to the shoot; Pi redistribution and reuse during reproductive growth; and the molecular mechanisms of arbuscular mycorrhizal symbiosis in rice (Oryza sativa L.) under Pi deficiency. Furthermore, we discuss several strategies for boosting P utilization efficiency and yield in rice.
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Affiliation(s)
- Hong Lu
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Fei Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Yan Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Rongbin Lin
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Zhiye Wang
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chuanzao Mao
- Hainan Institute of Zhejiang University, Yazhou Bay Science and Technology City, Yazhou District, Sanya, Hainan, China
- State Key Laboratory of Plant Physiology and Biochemistry, College of Life Sciences, Zhejiang University, Hangzhou, China
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5
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Sedaghatmehr M, Stüwe B, Mueller-Roeber B, Balazadeh S. Heat shock factor HSFA2 fine-tunes resetting of thermomemory via plastidic metalloprotease FtsH6. JOURNAL OF EXPERIMENTAL BOTANY 2022; 73:6394-6404. [PMID: 35705109 PMCID: PMC9578354 DOI: 10.1093/jxb/erac257] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/14/2022] [Indexed: 06/01/2023]
Abstract
Plants 'memorize' stressful events and protect themselves from future, often more severe, stresses. To maximize growth after stress, plants 'reset' or 'forget' memories of stressful situations, which requires an intricate balance between stress memory formation and the degree of forgetfulness. HEAT SHOCK PROTEIN 21 (HSP21) encodes a small heat shock protein in plastids of Arabidopsis thaliana. HSP21 functions as a key component of thermomemory, which requires a sustained elevated level of HSP21 during recovery from heat stress. A heat-induced metalloprotease, filamentation temperature-sensitive H6 (FtsH6), degrades HSP21 to its pre-stress abundance, thereby resetting memory during the recovery phase. The transcription factor heat shock factor A2 (HSFA2) activates downstream genes essential for mounting thermomemory, acting as a positive regulator in the process. Here, using a yeast one-hybrid screen, we identify HSFA2 as an upstream transactivator of the resetting element FtsH6. Constitutive and inducible overexpression of HSFA2 increases expression of FtsH6, whereas it is drastically reduced in the hsfa2 knockout mutant. Chromatin immunoprecipitation reveals in planta binding of HSFA2 to the FtsH6 promoter. Importantly, overexpression of HSFA2 improves thermomemory more profoundly in ftsh6 than wild-type plants. Thus, by activating both memory-supporting and memory-resetting genes, HSFA2 acts as a cellular homeostasis factor during thermomemory.
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Affiliation(s)
| | - Benno Stüwe
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
| | - Bernd Mueller-Roeber
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg, Potsdam-Golm, Germany
- Institute of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Straße, Haus, Potsdam-Golm, Germany
- Center of Plant Systems Biology and Biotechnology (CPSBB), Plovdiv, Bulgaria
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6
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Rakpenthai A, Apodiakou A, Whitcomb SJ, Hoefgen R. In silico analysis of cis-elements and identification of transcription factors putatively involved in the regulation of the OAS cluster genes SDI1 and SDI2. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2022; 110:1286-1304. [PMID: 35315155 DOI: 10.1111/tpj.15735] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/30/2021] [Revised: 02/09/2022] [Accepted: 03/01/2022] [Indexed: 06/14/2023]
Abstract
Arabidopsis thaliana sulfur deficiency-induced 1 and sulfur deficiency-induced 2 (SDI1 and SDI2) are involved in partitioning sulfur among metabolite pools during sulfur deficiency, and their transcript levels strongly increase in this condition. However, little is currently known about the cis- and trans-factors that regulate SDI expression. We aimed at identifying DNA sequence elements (cis-elements) and transcription factors (TFs) involved in regulating expression of the SDI genes. We performed in silico analysis of their promoter sequences cataloging known cis-elements and identifying conserved sequence motifs. We screened by yeast-one-hybrid an arrayed library of Arabidopsis TFs for binding to the SDI1 and SDI2 promoters. In total, 14 candidate TFs were identified. Direct association between particular cis-elements in the proximal SDI promoter regions and specific TFs was established via electrophoretic mobility shift assays: sulfur limitation 1 (SLIM1) was shown to bind SURE cis-element(s), the basic domain/leucine zipper (bZIP) core cis-element was shown to be important for HY5-homolog (HYH) binding, and G-box binding factor 1 (GBF1) was shown to bind the E box. Functional analysis of GBF1 and HYH using mutant and over-expressing lines indicated that these TFs promote a higher transcript level of SDI1 in vivo. Additionally, we performed a meta-analysis of expression changes of the 14 TF candidates in a variety of conditions that alter SDI expression. The presented results expand our understanding of sulfur pool regulation by SDI genes.
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Affiliation(s)
- Apidet Rakpenthai
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Anastasia Apodiakou
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Sarah J Whitcomb
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
| | - Rainer Hoefgen
- Max Planck Institute of Molecular Plant Physiology, Am Mühlenberg 1, 14476, Potsdam-Golm, Germany
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The BES1/BZR1-family transcription factor MpBES1 regulates cell division and differentiation in Marchantia polymorpha. Curr Biol 2021; 31:4860-4869.e8. [PMID: 34529936 DOI: 10.1016/j.cub.2021.08.050] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2021] [Revised: 05/24/2021] [Accepted: 08/18/2021] [Indexed: 11/24/2022]
Abstract
Brassinosteroids (BRs) play essential roles in growth and development in seed plants;1 disturbances in BR homeostasis lead to altered mitotic activity in meristems2,3 and organ boundaries4,5 and to changes in meristem determinacy.6 An intricate signaling cascade linking the perception of BRs at the plasma membrane to the regulation of master transcriptional regulators belonging to the BEH, for BES1 homologues, family7 has been described in great detail in model angiosperms. Homologs of these transcription factors are present in streptophyte algae and in land plant lineages where BR signaling or function is absent or has not yet been characterized. The genome of the bryophyte Marchantia polymorpha does not encode for BR receptors but includes one close ortholog of Arabidopsis thaliana BRI1-EMS-SUPPRESSOR 1 (AtBES1)8 and Arabidopsis thaliana BRASSINAZOLE-RESISTANT 1 (AtBZR1),9 MpBES1. Altered levels of MpBES1 severely compromised cell division and differentiation, resulting in stunted thalli that failed to differentiate adult tissues and reproductive organs. The transcriptome of Mpbes1 knockout plants revealed a significant overlap with homologous functions controlled by AtBES1 and AtBZR1, suggesting that members of this gene family share a subset of common targets. Indeed, MpBES1 behaved as a gain-of-function substitute of AtBES1/AtBZR1 when expressed in Arabidopsis, probably because it mediates conserved functions but evades the regulatory mechanisms that native counterparts are subject to. Our results show that this family of transcription factors plays an ancestral role in the control of cell division and differentiation in plants and that BR signaling likely co-opted this function and imposed additional regulatory checkpoints upon it.
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8
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Li GZ, Zheng YX, Chen SJ, Liu J, Wang PF, Wang YH, Guo TC, Kang GZ. TaWRKY74 participates copper tolerance through regulation of TaGST1 expression and GSH content in wheat. ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY 2021; 221:112469. [PMID: 34198190 DOI: 10.1016/j.ecoenv.2021.112469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Revised: 06/22/2021] [Accepted: 06/24/2021] [Indexed: 06/13/2023]
Abstract
Glutathione S-transferase (GST) is the key enzyme in glutathione (GSH) synthesis, and plays a crucial role in copper (Cu) detoxification. Nonetheless, its regulatory mechanisms remain largely unclear. In this study, we identified a Cu-induced glutathione S-transferase 1 (TaGST1) gene in wheat. Yeast one-hybrid (Y1H) screened out TaWRKY74, which was one member from the WRKY transcription factor family. The bindings between TaGST1 promoter and TaWRKY74 were further verified by using another Y1H and luciferase assays. Expression of TaWRKY74 was induced more than 30-folds by Cu stress. Functions of TaWRKY74 were tested by using transiently silence methods. In transiently TaWRKY74-silenced wheat plants, TaWRKY74 and TaGST1 expression, GST activity, and GSH content was significantly inhibited by 25.68%, 19.88%, 27.66%, and 12.68% in shoots, and 53.81%, 52.11%, 23.47%, and 17.11% in roots, respectively. However, contents of hydrogen peroxide, malondialdehyde, or Cu were significantly increased by 2.58%, 12.45%, or 37.74% in shoots, and 25.24%, 53.84%, and 103.99% in roots, respectively. Notably, exogenous application of GSH reversed the adverse effects of transiently TaWRKY74-silenced wheat plants during Cu stress. Taken together, our results suggesting that TaWRKY74 regulated TaGST1 expression and affected GSH accumulation under Cu stress, and could be useful to ameliorate Cu toxicity for crop food safety.
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Affiliation(s)
- Ge-Zi Li
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China; National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, China
| | - Yong-Xing Zheng
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Shi-Juan Chen
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Jin Liu
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Peng-Fei Wang
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Yong-Hua Wang
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Tian-Cai Guo
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China
| | - Guo-Zhang Kang
- National Engineering Research Center for Wheat, Henan Agricultural University, Zhengzhou 450046, China; National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, Zhengzhou 450046, China.
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9
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O’Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 PMCID: PMC8154064 DOI: 10.1093/plphys/kiab047] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/14/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O’Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
- Author for communication:
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10
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Ruffel S, Chaput V, Przybyla-Toscano J, Fayos I, Ibarra C, Moyano T, Fizames C, Tillard P, O'Brien JA, Gutiérrez RA, Gojon A, Lejay L. Genome-wide analysis in response to nitrogen and carbon identifies regulators for root AtNRT2 transporters. PLANT PHYSIOLOGY 2021; 186:696-714. [PMID: 33582801 DOI: 10.1101/822197] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Accepted: 01/19/2021] [Indexed: 05/26/2023]
Abstract
In Arabidopsis (Arabidopsis thaliana), the High-Affinity Transport System (HATS) for root nitrate (NO3-) uptake depends mainly on four NRT2 NO3- transporters, namely NRT2.1, NRT2.2, NRT2.4, and NRT2.5. The HATS is the target of many regulations to coordinate nitrogen (N) acquisition with the N status of the plant and with carbon (C) assimilation through photosynthesis. At the molecular level, C and N signaling pathways control gene expression of the NRT2 transporters. Although several regulators of these transporters have been identified in response to either N or C signals, the response of NRT2 gene expression to the interaction of these signals has never been specifically investigated, and the underlying molecular mechanisms remain largely unknown. To address this question we used an original systems biology approach to model a regulatory gene network targeting NRT2.1, NRT2.2, NRT2.4, and NRT2.5 in response to N/C signals. Our systems analysis of the data identified three transcription factors, TGA3, MYC1, and bHLH093. Functional analysis of mutants combined with yeast one-hybrid experiments confirmed that all three transcription factors are regulators of NRT2.4 or NRT2.5 in response to N or C signals. These results reveal a role for TGA3, MYC1, and bHLH093 in controlling the expression of root NRT2 transporter genes.
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Affiliation(s)
- Sandrine Ruffel
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Valentin Chaput
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | | | - Ian Fayos
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Catalina Ibarra
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Tomas Moyano
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Cécile Fizames
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Pascal Tillard
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Jose Antonio O'Brien
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Universidad Católica de Chile, Santiago 8331150, Chile
- Departamento de Fruticultura y Enología, Facultad de Agronomía e Ingeniería Forestal. Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Rodrigo A Gutiérrez
- Departamento de Genética Molecular y Microbiología, Facultad de Ciencias Biológicas, Millennium Institute for Integrative Biology, FONDAP Center for Genome Regulation, Pontificia Universidad Católica de Chile, Santiago 8331150, Chile
| | - Alain Gojon
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
| | - Laurence Lejay
- BPMP, University of Montpellier, CNRS, INRAE, Institut Agro, Montpellier 34060, France
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11
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Jacob P, Brisou G, Dalmais M, Thévenin J, van der Wal F, Latrasse D, Suresh Devani R, Benhamed M, Dubreucq B, Boualem A, Lepiniec L, Immink RGH, Hirt H, Bendahmane A. The Seed Development Factors TT2 and MYB5 Regulate Heat Stress Response in Arabidopsis. Genes (Basel) 2021; 12:genes12050746. [PMID: 34063415 PMCID: PMC8156827 DOI: 10.3390/genes12050746] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2021] [Revised: 04/30/2021] [Accepted: 05/10/2021] [Indexed: 11/16/2022] Open
Abstract
HEAT SHOCK FACTOR A2 (HSFA2) is a regulator of multiple environmental stress responses required for stress acclimation. We analyzed HSFA2 co-regulated genes and identified 43 genes strongly co-regulated with HSFA2 during multiple stresses. Motif enrichment analysis revealed an over-representation of the site II element (SIIE) in the promoters of these genes. In a yeast 1-hybrid screen with the SIIE, we identified the closely related R2R3-MYB transcription factors TT2 and MYB5. We found overexpression of MYB5 or TT2 rendered plants heat stress tolerant. In contrast, tt2, myb5, and tt2/myb5 loss of function mutants showed heat stress hypersensitivity. Transient expression assays confirmed that MYB5 and TT2 can regulate the HSFA2 promoter together with the other members of the MBW complex, TT8 and TRANSPARENT TESTA GLABRA 1 (TTG1) and that the SIIE was involved in this regulation. Transcriptomic analysis revealed that TT2/MYB5 target promoters were enriched in SIIE. Overall, we report a new function of TT2 and MYB5 in stress resistance and a role in SIIE-mediated HSFA2 regulation.
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Affiliation(s)
- Pierre Jacob
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Gwilherm Brisou
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Marion Dalmais
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Johanne Thévenin
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Froukje van der Wal
- Bioscience and Laboratory of Molecular Biology, Wageningen University and Research, 6708PB Wageningen, The Netherlands; (F.v.d.W.); (R.G.H.I.)
| | - David Latrasse
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Ravi Suresh Devani
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Moussa Benhamed
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Adnane Boualem
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
| | - Loic Lepiniec
- Institut Jean-Pierre Bourgin, INRAE, AgroParisTech, Université Paris-Saclay, 78000 Versailles, France; (J.T.); (B.D.); (L.L.)
| | - Richard G. H. Immink
- Bioscience and Laboratory of Molecular Biology, Wageningen University and Research, 6708PB Wageningen, The Netherlands; (F.v.d.W.); (R.G.H.I.)
| | - Heribert Hirt
- Darwin21, Biological and Environmental Science and Engineering Division (BESE), King Abdullah University of Science and Technology, Thuwal 23955-6900, Saudi Arabia;
- Max Perutz Laboratories, University of Vienna, 1030 Vienna, Austria
| | - Abdelhafid Bendahmane
- Institute of Plant Sciences Paris-Saclay, Université Paris-Saclay, Univ. Evry, INRAE, CNRS, 91405 Orsay, France; (P.J.); (G.B.); (M.D.); (D.L.); (R.S.D.); (M.B.); (A.B.)
- Correspondence:
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12
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A Molecular Signal Integration Network Underpinning Arabidopsis Seed Germination. Curr Biol 2020; 30:3703-3712.e4. [PMID: 32763174 PMCID: PMC7544511 DOI: 10.1016/j.cub.2020.07.012] [Citation(s) in RCA: 41] [Impact Index Per Article: 10.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2020] [Revised: 06/22/2020] [Accepted: 07/02/2020] [Indexed: 12/20/2022]
Abstract
Seed dormancy is an adaptive trait defining where and when plants are established. Diverse signals from the environment are used to decide when to initiate seed germination, a process driven by the expansion of cells within the embryo. How these signals are integrated and transduced into the biomechanical changes that drive embryo growth remains poorly understood. Using Arabidopsis seeds, we demonstrate that cell-wall-loosening EXPANSIN (EXPA) genes promote gibberellic acid (GA)-mediated germination, identifying EXPAs as downstream molecular targets of this developmental phase transition. Molecular interaction screening identified transcription factors (TFs) that bind to both EXPA promoter fragments and DELLA GA-response regulators. A subset of these TFs is targeted each by nitric oxide (NO) and the phytochrome-interacting TF PIL5. This molecular interaction network therefore directly links the perception of an external environmental signal (light) and internal hormonal signals (GA and NO) with downstream germination-driving EXPA gene expression. Experimental validation of this network established that many of these TFs mediate GA-regulated germination, including TCP14/15, RAP2.2/2.3/2.12, and ZML1. The reduced germination phenotype of the tcp14 tcp15 mutant seed was partially rescued through ectopic expression of their direct target EXPA9. The GA-mediated control of germination by TCP14/15 is regulated through EXPA-mediated control of cell wall loosening, providing a mechanistic explanation for this phenotype and a previously undescribed role for TCPs in the control of cell expansion. This network reveals the paths of signal integration that culminate in seed germination and provides a resource to uncover links between the genetic and biomechanical bases of plant growth. The network linking integration of environmental signals to seed growth is mapped EXPANSIN gene expression is redundantly regulated and promotes GA-mediated germination The TCP14 transcription factor directly regulates EXPANSIN9 expression The tcp14/15 germination phenotype is complemented by EXPANSIN9 expression
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13
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Yang Y, Zhang L, Chen P, Liang T, Li X, Liu H. UV-B photoreceptor UVR8 interacts with MYB73/MYB77 to regulate auxin responses and lateral root development. EMBO J 2020; 39:e101928. [PMID: 31777974 PMCID: PMC6960441 DOI: 10.15252/embj.2019101928] [Citation(s) in RCA: 68] [Impact Index Per Article: 17.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/13/2019] [Revised: 10/21/2019] [Accepted: 10/24/2019] [Indexed: 12/31/2022] Open
Abstract
The UV-B photoreceptor UVR8 mediates multiple UV-B responses in plants, but the function of UVR8 in regulating root development has not previously been investigated. Here, we show that UV-B light inhibits Arabidopsis lateral root growth in a UVR8-dependent manner. Monomeric UVR8 inhibits auxin responses in a tissue-autonomous manner and thereby regulates lateral root growth. Genome-wide gene expression analysis demonstrated that auxin and UV-B irradiation antagonistically regulate auxin-regulated gene expression. We further show that UVR8 physically interacts with MYB73/MYB77 (MYB DOMAIN PROTEIN 73/77) in a UV-B-dependent manner. UVR8 inhibits lateral root development via regulation of MYB73/MYB77. When activated by UV-B light, UVR8 localizes to the nucleus and inhibits the DNA-binding activities of MYB73/MYB77 and directly represses the transcription of their target auxin-responsive genes. Our results demonstrate that UV-B light and UVR8 are critical for both shoot morphogenesis and root development. The UV-B-dependent interaction of UVR8 and MYB73/MYB77 serves as an important module that integrates light and auxin signaling and represents a new UVR8 signaling mechanism in plants.
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Affiliation(s)
- Yu Yang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesShanghaiChina
| | - Libo Zhang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
| | - Ping Chen
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
- The Joint Center for Infection and Immunity between Guangzhou Institute of PediatricsGuangzhou Women and Children's Medical CenterGuangzhouChina
| | - Tong Liang
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
- University of Chinese Academy of SciencesShanghaiChina
| | - Xuan Li
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics (NKLPMG)CAS Center for Excellence in Molecular Plant SciencesInstitute of Plant Physiology and Ecology (SIPPE)Chinese Academy of SciencesShanghaiChina
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14
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Dong J, Zheng Y, Fu Y, Wang J, Yuan S, Wang Y, Zhu Q, Ou X, Li G, Kang G. PDIL1-2 can indirectly and negatively regulate expression of the AGPL1 gene in bread wheat. Biol Res 2019; 52:56. [PMID: 31699158 PMCID: PMC6839113 DOI: 10.1186/s40659-019-0263-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2018] [Accepted: 10/25/2019] [Indexed: 12/02/2022] Open
Abstract
Background ADP-glucose pyrophosphorylase (AGPase), the key enzyme in plant starch biosynthesis, is a heterotetramer composed of two identical large subunits and two identical small subunits. AGPase has plastidial and cytosolic isoforms in higher plants, whereas it is mainly detected in the cytosol of grain endosperms in cereal crops. Our previous results have shown that the expression of the TaAGPL1 gene, encoding the cytosolic large subunit of wheat AGPase, temporally coincides with the rate of starch accumulation and that its overexpression dramatically increases wheat AGPase activity and the rate of starch accumulation, suggesting an important role. Methods In this study, we performed yeast one-hybrid screening using the promoter of the TaAGPL1 gene as bait and a wheat grain cDNA library as prey to screen out the upstream regulators of TaAGPL1 gene. And the barley stripe mosaic virus-induced gene-silencing (BSMV-VIGS) method was used to verify the functional characterization of the identified regulators in starch biosynthesis. Results Disulfide isomerase 1-2 protein (TaPDIL1-2) was screened out, and its binding to the TaAGPL1-1D promoter was further verified using another yeast one-hybrid screen. Transiently silenced wheat plants of the TaPDIL1-2 gene were obtained by using BSMV-VIGS method under field conditions. In grains of BSMV-VIGS-TaPDIL1-2-silenced wheat plants, the TaAGPL1 gene transcription levels, grain starch contents, and 1000-kernel weight also significantly increased. Conclusions As important chaperones involved in oxidative protein folding, PDIL proteins have been reported to form hetero-dimers with some transcription factors, and thus, our results suggested that TaPDIL1-2 protein could indirectly and negatively regulate the expression of the TaAGPL1 gene and function in starch biosynthesis.
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Affiliation(s)
- Jie Dong
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China
| | - Yongxing Zheng
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Yihan Fu
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Jinxi Wang
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China
| | - Shasha Yuan
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Yonghua Wang
- The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China
| | - Qidi Zhu
- The School of Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Xingqi Ou
- The School of Science and Technology, Henan Institute of Science and Technology, Xinxiang, 453003, China
| | - Gezi Li
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China.
| | - Guozhang Kang
- The National Key Laboratory of Wheat and Maize Crop Science, Henan Agricultural University, #15 Longzihu College District, Zhengzhou, 450046, China. .,The National Engineering Research Center for Wheat, Henan Agricultural University, #63 Nongye Road, Zhengzhou, 450046, Henan, China.
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15
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Boter M, Calleja-Cabrera J, Carrera-Castaño G, Wagner G, Hatzig SV, Snowdon RJ, Legoahec L, Bianchetti G, Bouchereau A, Nesi N, Pernas M, Oñate-Sánchez L. An Integrative Approach to Analyze Seed Germination in Brassica napus. FRONTIERS IN PLANT SCIENCE 2019; 10:1342. [PMID: 31708951 PMCID: PMC6824160 DOI: 10.3389/fpls.2019.01342] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/12/2019] [Accepted: 09/26/2019] [Indexed: 05/23/2023]
Abstract
Seed germination is a complex trait determined by the interaction of hormonal, metabolic, genetic, and environmental components. Variability of this trait in crops has a big impact on seedling establishment and yield in the field. Classical studies of this trait in crops have focused mainly on the analyses of one level of regulation in the cascade of events leading to seed germination. We have carried out an integrative and extensive approach to deepen our understanding of seed germination in Brassica napus by generating transcriptomic, metabolic, and hormonal data at different stages upon seed imbibition. Deep phenotyping of different seed germination-associated traits in six winter-type B. napus accessions has revealed that seed germination kinetics, in particular seed germination speed, are major contributors to the variability of this trait. Metabolic profiling of these accessions has allowed us to describe a common pattern of metabolic change and to identify the levels of malate and aspartate metabolites as putative metabolic markers to estimate germination performance. Additionally, analysis of seed content of different hormones suggests that hormonal balance between ABA, GA, and IAA at crucial time points during this process might underlie seed germination differences in these accessions. In this study, we have also defined the major transcriptome changes accompanying the germination process in B. napus. Furthermore, we have observed that earlier activation of key germination regulatory genes seems to generate the differences in germination speed observed between accessions in B. napus. Finally, we have found that protein-protein interactions between some of these key regulator are conserved in B. napus, suggesting a shared regulatory network with other plant species. Altogether, our results provide a comprehensive and detailed picture of seed germination dynamics in oilseed rape. This new framework will be extremely valuable not only to evaluate germination performance of B. napus accessions but also to identify key targets for crop improvement in this important process.
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Affiliation(s)
- Marta Boter
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Julián Calleja-Cabrera
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Gerardo Carrera-Castaño
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Geoffrey Wagner
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Sarah Vanessa Hatzig
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Rod J. Snowdon
- Department of Plant Breeding, Justus Liebig University Giessen, Giessen, Germany
| | - Laurie Legoahec
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Grégoire Bianchetti
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Alain Bouchereau
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Nathalie Nesi
- Joint Laboratory for Genetics, Institute for Genetics, Environment and Plant Protection (IGEPP), Le Rheu, France
| | - Mónica Pernas
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, (Universidad Politécnica de Madrid –Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria), Madrid, Spain
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16
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Screening Arrayed Libraries with DNA and Protein Baits to Identify Interacting Proteins. Methods Mol Biol 2019; 1794:131-149. [PMID: 29855955 DOI: 10.1007/978-1-4939-7871-7_9] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/25/2023]
Abstract
Molecular interactions are an integral part of the regulatory mechanisms controlling gene expression. The yeast one- and two-hybrid systems (Y1H/Y2H) have been widely used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). The development of efficient cloning systems have promoted the generation of large open reading frame (ORF) clone collections (libraries) for several organisms. Functional analyses of such large collections require the establishment of adequate protocols. Here, we describe a simple straightforward procedure for high-throughput screenings of arrayed libraries with DNA or protein baits that can be carried out by one person with minimal labor and not requiring robotics. The protocol can also be scaled up or down and is compatible with several library formats. Procedures to make yeast stocks for long-term storage (tube and microplate formats) are also provided.
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17
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Roscoe TJ, Vaissayre V, Paszkiewicz G, Clavijo F, Kelemen Z, Michaud C, Lepiniec LC, Dubreucq B, Zhou DX, Devic M. Regulation of FUSCA3 Expression During Seed Development in Arabidopsis. PLANT & CELL PHYSIOLOGY 2019; 60:476-487. [PMID: 30462310 DOI: 10.1093/pcp/pcy224] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2018] [Accepted: 11/18/2018] [Indexed: 06/09/2023]
Abstract
FUSCA3 (FUS3) is a master regulator of seed development important in establishing and maintaining embryonic identity whose expression is tightly regulated at genetic and epigenetic levels. Despite this prominent role, the control of FUS3 expression remains poorly understood. Promoter and functional complementation analyses provided insight into the regulation of FUS3. W-boxes present in the promoter proximal to the start of transcription are recognized by WRKY type-1 factors which are necessary for the activation of FUS3 expression. The RY motif, the binding site of B3 factors, is important for the activation of FUS3 in the embryo proper but not in the suspensor. The loss of a negative regulatory sequence (NRS) leads to preferential expression of FUS3 in the vasculature of vegetative tissues. Since the NRS includes the RY motif, mechanisms of activation and repression target adjacent or overlapping regions. These findings discriminate the regulation of FUS3 from that of LEAFY COTYLEDON2 by the control exerted by WRKY factors and by the presence of the RY motif, yet also confirm conservation of certain regulatory elements, thereby implicating potential regulation by BASIC PENTACYSTEINE (BPC) factors and POLYCOMB REPRESSIVE COMPLEX2 (PRC2).
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Affiliation(s)
| | - Virginie Vaissayre
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Gael Paszkiewicz
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Fernando Clavijo
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Zsolt Kelemen
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Caroline Michaud
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
| | - Loï C Lepiniec
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Bertrand Dubreucq
- Institut Jean-Pierre Bourgin, INRA, AgroParisTech, CNRS, Universit� Paris-Saclay, Versailles Cedex, France
| | - Dao-Xiu Zhou
- Universit� Paris-sud 11, Institut de Biologie des Plantes, CNRS, UMR8618, Saclay Plant Science, Orsay, France
| | - Martine Devic
- DIADE, ERL 5300 CNRS-IRD, Universit� de Montpellier, Montpellier, France
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18
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Sánchez-Montesino R, Bouza-Morcillo L, Marquez J, Ghita M, Duran-Nebreda S, Gómez L, Holdsworth MJ, Bassel G, Oñate-Sánchez L. A Regulatory Module Controlling GA-Mediated Endosperm Cell Expansion Is Critical for Seed Germination in Arabidopsis. MOLECULAR PLANT 2019; 12:71-85. [PMID: 30419294 PMCID: PMC7086157 DOI: 10.1016/j.molp.2018.10.009] [Citation(s) in RCA: 48] [Impact Index Per Article: 9.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/31/2018] [Revised: 10/30/2018] [Accepted: 10/31/2018] [Indexed: 05/19/2023]
Abstract
A key component of seed germination is the interplay of mechanical forces governing embryo growth and the surrounding restraining endosperm tissue. Endosperm cell separation is therefore thought to play a critical role in the control of this developmental transition. Here we demonstrate that in Arabidopsis thaliana seeds, endosperm cell expansion is a key component of germination. Endosperm cells expand to accommodate embryo growth prior to germination. We show that this is an actively regulated process supported by spatiotemporal control of the cell expansion gene EXPANSIN 2 (EXPA2). The NAC transcription factors NAC25 and NAC1L were identified as upstream regulators of EXPA2 expression, gibberellin-mediated endosperm expansion, and seed germination. The DELLA protein RGL2 repressed activation of the EXPA2 promoter by NAC25/NAC1L. Taken together, our findings uncover a key role of the GA/DELLA-NAC25/NAC1L-EXPA2 network in regulating endosperm cell expansion to control the seed-to-seedling transition.
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Affiliation(s)
- Rocío Sánchez-Montesino
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Laura Bouza-Morcillo
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain
| | - Julietta Marquez
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | - Melania Ghita
- School of Biosciences, University of Nottingham, Loughborough LE12 5RD, UK
| | | | - Luis Gómez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain; Departamento de Sistemas y Recursos Naturales, E.T.S.I. Montes, Forestal y del Medio Natural, Campus de Moncloa, 28040 Madrid, Spain
| | | | - George Bassel
- School of Biosciences, University of Birmingham, Birmingham B15 2TT, UK.
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, Universidad Politécnica de Madrid - Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Campus de Montegancedo, Pozuelo de Alarcón, Madrid 28223, Spain.
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19
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Herrera-Ubaldo H, Lozano-Sotomayor P, Ezquer I, Di Marzo M, Chávez Montes RA, Gómez-Felipe A, Pablo-Villa J, Diaz-Ramirez D, Ballester P, Ferrándiz C, Sagasser M, Colombo L, Marsch-Martínez N, de Folter S. New roles of NO TRANSMITTING TRACT and SEEDSTICK during medial domain development in Arabidopsis fruits. Development 2019; 146:dev.172395. [PMID: 30538100 DOI: 10.1242/dev.172395] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Accepted: 12/03/2018] [Indexed: 01/11/2023]
Abstract
The gynoecium, the female reproductive part of the flower, is key for plant sexual reproduction. During its development, inner tissues such as the septum and the transmitting tract tissue, important for pollen germination and guidance, are formed. In Arabidopsis, several transcription factors are known to be involved in the development of these tissues. One of them is NO TRANSMITTING TRACT (NTT), essential for transmitting tract formation. We found that the NTT protein can interact with several gynoecium-related transcription factors, including several MADS-box proteins, such as SEEDSTICK (STK), known to specify ovule identity. Evidence suggests that NTT and STK control enzyme and transporter-encoding genes involved in cell wall polysaccharide and lipid distribution in gynoecial medial domain cells. The results indicate that the simultaneous loss of NTT and STK activity affects polysaccharide and lipid deposition and septum fusion, and delays entry of septum cells to their normal degradation program. Furthermore, we identified KAWAK, a direct target of NTT and STK, which is required for the correct formation of fruits in Arabidopsis These findings position NTT and STK as important factors in determining reproductive competence.
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Affiliation(s)
- Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Ignacio Ezquer
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Maurizio Di Marzo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Ricardo Aarón Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Andrea Gómez-Felipe
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV Universidad Politécnica de Valencia, 46022, Spain
| | - Martin Sagasser
- Bielefeld University, Faculty of Biology, Chair of Genetics and Genomics of Plants, Bielefeld 33615, Germany
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan 20133, Italy
| | - Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Unidad Irapuato, CINVESTAV-IPN, Irapuato 36824, Guanajuato, México
| | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato 36824, Guanajuato, México
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20
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Lepiniec L, Devic M, Roscoe TJ, Bouyer D, Zhou DX, Boulard C, Baud S, Dubreucq B. Molecular and epigenetic regulations and functions of the LAFL transcriptional regulators that control seed development. PLANT REPRODUCTION 2018; 31:291-307. [PMID: 29797091 DOI: 10.1007/s00497-018-0337-2] [Citation(s) in RCA: 55] [Impact Index Per Article: 9.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Accepted: 05/10/2018] [Indexed: 05/20/2023]
Abstract
The LAFL (i.e. LEC1, ABI3, FUS3, and LEC2) master transcriptional regulators interact to form different complexes that induce embryo development and maturation, and inhibit seed germination and vegetative growth in Arabidopsis. Orthologous genes involved in similar regulatory processes have been described in various angiosperms including important crop species. Consistent with a prominent role of the LAFL regulators in triggering and maintaining embryonic cell fate, their expression appears finely tuned in different tissues during seed development and tightly repressed in vegetative tissues by a surprisingly high number of genetic and epigenetic factors. Partial functional redundancies and intricate feedback regulations of the LAFL have hampered the elucidation of the underpinning molecular mechanisms. Nevertheless, genetic, genomic, cellular, molecular, and biochemical analyses implemented during the last years have greatly improved our knowledge of the LALF network. Here we summarize and discuss recent progress, together with current issues required to gain a comprehensive insight into the network, including the emerging function of LEC1 and possibly LEC2 as pioneer transcription factors.
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Affiliation(s)
- L Lepiniec
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France.
| | - M Devic
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - T J Roscoe
- Régulations Epigénétiques et Développement de la Graine, ERL 5300 CNRS-IRD UMR DIADE, IRD centre de Montpellier, 911 Avenue Agropolis, BP 64501, 34394, Montpellier, France
- Laboratoire d'Océanographie Microbienne, Observatoire Océanologique, Sorbonne Universités, Université Pierre et Marie Curie (Paris 06) & Centre National pour la Recherche Scientifique CNRS UMR 7621, 66650, Banyuls-sur-Mer, France
| | - D Bouyer
- Institut de Biologie de l'ENS, CNRS UMR8197, Ecole Normale Supérieure, 46 rue d'Ulm, 75230, Paris Cedex 05, France
| | - D-X Zhou
- Institute of Plant Sciences Paris-Saclay (IPS2), Université Paris Sud 11, Université Paris-Saclay, 91405, Orsay, France
| | - C Boulard
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - S Baud
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
| | - B Dubreucq
- IJPB (Institut Jean-Pierre Bourgin), INRA, AgroParisTech, CNRS, Université Paris-Saclay, RD10, 78026, Versailles, France
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21
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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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22
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Yang Y, Liang T, Zhang L, Shao K, Gu X, Shang R, Shi N, Li X, Zhang P, Liu H. UVR8 interacts with WRKY36 to regulate HY5 transcription and hypocotyl elongation in Arabidopsis. NATURE PLANTS 2018; 4:98-107. [PMID: 29379156 DOI: 10.1038/s41477-017-0099-0] [Citation(s) in RCA: 120] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/01/2017] [Accepted: 12/27/2017] [Indexed: 05/20/2023]
Abstract
UV RESISTANCE LOCUS 8 (UVR8) is an ultraviolet-B (UVB) radiation photoreceptor that mediates light responses in plants. How plant UVR8 acts in response to UVB light is not well understood. Here, we report the identification and characterization of the Arabidopsis WRKY DNA-BINDING PROTEIN 36 (WRKY36) protein. WRKY36 interacts with UVR8 in yeast and Arabidopsis cells and it promotes hypocotyl elongation by inhibiting HY5 transcription. Inhibition of hypocotyl elongation under UVB requires the inhibition of WRKY36. WRKY36 binds to the W-box motif of the HY5 promoter to inhibit its transcription, while nuclear localized UVR8 directly interacts with WRKY36 to inhibit WRKY36-DNA binding both in vitro and in vivo, leading to the release of inhibition of HY5 transcription. These results indicate that WRKY36 is a negative regulator of HY5 and that UVB represses WRKY36 via UVR8 to promote the transcription of HY5 and photomorphogenesis. The UVR8-WRKY36 interaction in the nucleus represents a novel mechanism of early UVR8 signal transduction in Arabidopsis.
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Affiliation(s)
- Yu Yang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Tong Liang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Libo Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Kai Shao
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Xingxing Gu
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Ruixin Shang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- Shanghai College of Life Science, University of Chinese Academy of Sciences, Shanghai, China
| | - Nan Shi
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Xu Li
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Peng Zhang
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Hongtao Liu
- National Key Laboratory of Plant Molecular Genetics, Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China.
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23
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Sheshadri SA, Nishanth MJ, Harita N, Brindha P, Bindu S. Comparative genome based cis-elements analysis in the 5' upstream and 3' downstream region of cell wall invertase and Phenylalanine ammonia lyase in Nicotiana benthamiana. Comput Biol Chem 2018; 72:181-191. [PMID: 29329783 DOI: 10.1016/j.compbiolchem.2017.11.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2016] [Revised: 10/12/2017] [Accepted: 11/11/2017] [Indexed: 11/18/2022]
Abstract
Plant secondary metabolites are widely used in human disease treatment; though primary metabolism provides precursors for secondary metabolism, not much has been studied to unravel the link connecting both the processes. Most common form of gene regulation interconnecting diverse metabolism occurs at the transcriptional and/or posttranscriptional level mediated by regulatory cis-elements. The present study aims at understanding the common cis-elements network connecting the major primary metabolic enzyme, cell wall invertase (CWIN) and secondary metabolism genes in Nicotiana benthamiana (N. benthamiana). The CWIN and thirty one other gene sequences were extracted from N. benthamiana genome, followed by cis-element analysis of their 5' upstream and 3' downstream region using different programs (Genomatix software suite; PLACE and PlantCARe). Comparative cis-element analysis of CWIN (N. benthamiana and other plant species) and other primary, secondary metabolism and transcription factor genes (N. benthamiana) revealed the occurrence of common stress associated cis-elements. Predominantly, AHBP, L1BX, MYBL, MADS, MYBS, GTBX, DOFF and CCAF were found in the 5' upstream region of all genes, whereas AHBP, MYBL, L1BX, HEAT, CCAF and KAN1 were largely occurring in the 3' downstream region of all genes; indicating common function of these elements in transcriptional and posttranscriptional gene regulation. Further, genomic analysis using FGENESH, GenScan and homology based methods (BlastX and BlastN) was performed on the N. benthamiana contigs harboring CWIN and PAL, in an attempt to identify genomic neighborhood genes. The 5' upstream and 3' downstream region of genes in the genomic neighborhood of CWIN and PAL were also subjected to similar cis-element analysis, and the results indicated cis-elements profile similar to CWIN, PAL and other primary, secondary metabolism and transcription factor genes. The results of evolutionary studies confirmed that the 5' upstream region of NbCWINs significantly showed more proximity to secondary metabolism genes 4CL and the redox gene SOD, followed by the phenylpropanoid pathway gene CHI. The 3' downstream regions of NbCWINs were more closely related to other plant CWINs, followed by the redox gene, SOD and primary metabolism gene FBA. Thus, the commonly found stress responsive cis-elements in our study can play a vital role in modulating key pathways of both primary and secondary metabolism; thereby postulating their role in regulating plant growth and metabolisms under unfavourable growth conditions.
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Affiliation(s)
- S A Sheshadri
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - M J Nishanth
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - N Harita
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India
| | - P Brindha
- Centre for Advanced Research in Indian System of Medicine (CARISM), SASTRA University, Thanjavur, 613401 India
| | - S Bindu
- School of Chemical and Biotechnology, SASTRA University, Thanjavur, 613401 India.
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24
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Abstract
Transitory gene expression systems in Nicotiana benthamiana leaves, in combination with the use of gene silencing suppressors as the p19 or HC-pro proteins that allow for elevated levels of gene expression, have proven to be a highly versatile tool to analyze transcriptional function of DNA binding factors in the activated or repressed expression of their gene targets. This experimental setup uses Agrobacterium-mediated infection to deliver the various DNA constructs into the cell, and offers the advantage with respect to mesophyll protoplast transfection procedures that it entails a much easier protocol, in addition to preserving the intact leaf tissue, thus being more amenable to the study of wound and stress signaling pathways or to the functional analyses of regulators that respond to Ca+2 signatures. Furthermore, by using reporter constructs based on the LUCIFERASE (LUC) gene, which does not require a destructive determination assay, this expression system can be used to test for changes in gene activity over time or in response to various treatments, thus providing a comprehensive understanding of the signaling pathways that modulate activity of the expressed regulators and therefore their in vivo function in the control of the analyzed promoter.
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Affiliation(s)
- Pilar Lasierra
- Dpto. Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Madrid, Spain
| | - Salomé Prat
- Dpto. Genética Molecular de Plantas, Centro Nacional de Biotecnología-CSIC, Madrid, Spain.
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25
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Filyushin MA, Slugina MA, Shchennikova AV, Kochieva EZ. YABBY3-Orthologous Genes in Wild Tomato Species: Structure, Variability, and Expression. Acta Naturae 2017; 9:101-109. [PMID: 29340223 PMCID: PMC5762834] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2017] [Indexed: 11/10/2022] Open
Abstract
Evolution of the genes encoding YABBY transcription factors is believed to be one of the key reasons for flat leaf emergence from the radially symmetrical stem and gynoecium diversity. YABBY genes determine the identity of the abaxial surface of all aboveground lateral organs in seed plants. In the present study, complete sequences of YABBY3-orthologous genes were identified and characterized in 13 accessions of cultivated and wild tomato species with diverse morphophysiology of leaves, flowers, and fruits. The obtained gene sequences showed high homology (95-99%) and an identical exon-intron structure with the known S. lycopersicum YABBY3 gene, and they contained sequences that encode the conserved HMG-like YABBY and Cys2Cys2-zinc-finger domains. In total, in the analyzed YABBY3 genes, 317 variable sites were found, wherein 8 of 24 exon-specific SNPs were nonsynonymous. In the vegetative and reproductive organs of red-fruited and green-fruited tomato species, YABBY3 gene expression was similar to that in S. pimpinellifolium described earlier, but it demonstrated interspecies differences at the leaf-, bud- and flower-specific expression levels.
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Affiliation(s)
- M. A. Filyushin
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky pr. 33, bldg. 2, Moscow, 119071, Russia
| | - M. A. Slugina
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky pr. 33, bldg. 2, Moscow, 119071, Russia
- Department of Biotechnology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
| | - A. V. Shchennikova
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky pr. 33, bldg. 2, Moscow, 119071, Russia
| | - E. Z. Kochieva
- Federal State Institution «Federal Research Centre «Fundamentals of Biotechnology» of the Russian Academy of Sciences», Leninsky pr. 33, bldg. 2, Moscow, 119071, Russia
- Department of Biotechnology, Faculty of Biology, Moscow State University, Leninskie Gory 1, bldg. 12, Moscow, 119991, Russia
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26
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Cis and trans determinants of epigenetic silencing by Polycomb repressive complex 2 in Arabidopsis. Nat Genet 2017; 49:1546-1552. [DOI: 10.1038/ng.3937] [Citation(s) in RCA: 150] [Impact Index Per Article: 21.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/08/2017] [Accepted: 07/21/2017] [Indexed: 12/12/2022]
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27
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Ortiz-Espín A, Iglesias-Fernández R, Calderón A, Carbonero P, Sevilla F, Jiménez A. Mitochondrial AtTrxo1 is transcriptionally regulated by AtbZIP9 and AtAZF2 and affects seed germination under saline conditions. JOURNAL OF EXPERIMENTAL BOTANY 2017; 68:1025-1038. [PMID: 28184497 PMCID: PMC5441863 DOI: 10.1093/jxb/erx012] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/10/2023]
Abstract
Mitochondrial thioredoxin-o (AtTrxo1) was characterized and its expression examined in different organs of Arabidopsis thaliana. AtTrxo1 transcript levels were particularly high in dry seeds and cotyledons where they reached a maximum 36 h after imbibition with water, coinciding with 50% germination. Expression was lower in seeds germinating in 100 mM NaCl. To gain insight into the transcriptional regulation of the AtTrxo1 gene, a phylogenomic analysis was coupled with the screening of an arrayed library of Arabidopsis transcription factors in yeast. The basic leucine zipper AtbZIP9 and the zinc finger protein AZF2 were identified as putative transcriptional regulators. Transcript regulation of AtbZIP9 and AtAFZ2 during germination was compatible with the proposed role in transcriptional regulation of AtTrxo1. Transient over-expression of AtbZIP9 and AtAZF2 in Nicotiana benthamiana leaves demonstrated an activation effect of AtbZIP9 and a repressor effect of AtAZF2 on AtTrxo1 promoter-driven reporter expression. Although moderate concentrations of salt delayed germination in Arabidopsis wild-type seeds, those of two different AtTrxo1 knock-out mutants germinated faster and accumulated higher H2O2 levels than the wild-type. All these data indicate that AtTrxo1 has a role in redox homeostasis during seed germination under salt conditions.
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Affiliation(s)
- Ana Ortiz-Espín
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, Campus Universitario de Espinardo, 30100-Murcia, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas (CBGP; UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Aingeru Calderón
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, Campus Universitario de Espinardo, 30100-Murcia, Spain
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas (CBGP; UPM-INIA), Campus de Montegancedo, Universidad Politécnica de Madrid, Pozuelo de Alarcón, 28223-Madrid, Spain
| | - Francisca Sevilla
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, Campus Universitario de Espinardo, 30100-Murcia, Spain
| | - Ana Jiménez
- Departamento de Biología del Estrés y Patología Vegetal, CEBAS-CSIC, Campus Universitario de Espinardo, 30100-Murcia, Spain
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Ebrahimian-Motlagh S, Ribone PA, Thirumalaikumar VP, Allu AD, Chan RL, Mueller-Roeber B, Balazadeh S. JUNGBRUNNEN1 Confers Drought Tolerance Downstream of the HD-Zip I Transcription Factor AtHB13. FRONTIERS IN PLANT SCIENCE 2017; 8:2118. [PMID: 29326734 PMCID: PMC5736527 DOI: 10.3389/fpls.2017.02118] [Citation(s) in RCA: 39] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2017] [Accepted: 11/28/2017] [Indexed: 05/05/2023]
Abstract
Low water availability is the major environmental factor limiting growth and productivity of plants and crops and is therefore considered of high importance for agriculture affected by climate change. Identifying regulatory components controlling the response and tolerance to drought stress is thus of major importance. The NAC transcription factor (TF) JUNGBRUNNEN1 (JUB1) from Arabidopsis thaliana extends leaf longevity under non-stress growth conditions, lowers cellular hydrogen peroxide (H2O2) level, and enhances tolerance against heat stress and salinity. Here, we additionally find that JUB1 strongly increases tolerance to drought stress in Arabidopsis when expressed from both, a constitutive (CaMV 35S) and an abiotic stress-induced (RD29A) promoter. Employing a yeast one-hybrid screen we identified HD-Zip class I TF AtHB13 as an upstream regulator of JUB1. AtHB13 has previously been reported to act as a positive regulator of drought tolerance. AtHB13 and JUB1 thereby establish a joint drought stress control module.
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Affiliation(s)
- Saghar Ebrahimian-Motlagh
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Pamela A. Ribone
- Instituto de Agrobiotecnología del Litoral, CONICET-Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Venkatesh P. Thirumalaikumar
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Annapurna D. Allu
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Raquel L. Chan
- Instituto de Agrobiotecnología del Litoral, CONICET-Universidad Nacional del Litoral, Facultad de Bioquímica y Ciencias Biológicas, Santa Fe, Argentina
| | - Bernd Mueller-Roeber
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
| | - Salma Balazadeh
- Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
- Max Planck Institute of Molecular Plant Physiology, Potsdam, Germany
- *Correspondence: Salma Balazadeh,
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29
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Abstract
Plants, like other eukaryotes, have evolved complex mechanisms to coordinate gene expression during development, environmental response, and cellular homeostasis. Transcription factors (TFs), accompanied by basic cofactors and posttranscriptional regulators, are key players in gene-regulatory networks (GRNs). The coordinated control of gene activity is achieved by the interplay of these factors and by physical interactions between TFs and DNA. Here, we will briefly outline recent technological progress made to elucidate GRNs in plants. We will focus on techniques that allow us to characterize physical interactions in GRNs in plants and to analyze their regulatory consequences. Targeted manipulation allows us to test the relevance of specific gene-regulatory interactions. The combination of genome-wide experimental approaches with mathematical modeling allows us to get deeper insights into key-regulatory interactions and combinatorial control of important processes in plants.
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Affiliation(s)
- Kerstin Kaufmann
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.
| | - Dijun Chen
- Department for Plant Cell and Molecular Biology, Institute for Biology, Humboldt-Universität zu Berlin, 10115, Berlin, Germany.,Institute for Biochemistry and Biology, University of Potsdam, Potsdam, Germany
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30
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Sánchez-Montesino R, Oñate-Sánchez L. Yeast One- and Two-Hybrid High-Throughput Screenings Using Arrayed Libraries. Methods Mol Biol 2017. [PMID: 28623579 DOI: 10.1007/978-1-4939-7125-1_5] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/04/2022]
Abstract
Since their original description more than 25 years ago, the yeast one- and two-hybrid systems (Y1H/Y2H) have been used by many laboratories to detect DNA-protein (Y1H) and protein-protein interactions (Y2H). These systems use yeast cells (Saccharomyces cerevisiae) as a eukaryotic "test tube" and are amenable for most labs in the world. The development of highly efficient cloning methods has fostered the generation of large collections of open reading frames (ORFs) for several organisms that have been used for yeast screenings. Here, we describe a simple mating based method for high-throughput screenings of arrayed ORF libraries with DNA (Y1H) or protein (Y2H) baits not requiring robotics. One person can easily carry out this protocol in approximately 10 h of labor spread over 5 days. It can also be scaled down to test one-to-one (few) interactions, scaled up (i.e., robotization) and is compatible with several library formats (i.e., 96, 384-well microtiter plates).
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Affiliation(s)
- Rocío Sánchez-Montesino
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas (UPM-INIA), Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223, Madrid, Spain.
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31
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Lozano-Sotomayor P, Chávez Montes RA, Silvestre-Vañó M, Herrera-Ubaldo H, Greco R, Pablo-Villa J, Galliani BM, Diaz-Ramirez D, Weemen M, Boutilier K, Pereira A, Colombo L, Madueño F, Marsch-Martínez N, de Folter S. Altered expression of the bZIP transcription factor DRINK ME affects growth and reproductive development in Arabidopsis thaliana. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2016; 88:437-451. [PMID: 27402171 DOI: 10.1111/tpj.13264] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/15/2015] [Revised: 06/24/2016] [Accepted: 07/06/2016] [Indexed: 05/05/2023]
Abstract
Here we describe an uncharacterized gene that negatively influences Arabidopsis growth and reproductive development. DRINK ME (DKM; bZIP30) is a member of the bZIP transcription factor family, and is expressed in meristematic tissues such as the inflorescence meristem (IM), floral meristem (FM), and carpel margin meristem (CMM). Altered DKM expression affects meristematic tissues and reproductive organ development, including the gynoecium, which is the female reproductive structure and is determinant for fertility and sexual reproduction. A microarray analysis indicates that DKM overexpression affects the expression of cell cycle, cell wall, organ initiation, cell elongation, hormone homeostasis, and meristem activity genes. Furthermore, DKM can interact in yeast and in planta with proteins involved in shoot apical meristem maintenance such as WUSCHEL, KNAT1/BP, KNAT2 and JAIBA, and with proteins involved in medial tissue development in the gynoecium such as HECATE, BELL1 and NGATHA1. Taken together, our results highlight the relevance of DKM as a negative modulator of Arabidopsis growth and reproductive development.
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Affiliation(s)
- Paulina Lozano-Sotomayor
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Ricardo A Chávez Montes
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Marina Silvestre-Vañó
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus de la Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | - Humberto Herrera-Ubaldo
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | | | - Jeanneth Pablo-Villa
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
| | - Bianca M Galliani
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - David Diaz-Ramirez
- Departamento de Biotecnología y Bioquímica, CINVESTAV-IPN, Irapuato, Gto., México
| | - Mieke Weemen
- Wageningen University and Research Centre, Bioscience, P.O. Box 619, 6700 AP, Wageningen, The Netherlands
| | - Kim Boutilier
- Wageningen University and Research Centre, Bioscience, P.O. Box 619, 6700 AP, Wageningen, The Netherlands
| | - Andy Pereira
- Crop, Soil and Environmental Sciences, University of Arkansas, 115 Plant Science Building, Fayetteville, AR, 72701, USA
| | - Lucia Colombo
- Dipartimento di Bioscienze, Università degli Studi di Milano, Milan, Italy
| | - Francisco Madueño
- Instituto de Biología Molecular y Celular de Plantas (UPV-CSIC), Campus de la Universidad Politécnica de Valencia, 46022, Valencia, Spain
| | | | - Stefan de Folter
- Unidad de Genómica Avanzada (LANGEBIO), Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Irapuato, Gto., México
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32
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Franco-Zorrilla JM, Solano R. Identification of plant transcription factor target sequences. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2016; 1860:21-30. [PMID: 27155066 DOI: 10.1016/j.bbagrm.2016.05.001] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2016] [Revised: 05/01/2016] [Accepted: 05/02/2016] [Indexed: 12/15/2022]
Abstract
Regulation of gene expression depends on specific cis-regulatory sequences located in the gene promoter regions. These DNA sequences are recognized by transcription factors (TFs) in a sequence-specific manner, and their identification could help to elucidate the regulatory networks that underlie plant physiological responses to developmental programs or to environmental adaptation. Here we review recent advances in high throughput methodologies for the identification of plant TF binding sites. Several approaches offer a map of the TF binding locations in vivo and of the dynamics of the gene regulatory networks. As an alternative, high throughput in vitro methods provide comprehensive determination of the DNA sequences recognized by TFs. These advances are helping to decipher the regulatory lexicon and to elucidate transcriptional network hierarchies in plants in response to internal or external cues. This article is part of a Special Issue entitled: Plant Gene Regulatory Mechanisms and Networks, edited by Dr. Erich Grotewold and Dr. Nathan Springer.
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Affiliation(s)
- José M Franco-Zorrilla
- Genomics Unit, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain.
| | - Roberto Solano
- Department of Plant Molecular Genetics, Centro Nacional de Biotecnología, Consejo Superior de Investigaciones Científicas, 28049 Madrid, Spain
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33
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Gu M, Chen A, Sun S, Xu G. Complex Regulation of Plant Phosphate Transporters and the Gap between Molecular Mechanisms and Practical Application: What Is Missing? MOLECULAR PLANT 2016; 9:396-416. [PMID: 26714050 DOI: 10.1016/j.molp.2015.12.012] [Citation(s) in RCA: 150] [Impact Index Per Article: 18.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Revised: 11/18/2015] [Accepted: 12/11/2015] [Indexed: 05/18/2023]
Abstract
It has been almost 25 years since the first report of the gene encoding a high-affinity phosphate transporter (PT), PHO84, in yeast. Since then, an increasing number of yeast PHO84 homologs as well as other genes encoding proteins with phosphate (Pi) transport activities have been identified and functionally characterized in diverse plant species. Great progress has been made also in deciphering the molecular mechanism underlying the regulation of the abundance and/or activity of these genes and their products. The regulatory genes affect plant Pi homeostasis commonly through direct or indirect regulation of the abundance of PTs at different levels. However, little has been achieved in the use of PTs for developing genetically modified crops with high phosphorus use efficiency (PUE). This might be a consequence of overemphasizing Pi uptake from the rhizosphere and lack of knowledge about the roles of PTs in Pi transport and recycling within the plant that are required to optimize PUE. Here, we mainly focused on the genes encoding proteins with Pi transport activities and the emerging understanding of their regulation at the transcriptional, post-transcriptional, translational, and post-translational levels. In addition, we propose potential strategies for effective use of PTs in improving plant growth and development.
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Affiliation(s)
- Mian Gu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Aiqun Chen
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Shubin Sun
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China
| | - Guohua Xu
- State Key Laboratory of Crop Genetics and Germplasm Enhancement, Nanjing Agricultural University, Nanjing 210095, China; MOA Key Laboratory of Plant Nutrition and Fertilization in Lower-Middle Reaches of the Yangtze River, Nanjing 210095, China.
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34
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Shahnejat-Bushehri S, Tarkowska D, Sakuraba Y, Balazadeh S. Arabidopsis NAC transcription factor JUB1 regulates GA/BR metabolism and signalling. NATURE PLANTS 2016; 2:16013. [PMID: 27249348 DOI: 10.1038/nplants.2016.13] [Citation(s) in RCA: 94] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/14/2015] [Accepted: 01/21/2016] [Indexed: 05/02/2023]
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35
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36
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Šimášková M, O'Brien JA, Khan M, Van Noorden G, Ötvös K, Vieten A, De Clercq I, Van Haperen JMA, Cuesta C, Hoyerová K, Vanneste S, Marhavý P, Wabnik K, Van Breusegem F, Nowack M, Murphy A, Friml J, Weijers D, Beeckman T, Benková E. Cytokinin response factors regulate PIN-FORMED auxin transporters. Nat Commun 2015; 6:8717. [PMID: 26541513 DOI: 10.1038/ncomms9717] [Citation(s) in RCA: 74] [Impact Index Per Article: 8.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2014] [Accepted: 09/24/2015] [Indexed: 01/22/2023] Open
Abstract
Auxin and cytokinin are key endogenous regulators of plant development. Although cytokinin-mediated modulation of auxin distribution is a developmentally crucial hormonal interaction, its molecular basis is largely unknown. Here we show a direct regulatory link between cytokinin signalling and the auxin transport machinery uncovering a mechanistic framework for cytokinin-auxin cross-talk. We show that the CYTOKININ RESPONSE FACTORS (CRFs), transcription factors downstream of cytokinin perception, transcriptionally control genes encoding PIN-FORMED (PIN) auxin transporters at a specific PIN CYTOKININ RESPONSE ELEMENT (PCRE) domain. Removal of this cis-regulatory element effectively uncouples PIN transcription from the CRF-mediated cytokinin regulation and attenuates plant cytokinin sensitivity. We propose that CRFs represent a missing cross-talk component that fine-tunes auxin transport capacity downstream of cytokinin signalling to control plant development.
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Affiliation(s)
- Mária Šimášková
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - José Antonio O'Brien
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Mamoona Khan
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Giel Van Noorden
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Krisztina Ötvös
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Anne Vieten
- Department of Developmental Genetics, Centre for Molecular Biology of Plants, University Tübingen, Auf der Morgenstelle 3, 72076 Tübingen, Germany
| | - Inge De Clercq
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | | | - Candela Cuesta
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Klára Hoyerová
- Institute of Experimental Botany, ASCR, Rozvojová 263, 16502 Prague, Czech Republic
| | - Steffen Vanneste
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Peter Marhavý
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Krzysztof Wabnik
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Frank Van Breusegem
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Moritz Nowack
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Angus Murphy
- Department of Plant Science and Landscape Architecture, University of Maryland, College Park, Maryland 20742, USA
| | - Jiří Friml
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
| | - Dolf Weijers
- Laboratory of Biochemistry, Wageningen University, Dreijenlaan 3, 6703HA Wageningen, the Netherlands
| | - Tom Beeckman
- Department of Plant Systems Biology, VIB, Technologiepark 927, B-9052 Gent, Belgium.,Department of Plant Biotechnology and Bioinformatics, Ghent University, Technologiepark 927, B-9052 Gent, Belgium
| | - Eva Benková
- Institute of Science and Technology Austria (IST Austria), Am Campus 1, 3400 Klosterneuburg, Austria
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37
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Ballester P, Navarrete-Gómez M, Carbonero P, Oñate-Sánchez L, Ferrándiz C. Leaf expansion in Arabidopsis is controlled by a TCP-NGA regulatory module likely conserved in distantly related species. PHYSIOLOGIA PLANTARUM 2015; 155:21-32. [PMID: 25625546 DOI: 10.1111/ppl.12327] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/03/2014] [Revised: 01/15/2015] [Accepted: 01/19/2015] [Indexed: 05/10/2023]
Abstract
The NGATHA (NGA) clade of transcription factors (TFs) forms a small subfamily of four members in Arabidopsis thaliana. NGA genes act redundantly to direct the development of apical tissues in the gynoecium, where they have been shown to be essential for style and stigma specification. In addition, NGA genes have a more general role in controlling lateral organ growth. The four NGA genes in Arabidopsis are expressed in very similar domains, although little is known about the nature of their putative regulators. Here, we have identified a conserved region within the four NGA promoters that we have used as a bait to screen a yeast library, aiming to identify such NGA regulators. Three members of the TCP family of TFs, named after the founding factors TEOSINTE BRANCHED 1, CYCLOIDEA and PROLIFERATING CELL FACTOR 1 AND 2), were recovered from this screening, of which two [TCP2 and TCP3, members of the CINCINNATA (CIN) family of TCP genes (CIN-TCP) subclade] were shown to activate the NGA3 promoter in planta. We provide evidence that support that CIN-TCP genes are true regulators of NGA gene expression, and that part of the CIN-TCP role in leaf development is mediated by NGA upregulation. Moreover, we have found that this TCP-NGA regulatory interaction is likely conserved in angiosperms, including important crop species, for which the regulation of leaf development is a target for biotechnological improvement.
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Affiliation(s)
- Patricia Ballester
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, 46022, Spain
| | - Marisa Navarrete-Gómez
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, 46022, Spain
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, 28223, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Madrid, 28223, Spain
| | - Cristina Ferrándiz
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas, Universidad Politécnica de Valencia, Valencia, 46022, Spain
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38
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Identification of 7 stress-related NAC transcription factor members in maize (Zea mays L.) and characterization of the expression pattern of these genes. Biochem Biophys Res Commun 2015; 462:144-50. [PMID: 25937463 DOI: 10.1016/j.bbrc.2015.04.113] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2015] [Accepted: 04/22/2015] [Indexed: 11/20/2022]
Abstract
NAC proteins are plant-specific transcription factors that play essential roles in plant development and various abiotic stress responses. A comprehensive analysis of maize NAC genes was performed in this study. A total of 157 non-redundant maize NAC genes including seven membrane-bound members were identified and found to be unevenly distributed on 10 maize chromosomes. Motif composition analysis indicated that the maize NAC proteins share three relatively conserved motifs in the NAC domain within the N-terminal region. Phylogenetic analysis of 157 maize NAC proteins accompanied by 117 NAC proteins from Arabidopsis and 151 from rice were presented. The NAC proteins evaluated were divided into two large groups including 18 subgroups. Gene duplication analysis indicated that gene loss occurred during maize evolution. Seven NAC members that belong to the same clade of maize NAC domain genes were isolated, and overlapping expression patterns were observed under various abiotic stresses, including low temperature, high salinity and dehydration, and phytohormone abscisic acid treatments. This suggested that NAC members function as stress-responsive transcription factors in ABA-dependent signaling pathways. Relatively higher expression levels of these selected maize NAC genes were detected in roots. The stress responsive NAC genes may have applications in molecular breeding to improve crop stress tolerance.
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39
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Zaag R, Tamby JP, Guichard C, Tariq Z, Rigaill G, Delannoy E, Renou JP, Balzergue S, Mary-Huard T, Aubourg S, Martin-Magniette ML, Brunaud V. GEM2Net: from gene expression modeling to -omics networks, a new CATdb module to investigate Arabidopsis thaliana genes involved in stress response. Nucleic Acids Res 2014; 43:D1010-7. [PMID: 25392409 PMCID: PMC4383956 DOI: 10.1093/nar/gku1155] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/29/2023] Open
Abstract
CATdb (http://urgv.evry.inra.fr/CATdb) is a database providing a public access to a large collection of transcriptomic data, mainly for Arabidopsis but also for other plants. This resource has the rare advantage to contain several thousands of microarray experiments obtained with the same technical protocol and analyzed by the same statistical pipelines. In this paper, we present GEM2Net, a new module of CATdb that takes advantage of this homogeneous dataset to mine co-expression units and decipher Arabidopsis gene functions. GEM2Net explores 387 stress conditions organized into 18 biotic and abiotic stress categories. For each one, a model-based clustering is applied on expression differences to identify clusters of co-expressed genes. To characterize functions associated with these clusters, various resources are analyzed and integrated: Gene Ontology, subcellular localization of proteins, Hormone Families, Transcription Factor Families and a refined stress-related gene list associated to publications. Exploiting protein–protein interactions and transcription factors-targets interactions enables to display gene networks. GEM2Net presents the analysis of the 18 stress categories, in which 17 264 genes are involved and organized within 681 co-expression clusters. The meta-data analyses were stored and organized to compose a dynamic Web resource.
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Affiliation(s)
- Rim Zaag
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean Philippe Tamby
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Cécile Guichard
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Zakia Tariq
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Guillem Rigaill
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Etienne Delannoy
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Jean-Pierre Renou
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Sandrine Balzergue
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Tristan Mary-Huard
- INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France UMRGV, INRA, Université Paris-Sud, CNRS, F-91190 Gif-sur-Yvette, Paris, France
| | - Sébastien Aubourg
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
| | - Marie-Laure Martin-Magniette
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France INRA, UMR 518 MIA, 75005 Paris, France AgroParisTech, UMR 518 MIA, 75005 Paris, France
| | - Véronique Brunaud
- INRA, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France UEVE, Unité de Recherche en Génomique Végétale, UMR 1165, ERL CNRS 8196, Saclay Plant Sciences, CP 5708, F-91057 Evry, France
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Burdo B, Gray J, Goetting-Minesky MP, Wittler B, Hunt M, Li T, Velliquette D, Thomas J, Gentzel I, Brito MDS, Mejía-Guerra MK, Connolly LN, Qaisi D, Li W, Casas MI, Doseff AI, Grotewold E. The Maize TFome--development of a transcription factor open reading frame collection for functional genomics. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:356-66. [PMID: 25053252 PMCID: PMC4283594 DOI: 10.1111/tpj.12623] [Citation(s) in RCA: 44] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/05/2014] [Revised: 06/09/2014] [Accepted: 07/18/2014] [Indexed: 05/19/2023]
Abstract
Establishing the architecture of the gene regulatory networks (GRNs) responsible for controlling the transcription of all genes in an organism is a natural development that follows elucidation of the genome sequence. Reconstruction of the GRN requires the availability of a series of molecular tools and resources that so far have been limited to a few model organisms. One such resource consists of collections of transcription factor (TF) open reading frames (ORFs) cloned into vectors that facilitate easy expression in plants or microorganisms. In this study, we describe the development of a publicly available maize TF ORF collection (TFome) of 2034 clones corresponding to 2017 unique gene models in recombination-ready vectors that make possible the facile mobilization of the TF sequences into a number of different expression vectors. The collection also includes several hundred co-regulators (CoREGs), which we classified into well-defined families, and for which we propose here a standard nomenclature, as we have previously done for TFs. We describe the strategies employed to overcome the limitations associated with cloning ORFs from a genome that remains incompletely annotated, with a partial full-length cDNA set available, and with many TF/CoREG genes lacking experimental support. In many instances this required the combination of genome-wide expression data with gene synthesis approaches. The strategies developed will be valuable for developing similar resources for other agriculturally important plants. Information on all the clones generated is available through the GRASSIUS knowledgebase (http://grassius.org/).
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Affiliation(s)
- Brett Burdo
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - John Gray
- Department of Biology, University of ToledoToledo, OH, 43606, USA
| | | | - Bettina Wittler
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - Matthew Hunt
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - Tai Li
- Department of Biology, University of ToledoToledo, OH, 43606, USA
| | | | - Julie Thomas
- Department of Biology, University of ToledoToledo, OH, 43606, USA
| | - Irene Gentzel
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - Michael dos Santos Brito
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
- Department of Plant Biology, Institute of Biology, State University of CampinasCampinas, Sao Paulo, 13083-970, Brazil
| | - Maria Katherine Mejía-Guerra
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State UniversityColumbus, OH, 43210, USA
| | - Layne N Connolly
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - Dalya Qaisi
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
| | - Wei Li
- Department of Internal Medicine and The Heart and Lung Research Institute, The Ohio State UniversityColumbus, OH, 43210, USA
| | - Maria I Casas
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
- Molecular, Cellular and Developmental Biology Graduate Program, The Ohio State UniversityColumbus, OH, 43210, USA
| | - Andrea I Doseff
- Department of Plant Biology, Institute of Biology, State University of CampinasCampinas, Sao Paulo, 13083-970, Brazil
- Department of Molecular Genetics, The Ohio State UniversityColumbus, OH, 43210, USA
| | - Erich Grotewold
- Center for Applied Plant Sciences (CAPS), The Ohio State UniversityColumbus, OH, 43210, USA
- Department of Molecular Genetics, The Ohio State UniversityColumbus, OH, 43210, USA
- *For correspondence (e-mail )
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41
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Marín-de la Rosa N, Sotillo B, Miskolczi P, Gibbs DJ, Vicente J, Carbonero P, Oñate-Sánchez L, Holdsworth MJ, Bhalerao R, Alabadí D, Blázquez MA. Large-scale identification of gibberellin-related transcription factors defines group VII ETHYLENE RESPONSE FACTORS as functional DELLA partners. PLANT PHYSIOLOGY 2014; 166:1022-32. [PMID: 25118255 PMCID: PMC4213073 DOI: 10.1104/pp.114.244723] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/06/2014] [Accepted: 08/06/2014] [Indexed: 05/17/2023]
Abstract
DELLA proteins are the master negative regulators in gibberellin (GA) signaling acting in the nucleus as transcriptional regulators. The current view of DELLA action indicates that their activity relies on the physical interaction with transcription factors (TFs). Therefore, the identification of TFs through which DELLAs regulate GA responses is key to understanding these responses from a mechanistic point of view. Here, we have determined the TF interactome of the Arabidopsis (Arabidopsis thaliana) DELLA protein GIBBERELLIN INSENSITIVE and screened a collection of conditional TF overexpressors in search of those that alter GA sensitivity. As a result, we have found RELATED TO APETALA2.3, an ethylene-induced TF belonging to the group VII ETHYLENE RESPONSE FACTOR of the APETALA2/ethylene responsive element binding protein superfamily, as a DELLA interactor with physiological relevance in the context of apical hook development. The combination of transactivation assays and chromatin immunoprecipitation indicates that the interaction with GIBBERELLIN INSENSITIVE impairs the activity of RELATED TO APETALA2.3 on the target promoters. This mechanism represents a unique node in the cross regulation between the GA and ethylene signaling pathways controlling differential growth during apical hook development.
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Affiliation(s)
- Nora Marín-de la Rosa
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Berta Sotillo
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Pal Miskolczi
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Daniel J Gibbs
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Jorge Vicente
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Pilar Carbonero
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Luis Oñate-Sánchez
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Michael J Holdsworth
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Rishikesh Bhalerao
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - David Alabadí
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
| | - Miguel A Blázquez
- Instituto de Biología Molecular y Celular de Plantas, 46022 Valencia, Spain (N.M.-d.l.R., B.S., D.A., M.A.B.);Department of Forest Genetics and Plant Physiology, Umeå Plant Science Center, Swedish University of Agricultural Sciences, 90187 Umea, Sweden (P.M., R.B.);Division of Plant and Crop Sciences, School of Biosciences, University of Nottingham, Loughborough LE12 5RD, United Kingdom (D.J.G., J.V., M.J.H.);Centro de Biotecnología y Genómica de Plantas, Escuela Técnica Superior de Ingenieros Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, 28223 Pozuelo de Alarcón, Spain (P.C., L.O.-S.); andCollege of Science, King Saud University, Riyadh 11451, Kingdom of Saudi Arabia (R.B.)
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42
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Marsch-Martínez N, Zúñiga-Mayo VM, Herrera-Ubaldo H, Ouwerkerk PBF, Pablo-Villa J, Lozano-Sotomayor P, Greco R, Ballester P, Balanzá V, Kuijt SJH, Meijer AH, Pereira A, Ferrándiz C, de Folter S. The NTT transcription factor promotes replum development in Arabidopsis fruits. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 80:69-81. [PMID: 25039392 DOI: 10.1111/tpj.12617] [Citation(s) in RCA: 40] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2014] [Revised: 07/03/2014] [Accepted: 07/09/2014] [Indexed: 05/21/2023]
Abstract
Fruits are complex plant structures that nurture seeds and facilitate their dispersal. The Arabidopsis fruit is termed silique. It develops from the gynoecium, which has a stigma, a style, an ovary containing the ovules, and a gynophore. Externally, the ovary consists of two valves, and their margins lay adjacent to the replum, which is connected to the septum that internally divides the ovary. In this work we describe the role for the zinc-finger transcription factor NO TRANSMITTING TRACT (NTT) in replum development. NTT loss of function leads to reduced replum width and cell number, whereas increased expression promotes replum enlargement. NTT activates the homeobox gene BP, which, together with RPL, is important for replum development. In addition, the NTT protein is able to bind the BP promoter in yeast, and when this binding region is not present, NTT fails to activate BP in the replum. Furthermore, NTT interacts with itself and different proteins involved in fruit development: RPL, STM, FUL, SHP1 and SHP2 in yeast and in planta. Moreover, its genetic interactions provide further evidence about its biological relevance in replum development.
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Affiliation(s)
- Nayelli Marsch-Martínez
- Departamento de Biotecnología y Bioquímica, Centro de Investigación y de Estudios Avanzados del Instituto Politécnico Nacional (CINVESTAV-IPN), Km. 9.6 Libramiento Norte, Carretera Irapuato-León, A.P. 629, CP 36821 Irapuato, Guanajuato, Mexico
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43
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Pruneda-Paz JL, Breton G, Nagel DH, Kang SE, Bonaldi K, Doherty CJ, Ravelo S, Galli M, Ecker JR, Kay SA. A genome-scale resource for the functional characterization of Arabidopsis transcription factors. Cell Rep 2014; 8:622-32. [PMID: 25043187 DOI: 10.1016/j.celrep.2014.06.033] [Citation(s) in RCA: 138] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2014] [Revised: 05/28/2014] [Accepted: 06/19/2014] [Indexed: 12/31/2022] Open
Abstract
Extensive transcriptional networks play major roles in cellular and organismal functions. Transcript levels are in part determined by the combinatorial and overlapping functions of multiple transcription factors (TFs) bound to gene promoters. Thus, TF-promoter interactions provide the basic molecular wiring of transcriptional regulatory networks. In plants, discovery of the functional roles of TFs is limited by an increased complexity of network circuitry due to a significant expansion of TF families. Here, we present the construction of a comprehensive collection of Arabidopsis TFs clones created to provide a versatile resource for uncovering TF biological functions. We leveraged this collection by implementing a high-throughput DNA binding assay and identified direct regulators of a key clock gene (CCA1) that provide molecular links between different signaling modules and the circadian clock. The resources introduced in this work will significantly contribute to a better understanding of the transcriptional regulatory landscape of plant genomes.
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Affiliation(s)
- Jose L Pruneda-Paz
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
| | - Ghislain Breton
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Dawn H Nagel
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - S Earl Kang
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Katia Bonaldi
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Colleen J Doherty
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA
| | - Stephanie Ravelo
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA
| | - Mary Galli
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Joseph R Ecker
- Genomic Analysis Laboratory, Howard Hughes Medical Institute and The Salk Institute for Biological Studies, La Jolla, CA 92037, USA
| | - Steve A Kay
- Division of Biological Sciences, University of California, San Diego, La Jolla, CA 92093, USA; Center for Chronobiology, University of California, San Diego, La Jolla, CA 92093, USA.
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44
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Rombolá-Caldentey B, Rueda-Romero P, Iglesias-Fernández R, Carbonero P, Oñate-Sánchez L. Arabidopsis DELLA and two HD-ZIP transcription factors regulate GA signaling in the epidermis through the L1 box cis-element. THE PLANT CELL 2014; 26:2905-19. [PMID: 24989044 PMCID: PMC4145122 DOI: 10.1105/tpc.114.127647] [Citation(s) in RCA: 53] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/13/2014] [Revised: 05/13/2014] [Accepted: 06/13/2014] [Indexed: 05/21/2023]
Abstract
Gibberellins (GAs) are plant hormones that affect plant growth and regulate gene expression differentially across tissues. To study the molecular mechanisms underlying GA signaling in Arabidopsis thaliana, we focused on a GDSL lipase gene (LIP1) induced by GA and repressed by DELLA proteins. LIP1 contains an L1 box promoter sequence, conserved in the promoters of epidermis-specific genes, that is bound by ATML1, an HD-ZIP transcription factor required for epidermis specification. In this study, we demonstrate that LIP1 is specifically expressed in the epidermis and that its L1 box sequence mediates GA-induced transcription. We show that this sequence is overrepresented in the upstream regulatory regions of GA-induced and DELLA-repressed transcriptomes and that blocking GA signaling in the epidermis represses the expression of L1 box-containing genes and negatively affects seed germination. We show that DELLA proteins interact directly with ATML1 and its paralogue PDF2 and that silencing of both HD-ZIP transcription factors inhibits epidermal gene expression and delays germination. Our results indicate that, upon seed imbibition, increased GA levels reduce DELLA protein abundance and release ATML1/PDF2 to activate L1 box gene expression, thus enhancing germination potential.
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Affiliation(s)
- Belén Rombolá-Caldentey
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Paloma Rueda-Romero
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Raquel Iglesias-Fernández
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Pilar Carbonero
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
| | - Luis Oñate-Sánchez
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and E.T.S.I. Agrónomos, Universidad Politécnica de Madrid, Campus de Montegancedo, Pozuelo de Alarcón, 28223 Madrid, Spain
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45
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Parapunova V, Busscher M, Busscher-Lange J, Lammers M, Karlova R, Bovy AG, Angenent GC, de Maagd RA. Identification, cloning and characterization of the tomato TCP transcription factor family. BMC PLANT BIOLOGY 2014; 14:157. [PMID: 24903607 PMCID: PMC4070083 DOI: 10.1186/1471-2229-14-157] [Citation(s) in RCA: 99] [Impact Index Per Article: 9.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/21/2014] [Accepted: 05/22/2014] [Indexed: 05/06/2023]
Abstract
BACKGROUND TCP proteins are plant-specific transcription factors, which are known to have a wide range of functions in different plant species such as in leaf development, flower symmetry, shoot branching, and senescence. Only a small number of TCP genes has been characterised from tomato (Solanum lycopersicum). Here we report several functional features of the members of the entire family present in the tomato genome. RESULTS We have identified 30 Solanum lycopersicum SlTCP genes, most of which have not been described before. Phylogenetic analysis clearly distinguishes two homology classes of the SlTCP transcription factor family - class I and class II. Class II differentiates in two subclasses, the CIN-TCP subclass and the CYC/TB1 subclass, involved in leaf development and axillary shoots formation, respectively. The expression patterns of all members were determined by quantitative PCR. Several SlTCP genes, like SlTCP12, SlTCP15 and SlTCP18 are preferentially expressed in the tomato fruit, suggesting a role during fruit development or ripening. These genes are regulated by RIN (RIPENING INHIBITOR), CNR (COLORLESS NON-RIPENING) and SlAP2a (APETALA2a) proteins, which are transcription factors with key roles in ripening. With a yeast one-hybrid assay we demonstrated that RIN binds the promoter fragments of SlTCP12, SlTCP15 and SlTCP18, and that CNR binds the SlTCP18 promoter. This data strongly suggests that these class I SlTCP proteins are involved in ripening. Furthermore, we demonstrate that SlTCPs bind the promoter fragments of members of their own family, indicating that they regulate each other. Additional yeast one-hybrid studies performed with Arabidopsis transcription factors revealed binding of the promoter fragments by proteins involved in the ethylene signal transduction pathway, contributing to the idea that these SlTCP genes are involved in the ripening process. Yeast two-hybrid data shows that SlTCP proteins can form homo and heterodimers, suggesting that they act together in order to form functional protein complexes and together regulate developmental processes in tomato. CONCLUSIONS The comprehensive analysis we performed, like phylogenetic analysis, expression studies, identification of the upstream regulators and the dimerization specificity of the tomato TCP transcription factor family provides the basis for functional studies to reveal the role of this family in tomato development.
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Affiliation(s)
- Violeta Parapunova
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Marco Busscher
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | | | - Michiel Lammers
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Rumyana Karlova
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
- Molecular Plant Physiology, Utrecht University, Padualaan 8, 3584 CH Utrecht, the Netherlands
| | - Arnaud G Bovy
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Gerco C Angenent
- Laboratory of Molecular Biology, Department of Plant Sciences, Wageningen-UR, PO Box 386, 6700 AJ Wageningen, the Netherlands
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
| | - Ruud A de Maagd
- Plant Research International, P.O. Box 619, 6700 AP Wageningen, the Netherlands
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Andriankaja ME, Danisman S, Mignolet-Spruyt LF, Claeys H, Kochanke I, Vermeersch M, De Milde L, De Bodt S, Storme V, Skirycz A, Maurer F, Bauer P, Mühlenbock P, Van Breusegem F, Angenent GC, Immink RGH, Inzé D. Transcriptional coordination between leaf cell differentiation and chloroplast development established by TCP20 and the subgroup Ib bHLH transcription factors. PLANT MOLECULAR BIOLOGY 2014; 85:233-45. [PMID: 24549883 DOI: 10.1007/s11103-014-0180-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/02/2013] [Accepted: 02/04/2014] [Indexed: 05/20/2023]
Abstract
The establishment of the photosynthetic apparatus during chloroplast development creates a high demand for iron as a redox metal. However, iron in too high quantities becomes toxic to the plant, thus plants have evolved a complex network of iron uptake and regulation mechanisms. Here, we examined whether four of the subgroup Ib basic helix-loop-helix transcription factors (bHLH38, bHLH39, bHLH100, bHLH101), previously implicated in iron homeostasis in roots, also play a role in regulating iron metabolism in developing leaves. These transcription factor genes were strongly up-regulated during the transition from cell proliferation to expansion, and thus sink-source transition, in young developing leaves of Arabidopsis thaliana. The four subgroup Ib bHLH genes also showed reduced expression levels in developing leaves of plants treated with norflurazon, indicating their expression was tightly linked to the onset of photosynthetic activity in young leaves. In addition, we provide evidence for a mechanism whereby the transcriptional regulators SAC51 and TCP20 antagonistically regulate the expression of these four subgroup Ib bHLH genes. A loss-of-function mutant analysis also revealed that single mutants of bHLH38, bHLH39, bHLH100, and bHLH101 developed smaller rosettes than wild-type plants in soil. When grown in agar plates with reduced iron concentration, triple bhlh39 bhlh100 bhlh101 mutant plants were smaller than wild-type plants. However, measurements of the iron content in single and multiple subgroup Ib bHLH genes, as well as transcript profiling of iron response genes during early leaf development, do not support a role for bHLH38, bHLH39, bHLH100, and bHLH101 in iron homeostasis during early leaf development.
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Affiliation(s)
- Megan E Andriankaja
- Department of Plant Systems Biology, VIB, Technologiepark 927, 9052, Ghent, Belgium
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Iglesias-Fernández R, Wozny D, Iriondo-de Hond M, Oñate-Sánchez L, Carbonero P, Barrero-Sicilia C. The AtCathB3 gene, encoding a cathepsin B-like protease, is expressed during germination of Arabidopsis thaliana and transcriptionally repressed by the basic leucine zipper protein GBF1. JOURNAL OF EXPERIMENTAL BOTANY 2014; 65:2009-21. [PMID: 24600022 PMCID: PMC3991739 DOI: 10.1093/jxb/eru055] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/21/2023]
Abstract
Protein hydrolysis plays an important role during seed germination and post-germination seedling establishment. In Arabidopsis thaliana, cathepsin B-like proteases are encoded by a gene family of three members, but only the AtCathB3 gene is highly induced upon seed germination and at the early post-germination stage. Seeds of a homozygous T-DNA insertion mutant in the AtCathB3 gene have, besides a reduced cathepsin B activity, a slower germination than the wild type. To explore the transcriptional regulation of this gene, we used a combined phylogenetic shadowing approach together with a yeast one-hybrid screening of an arrayed library of approximately 1200 transcription factor open reading frames from Arabidopsis thaliana. We identified a conserved CathB3-element in the promoters of orthologous CathB3 genes within the Brassicaceae species analysed, and, as its DNA-interacting protein, the G-Box Binding Factor1 (GBF1). Transient overexpression of GBF1 together with a PAtCathB3::uidA (β-glucuronidase) construct in tobacco plants revealed a negative effect of GBF1 on expression driven by the AtCathB3 promoter. In stable P35S::GBF1 lines, not only was the expression of the AtCathB3 gene drastically reduced, but a significant slower germination was also observed. In the homozygous knockout mutant for the GBF1 gene, the opposite effect was found. These data indicate that GBF1 is a transcriptional repressor of the AtCathB3 gene and affects the germination kinetics of Arabidopsis thaliana seeds. As AtCathB3 is also expressed during post-germination in the cotyledons, a role for the AtCathB3-like protease in reserve mobilization is also inferred.
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Affiliation(s)
| | - Dorothee Wozny
- * Present address: Max Planck Institute for Plant Breeding Research, Carl-von-Linné-Weg 10, 50829 Köln, Germany
| | | | | | | | - Cristina Barrero-Sicilia
- To whom correspondence should be addressed. Present address: Department of Biological Chemistry and Crop Protection, Rothamsted Research, West Common, Harpenden AL5 2JQ, UK. E-mail:
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Dubos C, Kelemen Z, Sebastian A, Bülow L, Huep G, Xu W, Grain D, Salsac F, Brousse C, Lepiniec L, Weisshaar B, Contreras-Moreira B, Hehl R. Integrating bioinformatic resources to predict transcription factors interacting with cis-sequences conserved in co-regulated genes. BMC Genomics 2014; 15:317. [PMID: 24773781 PMCID: PMC4234446 DOI: 10.1186/1471-2164-15-317] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2013] [Accepted: 04/16/2014] [Indexed: 11/22/2022] Open
Abstract
Background Using motif detection programs it is fairly straightforward to identify conserved cis-sequences in promoters of co-regulated genes. In contrast, the identification of the transcription factors (TFs) interacting with these cis-sequences is much more elaborate. To facilitate this, we explore the possibility of using several bioinformatic and experimental approaches for TF identification. This starts with the selection of co-regulated gene sets and leads first to the prediction and then to the experimental validation of TFs interacting with cis-sequences conserved in the promoters of these co-regulated genes. Results Using the PathoPlant database, 32 up-regulated gene groups were identified with microarray data for drought-responsive gene expression from Arabidopsis thaliana. Application of the binding site estimation suite of tools (BEST) discovered 179 conserved sequence motifs within the corresponding promoters. Using the STAMP web-server, 49 sequence motifs were classified into 7 motif families for which similarities with known cis-regulatory sequences were identified. All motifs were subjected to a footprintDB analysis to predict interacting DNA binding domains from plant TF families. Predictions were confirmed by using a yeast-one-hybrid approach to select interacting TFs belonging to the predicted TF families. TF-DNA interactions were further experimentally validated in yeast and with a Physcomitrella patens transient expression system, leading to the discovery of several novel TF-DNA interactions. Conclusions The present work demonstrates the successful integration of several bioinformatic resources with experimental approaches to predict and validate TFs interacting with conserved sequence motifs in co-regulated genes.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | - Reinhard Hehl
- Institut für Genetik, Technische Universität Braunschweig, Spielmannstr, 7, 38106 Braunschweig, Germany.
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Coego A, Brizuela E, Castillejo P, Ruíz S, Koncz C, del Pozo JC, Piñeiro M, Jarillo JA, Paz-Ares J, León J. The TRANSPLANTA collection of Arabidopsis lines: a resource for functional analysis of transcription factors based on their conditional overexpression. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2014; 77:944-53. [PMID: 24456507 DOI: 10.1111/tpj.12443] [Citation(s) in RCA: 69] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Revised: 01/08/2014] [Accepted: 01/13/2014] [Indexed: 05/07/2023]
Abstract
Transcription factors (TFs) are key regulators of gene expression in all organisms. In eukaryotes, TFs are often represented by functionally redundant members of large gene families. Overexpression might prove a means to unveil the biological functions of redundant TFs; however, constitutive overexpression of TFs frequently causes severe developmental defects, preventing their functional characterization. Conditional overexpression strategies help to overcome this problem. Here, we report on the TRANSPLANTA collection of Arabidopsis lines, each expressing one of 949 TFs under the control of a β-estradiol-inducible promoter. Thus far, 1636 independent homozygous lines, representing an average of 2.6 lines for every TF, have been produced for the inducible expression of 634 TFs. Along with a GUS-GFP reporter, randomly selected TRANSPLANTA lines were tested and confirmed for conditional transgene expression upon β-estradiol treatment. As a proof of concept for the exploitation of this resource, β-estradiol-induced proliferation of root hairs, dark-induced senescence, anthocyanin accumulation and dwarfism were observed in lines conditionally expressing full-length cDNAs encoding RHD6, WRKY22, MYB123/TT2 and MYB26, respectively, in agreement with previously reported phenotypes conferred by these TFs. Further screening performed with other TRANSPLANTA lines allowed the identification of TFs involved in different plant biological processes, illustrating that the collection is a powerful resource for the functional characterization of TFs. For instance, ANAC058 and a TINY/AP2 TF were identified as modulators of ABA-mediated germination potential, and RAP2.10/DEAR4 was identified as a regulator of cell death in the hypocotyl-root transition zone. Seeds of TRANSPLANTA lines have been deposited at the Nottingham Arabidopsis Stock Centre for further distribution.
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Affiliation(s)
- Alberto Coego
- Instituto de Biología Molecular y Celular de Plantas, Valencia (CSIC-UPV), CPI, Edificio 8E, Av. Fausto Elio s/n, 46022, Valencia, Spain
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Elevated levels of MYB30 in the phloem accelerate flowering in Arabidopsis through the regulation of FLOWERING LOCUS T. PLoS One 2014; 9:e89799. [PMID: 24587042 PMCID: PMC3934951 DOI: 10.1371/journal.pone.0089799] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2013] [Accepted: 01/27/2014] [Indexed: 01/07/2023] Open
Abstract
In Arabidopsis thaliana, the R2R3 MYB-like transcription factor MYB30 is a positive regulator of the pathogen-induced hypersensitive response and of brassinosteroid and abscisic acid signaling. Here, we show that MYB30 expressed under the control of the strong phloem-specific SUC2 promoter accelerates flowering both in long and short days. Early flowering is mediated by elevated expression of flowering locus T (FT), which can be observed in the absence and presence of CONSTANS (CO), the main activator of FT. CO-independent activation by high MYB30 expression results in FT levels that remain below those observed in the wild-type plants, which show an additive CO-dependent activation. In contrast, twin sister of FT (TSF) is repressed in plants expressing high levels of MYB30 in the phloem. In transient assays, MYB30 and CO additively increase the activity of a reporter construct driven by a 1 kb FT promoter. Acceleration of flowering by MYB30 does not require the presence of salicylic acid and is independent of FLC. Taken together, increased levels of MYB30, which was reported to be induced in response to the perception of pathogens, can accelerate flowering and MYB30 may thus be a candidate to mediate cross-talk between gene networks involved in biotic stress perception and flowering time.
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