DOCSLIB.ORG

Arabidopsis Thaliana NGATHA1 Transcription Factor Induces ABA Biosynthesis by Activating NCED3 Gene During Dehydration Stress

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Arabidopsis Thaliana NGATHA1 Transcription Factor Induces ABA Biosynthesis by Activating NCED3 Gene During Dehydration Stress Arabidopsis thaliana NGATHA1 transcription factor induces ABA biosynthesis by activating NCED3 gene during dehydration stress Hikaru Satoa,1, Hironori Takasakia,2, Fuminori Takahashia, Takamasa Suzukib, Satoshi Iuchic, Nobutaka Mitsudad, Masaru Ohme-Takagid,e, Miho Ikedad,e, Mitsunori Seof, Kazuko Yamaguchi-Shinozakig, and Kazuo Shinozakia,1 aGene Discovery Research Group, RIKEN Center for Sustainable Resource Science, Tsukuba, 305-0074 Ibaraki, Japan; bCollege of Bioscience and Biotechnology, Chubu University, Kasugai, 487-8501 Aichi, Japan; cExperimental Plant Division, BioResource Research Center, RIKEN, Tsukuba, 305-0074 Ibaraki, Japan; dPlant Gene Regulation Research Group, Bioproduction Research Institute, National Institute of Advanced Industrial Science and Technology, Tsukuba, 305-8566 Ibaraki, Japan; eGraduate School of Science and Engineering, Saitama University, Saitama, 338-8570 Saitama, Japan; fDormancy and Adaptation Research Unit, RIKEN Center for Sustainable Resource Science, Yokohama, 230-0045 Kanagawa, Japan; and gLaboratory of Plant Molecular Physiology, Graduate School of Agricultural and Life Sciences, University of Tokyo, 113-8657 Tokyo, Japan Edited by Julian I. Schroeder, Cell and Developmental Biology Section, Division of Biological Sciences, University of California, San Diego, La Jolla, CA, and approved October 1, 2018 (received for review July 10, 2018) The plant hormone abscisic acid (ABA) is accumulated after the NCED3 gene is highly induced in the vascular tissues by drought stress and plays critical roles in the responses to drought drought stress, and its knockout mutants revealed decreased ABA stress in plants, such as gene regulation, stomatal closure, seed accumulation under drought-stress conditions and drought-stress- maturation, and dormancy. Although previous reports revealed sensitive phenotypes (10, 11). The NCED3 promoter has a G-box detailed molecular roles of ABA in stress responses, the factors sequence as a long-range enhancer that is essential for gene in- that contribute to the drought-stress responses—in particular, reg- duction in the vascular tissues during dehydration stress (12, 13). ulation of ABA accumulation—remain unclear. The enzyme NINE- This G-box is located ∼2.3 kb upstream from its translational start CIS-EPOXYCAROTENOID DIOXYGENASE 3 (NCED3) is essential for site; however, the detailed molecular mechanisms by which the ABA biosynthesis during drought stress, and the NCED3 gene is unidentified transcription factors activate the NCED3 gene before PLANT BIOLOGY highly induced by drought stress. In the present study, we isolated ABA accumulation have not been elucidated. In the present study, NCED3 NGATHAs (NGAs) as candidate transcriptional regulators of we identified a transcription factor, NGATHA1 (NGA1), that through a screen of a plant library harboring the transcription activates the NCED3 gene during dehydration stress and charac- factors fused to a chimeric repressor domain, SRDX. The NGA pro- terized a cis-acting sequence, NGA-binding element (NBE), in the teins were directly bound to a cis-element NGA-binding element ′ ′ ′ ′ NCED3 5 untranslated region (5 UTR) of the NCED3 promoter that is (NBE) in the 5 untranslated region (5 UTR) of the promoter necessary for gene induction (in this work, we use “promoter” and were suggested to be transcriptional activators of NCED3. to refer to the region upstream from the translational start site Among the single-knockout mutants of four NGA family genes, of a protein coding gene and include the 5′ UTR region). More- we found that the NGATHA1 (NGA1) knockout mutant was drought- over, it also was suggested that ABA-independent posttranslational stress-sensitive with a decreased expression level of NCED3 during de- hydration stress. These results suggested that NGA1 essentially func- tions as a transcriptional activator of NCED3 among the NGA family Significance proteins. Moreover, the NGA1 protein was degraded under non- stressed conditions, and dehydration stress enhanced the accu- The plant hormone abscisic acid (ABA) is essential for drought- mulation of NGA1 proteins, even in ABA-deficient mutant plants, stress responses in plants, and its functions have been well indicating that there should be ABA-independent posttranslational studied; however, the detailed molecular mechanisms of ABA regulations. These findings emphasize the regulatory mechanisms of biosynthesis during early drought stress need to be further ABA biosynthesis during early drought stress. explored. The present study identified a transcription factor, NGTHA1 (NGA1), which positively regulates ABA accumulation drought stress | ABA biosynthesis | transcriptional regulation | NCED3 | during dehydration stress by activating the NCED3 gene encoding NGA a key ABA biosynthetic enzyme. We also identified a cis-acting element bound by NGA1 in the 5′ untranslated region (5′ UTR) NCED3 lants have developed various systems to survive adverse and of the promoter. The NGA1 protein was degraded under Pfluctuating environmental conditions, such as drought, high nonstressed conditions, but it was stabilized during dehydration salt, and extreme temperature, as sessile organisms. Drought stress in an ABA-independent pathway. stress has negative effects on the plant growth and crop yield (1) Author contributions: H.S., H.T., F.T., K.Y.-S., and K.S. designed research; H.S., H.T., T.S., and often causes severe damage to the agricultural crops (2). The and M.S. performed research; H.S., S.I., N.M., M.O.-T., and M.I. contributed new reagents/ plant hormone abscisic acid (ABA) is known as an essential factor analytic tools; H.S., H.T., and T.S. analyzed data; and H.S. and K.S. wrote the paper. that positively regulates the plant drought-stress responses, such as The authors declare no conflict of interest. stomatal closure, induction of drought-inducible genes, and re- This article is a PNAS Direct Submission. pression of plant growth (3). Previous studies revealed the de- Published under the PNAS license. tailed molecular mechanisms by which ABA is transported (4), Data deposition: Transcriptome datasets have been deposited in the DNA Data Bank of received (5) to activate the cellular signal cascades (6, 7), and then Japan (accession no. DRA006360). induces drought-stress-responsive gene expression (8); however, 1To whom correspondence may be addressed. Email: [email protected] or kazuo. the factors that regulate early drought-stress responses before [email protected]. ABA accumulation need to be further explored. 2Present address: Graduate School of Science and Engineering, Saitama University, Sai- Among the various enzymatic proteins involved in several ABA bio- tama, 338-8570 Saitama, Japan. synthetic pathways in plants (9), NINE-CIS-EPOXYCAROTENOID This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10. DIOXYGENASE 3 (NCED3) is known as an important enzyme 1073/pnas.1811491115/-/DCSupplemental. for ABA accumulation during drought stress because expression of www.pnas.org/cgi/doi/10.1073/pnas.1811491115 PNAS Latest Articles | 1of10 Downloaded by guest on September 29, 2021 regulation should be involved in the stabilization of the NGA1 NCED3 knockout mutants (nc3-2)(Fig.1E and F and SI Ap- protein. NGA proteins are B3-type transcription factors, and Ara- pendix,Fig.S1A–C). (In this work, “dehydration” and “drought” bidopsis thaliana has four NGA family proteins. Previous work stresses are defined as water-deficit stress treatments of plants on revealed that the NGA proteins regulate the developmental pro- parafilms from agar plates and plants on soil without a water cess in the reproductive organs or leaves (14–16). In the present supply, respectively.) ABA accumulation during dehydration stress work, we revealed functions of NGA1, which acts as a positive was significantly suppressed in line 1008-2 (Fig. 1G)inaccordwith regulator of ABA biosynthesis during the drought-stress responses the repression of NCED3 (Fig. 1D). The low level of ABA accu- by directly activating the expression of NCED3. mulation in nc3-2 likely results from low induction of another NCED family gene in nc3-2 that was not induced in the wild-type Results plant (21). Thus, we hypothesized that the NGA family proteins NGA2–SRDX-Overexpressing Plants Reveal Repressed Expression of are involved in the transcription of NCED3 during drought stress. NCED3. To identify the transcription factors that regulate ABA NGA proteins are B3-type transcription factors, and Arabi- biosynthesis during early drought responses, we screened a library dopsis thaliana has four NGA family proteins and three NGA- of transgenic plants overexpressing the transcription factors fused like (NGAL) family proteins (SI Appendix, Fig. S1D). RAV to the repressive domain SRDX (CRES-T; chimeric repressor subfamily proteins have the conserved B3 domain with high gene silencing technology) (17). ABA-deficient mutants have been homology to NGA; however, the protein structures are quite reported to show sucrose-insensitive phenotypes during germina- different because they also have conserved AP2 domains. An tion (18). Previous studies reported that sucrose or other sugar- amino acid sequence, K/RLFGV, was found in all of the NGA, insensitive mutants often carried mutations in the genes involved NGAL, and RAV subfamily proteins, which was reported as a in ABA biosynthesis (19, 20). Therefore, we screened 1,795 CRES- putative repressor motif (22). More comprehensive and detailed T plant lines of the
Load more

Recommended publications
  • Document Downloaded From: This Paper Must Be Cited As: the Final
    Document downloaded from: http://hdl.handle.net/10251/83362 This paper must be cited as: Fourquin ., C.; Ferrandiz Maestre, C. (2014). The essential role of NGATHA genes in style and stigma specification is widely conserved across eudicots. New Phytologist. 202(3):1001- 1013. doi:10.1111/nph.12703. The final publication is available at http://doi.org/10.1111/nph.12703 Copyright Wiley Additional Information 1 The essential role of NGATHA genes in style and stigma specification is widely 2 conserved across eudicots 3 Chloé Fourquin and Cristina Ferrándiz1 4 Instituto de Biología Molecular y Celular de Plantas, UPV-CSIC, 46022 Valencia, Spain 5 6 1 For correspondence : 7 Cristina Ferrándiz 8 Instituto de Biología Molecular y Celular de Plantas, UPV-CSIC, 46022 Valencia, Spain 9 Tel. +34 963877892; Fax +34 963877859; e-mail: [email protected] 10 11 Total word count for the main body of the text: 5721 12 13 Word count for individual sections are as follows: 14 • Introduction, 947 15 • Materials and Methods, 765 16 • Results, 2035 17 • Discussion, 1868 18 • Acknowledgements, 106 19 20 The manuscript contains 6 figures (5 in color) and 1 table. 21 Supplementary material consists of 4 figures and 1 table. 22 23 SUMMARY 24 • Carpel development and evolution is a central issue for plant biology. The 25 conservation of genetic functions conferring carpel identity has been widely studied 26 in higher plants. However, although genetic networks directing the development of 27 characteristic features of angiosperm carpels such as stigma and style are 28 increasingly known in Arabidopsis thaliana, little information is available on the 29 conservation and diversification of these networks in other species.
    [Show full text]
  • Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis Vinifera L.): Insights Into the Roles in the Pollen Development Regulation
    G C A T T A C G G C A T genes Article Comprehensive Genome-Wide Exploration of C2H2 Zinc Finger Family in Grapevine (Vitis vinifera L.): Insights into the Roles in the Pollen Development Regulation Oscar Arrey-Salas 1,* , José Carlos Caris-Maldonado 2, Bairon Hernández-Rojas 3 and Enrique Gonzalez 1 1 Laboratorio de Genómica Funcional, Instituto de Ciencias Biológicas, Universidad de Talca, 3460000 Talca, Chile; [email protected] 2 Center for Research and Innovation (CRI), Viña Concha y Toro, Ruta k-650 km 10, 3550000 Pencahue, Chile; [email protected] 3 Ph.D Program in Sciences Mention in Modeling of Chemical and Biological Systems, Faculty of Engineering, University of Talca, Calle 1 Poniente, 1141, 3462227 Talca, Chile; [email protected] * Correspondence: [email protected] Abstract: Some C2H2 zinc-finger proteins (ZFP) transcription factors are involved in the development of pollen in plants. In grapevine (Vitis vinifera L.), it has been suggested that abnormalities in pollen development lead to the phenomenon called parthenocarpy that occurs in some varieties of this cultivar. At present, a network involving several transcription factors types has been revealed and key roles have been assigned to members of the C2H2 zinc-finger proteins (ZFP) family in model plants. However, particularities of the regulatory mechanisms controlling pollen formation in grapevine Citation: Arrey-Salas, O.; remain unknown. In order to gain insight into the participation of ZFPs in grapevine gametophyte Caris-Maldonado, J.C.; development, we performed a genome-wide identification and characterization of genes encoding Hernández-Rojas, B.; Gonzalez, E. ZFP (VviZFP family).
    [Show full text]
  • Genome-Wide Analysis of the AP2/ERF Superfamily in Apple and Transcriptional Evidence of ERF Involvement in Scab Pathogenesis
    View metadata, citation and similar papers at core.ac.uk brought to you by CORE provided by Open Archive Toulouse Archive Ouverte Open Archive Toulouse Archive Ouverte ( OATAO ) OATAO is an open access repository that collects the work of Toulouse researchers and makes it freely available over the web where possible. This is an author-deposited version published in: http://oatao.univ- toulouse.fr/ Eprints ID: 11480 To link to this article : DOI:10.1016/j.scienta.2012.12.017 URL: http://dx.doi.org/10.1016/j.scienta.2012.12.017 To cite this version: Girardi, Cesar Luis and Rombaldi, César Valmor and Dal Cero, Joceani and Nobile, Paula M. and Laurent, François and Bouzayen, Mondher and Quecini, Vera Genome-wide analysis of the AP2/ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis. (2013) Scientia Horticulturae, vol. 151. pp. 112-121. ISSN 0304-4238 Any correspondence concerning this service should be sent to the repository administrator: [email protected] ! Genome•wide analysis of the AP2 /ERF superfamily in apple and transcriptional evidence of ERF involvement in scab pathogenesis a b b c c César Luís Girardi , César Valmor Rombaldi , Joceani Dal Cero , Paula M. Nobile , Franc¸ ois Laurens , d a,∗ Mondher Bouzayen , Vera Quecini a Embrapa Uva e Vinho, Caixa Postal 130, 95700•000 Bento Gonc¸ alves, RS, Brazil b ◦ Universidade Federal de Pelotas, Faculdade de Agronomia Eliseu Maciel, Departamento de Ciência e Tecnologia Agroindustrial, s/n caixa postal 354, 96010•900 Pelotas, RS, Brazil c UMR 1259 Génétique et Horticulture (GenHort), Angers, France d UMR 990, Génomique et Biotechnologie des Fruits, INP, ENSAT, INRA, F•31320 Castanet Tolosan, France a b s t r a c t The APETALA2 (AP2)/ETHYLENE RESPONSE FACTOR (ERF) superfamily of transcriptional regulators is involved in several growth, development and stress responses processes in higher plants.
    [Show full text]
  • Gene Family in Panax Ginseng CA Meyer
    bioRxiv preprint doi: https://doi.org/10.1101/850164; this version posted November 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY 4.0 International license. 1 Structural variation, functional differentiation and 2 expression characteristics of the AP2/ERF gene family and 3 its response to cold stress and methyl jasmonate in Panax 4 ginseng C.A. Meyer 5 Short title: Structural and functional Analysis of AP2/ERF 6 gene family in Panax ginseng C.A. Meyer 1,2 1 1 1 1,2 1,2 7 Jing Chen ☯,Yuanhang Zhou ☯, Qi Zhang , Li Li , Chunyu Sun , Kangyu Wang , 8 Yanfang Wang2,3, Mingzhu Zhao1,2, Hongjie Li1, Yilai Han1, Ping Chen1, Ruiqi Li1, 9 Jun Lei1, Meiping Zhang 1,2*, and Yi Wang 1,2* 10 1 College of Life Science, Jilin Agricultural University, 2888 Xincheng Street, 11 Changchun, Jilin 130118, China. 12 2 Research Center for Ginseng Genetic Resources Development and Utilization, 13 2888 Xincheng Street, Changchun, Jilin 130118, China. 14 3 College of Chinese Medicinal Materials, Jilin Agricultural University, 2888 15 Xincheng Street, Changchun 130118, Jilin, China. 16 17 ☯These authors contributed equally to this work. 18 Correspondence should be addressed to [email protected] and 19 [email protected] 1 bioRxiv preprint doi: https://doi.org/10.1101/850164; this version posted November 20, 2019. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity.
    [Show full text]
  • An Updated Overview on the Regulation of Seed Germination
    An Updated Overview on the Regulation of Seed Germination Table S1. Selected recent reviews on seed germination-related aspects. Subject (Keywords) References Generalists ABA, Arabidopsis, dormancy, germination, GA, seed maturation. [3] GAs and ABA GAs, ABA, hormone signaling, seed germination, abiotic stresses, crosstalk of [10] hormone signaling. DELLAs, GAs, hormone crosstalk, phenotypic plasticity, plant development. [20] DELLA, GRAS, GAs, Arabidopsis, rice, GID1, crosstalk, [22] ABA, ABA synthesis, ABA signaling, ABA response. [35] PYR1, RCAR, ABA transduction, SnRK2, PP2C. [42] ABI5, abiotic stress response, phytohormone crosstalk, ABA, brassinosteroids, GAs, [81] jasmonates, posttranslational modification. Hormones transport GA biosynthesis, GA action, GA transport, evolution, Gibberella fujikuroi. [48] GA, plant hormone, hormone transport and localization, GA transporters, NPF, [49] SWEET. ABA; guard cell; transporter; water stress. [50] GA metabolism, GA transport, GA gradients, cellular growth. [51] Plant NRT1/PTR transporters, phylogenetic relationships, substrates. [72] Glucosinolate, hormone, nitrate, nitrite, peptide, transporter. [73] NIN-like protein (NLP), nitrate, nitrate-responsive gene expression, post- translational regulation, transcription factor, [77] nitrate signalling. Light regulation PIF signaling, Phytochromes, plant development. [109] Chromatin dynamics Shoot apical meristem, quiescent center, floral homeotic gene, polycomb repression, [162] seed development, dormancy, germination and greening. DNA methylation,
    [Show full text]
  • Roles of Wrky Proteins in Mediating the Crosstalk of Hormone Signaling Pathways: an Approach Integrating Bioinformatics and Experimental Biology
    UNLV Retrospective Theses & Dissertations 1-1-2006 Roles of Wrky proteins in mediating the crosstalk of hormone signaling pathways: An approach integrating bioinformatics and experimental biology Zhen Xie University of Nevada, Las Vegas Follow this and additional works at: https://digitalscholarship.unlv.edu/rtds Repository Citation Xie, Zhen, "Roles of Wrky proteins in mediating the crosstalk of hormone signaling pathways: An approach integrating bioinformatics and experimental biology" (2006). UNLV Retrospective Theses & Dissertations. 2711. http://dx.doi.org/10.25669/0cw1-sipg This Dissertation is protected by copyright and/or related rights. It has been brought to you by Digital Scholarship@UNLV with permission from the rights-holder(s). You are free to use this Dissertation in any way that is permitted by the copyright and related rights legislation that applies to your use. For other uses you need to obtain permission from the rights-holder(s) directly, unless additional rights are indicated by a Creative Commons license in the record and/or on the work itself. This Dissertation has been accepted for inclusion in UNLV Retrospective Theses & Dissertations by an authorized administrator of Digital Scholarship@UNLV. For more information, please contact [email protected]. ROLES OF WRKY PROTEINS IN MEDIATING THE CROSSTALK OF HORMONE SIGNALING PATHWAYS: AN APPROACH INTEGRATING BIOINFORMATICS AND EXPERIMENTAL BIOLOGY by Zhen Xie Bachelor of Sciences Shandong Agricultural University 1998 Master of Sciences Shandong Agricultural University 2001 A dissertation submitted in partial fulfillment of the requirements for the Doctor of Philosophy Degree in Biological Sciences Department of Biological Sciences College of Sciences Graduate College University of Nevada, Las Vegas December 2006 Reproduced with permission of the copyright owner.
    [Show full text]
  • LEAFY COTYLEDON2 Encodes a B3 Domain Transcription Factor That Induces Embryo Development
    LEAFY COTYLEDON2 encodes a B3 domain transcription factor that induces embryo development Sandra L. Stone*†, Linda W. Kwong*†, Kelly Matsudaira Yee*, Julie Pelletier*, Loı¨c Lepiniec‡, Robert L. Fischer§, Robert B. Goldberg¶, and John J. Harada*ʈ *Section of Plant Biology, Division of Biological Sciences, University of California, One Shields Avenue, Davis, CA 95616; ‡Seed Biology Laboratory, Laboratoire de Biologie des Semences, Institut National de la Recherche Agronomique, Route de St-Cyr, 78026 Versailles, France; §Department of Plant and Microbial Biology, University of California, Berkeley, CA 94720; and ¶Department of Molecular, Cell, and Developmental Biology, University of California, Los Angeles, CA 90024-1606 Contributed by Robert B. Goldberg, August 6, 2001 The Arabidopsis LEAFY COTYLEDON2(LEC2) gene is a central Early in embryogenesis, LEC genes are required to specify embryonic regulator that serves critical roles both early and late suspensor cell fate and cotyledon identity (12–16). Late in during embryo development. LEC2 is required for the maintenance embryogenesis, LEC genes are needed during the maturation of suspensor morphology, specification of cotyledon identity, phase for the acquisition of desiccation tolerance and the progression through the maturation phase, and suppression of expression of many maturation-specific genes (13–17). Consis- premature germination. We cloned the LEC2 gene on the basis of tent with the finding that conditions that promote maturation its chromosomal position and showed that the predicted polypep- suppress germination (6), lec mutant embryos prematurely ac- tide contains a B3 domain, a DNA-binding motif unique to plants tivate the postgermination program (13, 15, 16, 18). Thus, LEC that is characteristic of several transcription factors.
    [Show full text]
  • RKD Genes: a Novel Transcription Factor Family Involved in the Female Gametophyte Development of Arabidopsis and Wheat
    RKD genes: a novel transcription factor family involved in the female gametophyte development of Arabidopsis and wheat Dissertation zur Erlangung des akademischen Grades doctor rerum naturalium (Dr. rer. nat.) vorgelegt der Mathematisch-Naturwissenschaftlich-Technischen Fakultät (mathematisch-naturwissenschaftlicher Bereich) Martin-Luther-Universität Halle-Wittenberg von Dávid Kőszegi geboren am 20. Februar 1979 in Budapest, Ungarn Gutachter : 1. Prof. Dr. Gerd Jürgens 2. Prof. Dr. Gunter Reuter 3. Prof. Dr. Ulrich Wobus Halle (Saale), den 25. September 2008 To my wife and my family „Mert az őssejtig vagyok minden ős- Az Ős vagyok, mely sokasodni foszlik: Apám- s anyámmá válok boldogon, S apám, anyám maga is kettéoszlik S én lelkes Eggyé így szaporodom!” “that I am every parent in the boundless succession to the primal lonely cell. till I become my father and mother, then father splits and mother, procreating the multiplying me and none other!” (Dunánál, By the Danube, Attila József, Hungarian poet, 1905-1937) ii Table of contents List of abbreviations vi 1. Introduction 1 1.1. Alternation of generations – speciality of plants: gametophyte proliferation 1 1.2. Development of the female sexual organs 1 1.3. Apomixis - avoidance of sexuality 4 1.4. Genetic analysis of plant reproduction 5 1.4.1. The sexual pathway 5 1.4.2. The apomictic pathway 7 1.5. The Salmon system of wheat 8 1.6. Main objectives 9 2. Materials and methods 11 2.1. Plant material 11 2.2. Cloning methods 11 2.3. Arabidopsis transformation 11 2.4. cDNA array hybridisation 11 2.5. RT-PCR 12 2.6.
    [Show full text]
  • Transcriptional Regulation in Plants: the Importance of Combinatorial Control
    Plant Physiol. (1998) 118: 1111–1120 Update on Gene Regulation Transcriptional Regulation in Plants: The Importance of Combinatorial Control Karam B. Singh Department of Molecular, Cell and Developmental Biology, University of California, Los Angeles, California 90095–1606 GLOSSARY OF TERMS plant-defense/stress response. A major level at which gene expression is regulated is the initiation of transcription, Combinatorial control: use of a discrete number of tran- and this is reflected in the percentage of the genome ded- scription factors in different combinations to give rise to icated to transcription factors in plants and other eu- a wide spectrum of expression patterns. karyotes. For example, an analysis of 1.9 Mb of Arabidopsis Enhanceosome: a higher-order nucleoprotein complex that genomic sequence from chromosome 4 revealed that about is formed by the binding of a specific combination of 15% of the genes with predicted or known functions were transcription factors to the transcriptional regulatory se- involved in transcription, a percentage similar to what has quences of a particular gene. been found in other eukaryotes (Bevan et al., 1998). General transcription factors: components of the Pol II In eukaryotic cells, genomic DNA is complexed with transcription-initiation complex that are thought to be proteins to form chromatin. One of chromatin’s major roles common to all Pol II promoters. is to facilitate the packaging of DNA in the nucleus, but the Holoenzyme: a large protein complex that is preformed structure of chromatin also leads to a general suppression off of the DNA and contains Pol II and many of the of gene activity.
    [Show full text]
  • MADS Interactomics
    MADS interactomics Towards understanding the molecular mechanisms of plant MADS-domain transcription factor function Cezary Smaczniak MADS interactomics Towards understanding the molecular mechanisms of plant MADS-domain transcription factor function Cezary Smaczniak Thesis Committee Promotor Prof. dr. ir. G.C. Angenent Personal chair at the Laboratory of Molecular Biology Wageningen University Co-promotor Dr. K. Kaufmann Assistant Professor, Laboratory of Molecular Biology Wageningen University Other members Prof. dr. ir. B.J.G. Scheres, Wageningen University Prof. dr. B. Davies, University of Leeds, United Kingdom Dr. C.C. Carles, Joseph Fourier University, Grenoble, France Dr. ir. J.J.M. Vervoort, Wageningen University This research was conducted under the auspices of the Graduate School of Experimental Plant Sciences. MADS interactomics Towards understanding the molecular mechanisms of plant MADS-domain transcription factor function Cezary Dominik Smaczniak Thesis submitted in fulfillment of the requirements for the degree of doctor at Wageningen University by the authority of the Rector Magnificus Prof. dr. M.J. Kropff, in the presence of the Thesis Committee appointed by the Academic Board to be defended in public on Wednesday 16 January 2013 at 1.30 p.m. in the Aula. Cezary Dominik Smaczniak MADS interactomics. Towards understanding the molecular mechanisms of plant MADS- domain transcription factor function. 178 pages Thesis, Wageningen University, Wageningen, NL (2013). With references, with summaries in Dutch, English and Polish.
    [Show full text]
  • Transcriptomic Analysis and Specific Expression of Transcription Factor
    International Journal of Molecular Sciences Article Transcriptomic Analysis and Specific Expression of Transcription Factor Genes in the Root and Sporophyll of Dryopteris fragrans (L.) Schott Lingling Chen, Dongrui Zhang, Chunhua Song, Hemeng Wang, Xun Tang and Ying Chang * College of Life Sciences, Northeast Agricultural University, Harbin 150030, Heilongjiang Province, China; [email protected] (L.C.); [email protected] (D.Z.); [email protected] (C.S.); [email protected] (H.W.); [email protected] (X.T.) * Correspondence: [email protected] Received: 28 July 2020; Accepted: 28 September 2020; Published: 2 October 2020 Abstract: Background: Dryopteris fragrans, which is densely covered with glandular trichomes, is considered to be one of the ferns with the most medicinal potential. The transcriptomes from selected tissues of D. fragrans were collected and analyzed for functional and comparative genomic studies. The aim of this study was to determine the transcriptomic characteristics of wild D. fragrans sporangium in tissues from the SR (root), SL (sporophyll), and TRL (sporophyll with glandular trichomes removed). Results: Cluster analysis identified genes that were highly expressed in an organ-specific manner according to read mapping, feature counting, and normalization. The functional map identified gene clusters that can uniquely describe the function of each tissue. We identified a group of three tissue-specific transcription factors targeting the SL, SR, and TRL. In addition, highly expressed transcription factors (TFs) were found in each tissue-specific gene cluster, where ERF and bHLH transcription factors were the two types showing the most distinct expression patterns between the three different tissues. The specific expression of transcription factor genes varied between the different types of tissues.
    [Show full text]
  • DNA-Binding Specificities of Plant Transcription Factors and Their Potential to Define Target Genes
    DNA-binding specificities of plant transcription factors and their potential to define target genes José M. Franco-Zorrillaa,1, Irene López-Vidrieroa, José L. Carrascob, Marta Godoya, Pablo Verab, and Roberto Solanoc,1 aGenomics Unit and cDepartment of Plant Molecular Genetics, Centro Nacional de Biotecnología (CNB)-Consejo Superior de Investigaciones Científicas (CSIC), Darwin 3, 28049 Madrid, Spain; and bInstituto de Biología Molecular y Celular de Plantas, Universidad Politécnica de Valencia-Consejo Superior de Investigaciones Científicas, 46022 Valencia, Spain Edited by Philip N. Benfey, Duke University, Durham, NC, and approved January 2, 2014 (received for review August 29, 2013) Transcription factors (TFs) regulate gene expression through bind- The application of high-throughput in vitro techniques is ing to cis-regulatory specific sequences in the promoters of their making the identification of the binding-sequences of all of the target genes. In contrast to the genetic code, the transcriptional TFs in a genome an affordable task. SELEX-seq and protein- regulatory code is far from being deciphered and is determined binding microarrays (PBMs) have yielded information of binding by sequence specificity of TFs, combinatorial cooperation between motifs for hundreds of TFs in mammals but these studies still TFs and chromatin competence. Here we addressed one of these lack of a simple and systematic analysis of the biological rele- determinants by characterizing the target sequence specificity of vance of the motifs (3, 4). In this study, we defined the DNA- 63 plant TFs representing 25 families, using protein-binding micro- binding motifs for 63 Arabidopsis thaliana TFs in vitro by means arrays. Remarkably, almost half of these TFs recognized secondary of PBM analysis, with a particular emphasis of plant-specific motifs, which in some cases were completely unrelated to the pri- families, and observed that approximately half of them may mary element.
    [Show full text]