DOCSLIB.ORG

Effect of Nitric Oxide on Gene Transcription – S-Nitrosylation of Nuclear Proteins

Total Page：16

File Type：pdf, Size：1020Kb

Download full-text PDF Read full-text
Effect of Nitric Oxide on Gene Transcription – S-Nitrosylation of Nuclear Proteins REVIEW ARTICLE published: 01 August 2013 doi: 10.3389/fpls.2013.00293 Effect of nitric oxide on gene transcription – S-nitrosylation of nuclear proteins Alexander Mengel, Mounira Chaki, Azam Shekariesfahlan and Christian Lindermayr* Institute of Biochemical Plant Pathology, Helmholtz Zentrum München – German Research Center for Environmental Health, Neuherberg, Germany Edited by: Nitric oxide (NO) plays an important role in many different physiological processes in plants. Emmanuel Baudouin, Université It mainly acts by post-translationally modifying proteins. Modification of cysteine residues Pierre et Marie Curie - Paris 6, France termed as S-nitrosylation is believed to be the most important mechanism for transduction Reviewed by: of bioactivity of NO. The first proteins found to be nitrosylated were mainly of cytoplasmic Georgia Tanou, Aristotle University of Thessaloniki, Greece origin or isolated from mitochondria and peroxisomes. Interestingly, it was shown that David Wendehenne, University of redox-sensitive transcription factors are also nitrosylated and that NO influences the redox- Burgundy, France dependent nuclear transport of some proteins.This implies that NO plays a role in regulating *Correspondence: transcription and/or general nuclear metabolism which is a fascinating new aspect of NO Christian Lindermayr, Institute of signaling in plants. In this review, we will discuss the impact of S-nitrosylation on nuclear Biochemical Plant Pathology, Helmholtz Zentrum München – plant proteins with a focus on transcriptional regulation, describe the function of this German Research Center for modification and draw also comparisons to the animal system in which S-nitrosylation Environmental Health, Ingolstädter of nuclear proteins is a well characterized concept. Landstrasse 1, 85764 Neuherberg, Germany Keywords: protein S-nitrosylation, nitric oxide, post-translational modification, nuclear proteins, redox- e-mail: lindermayr@helmholtz- modification muenchen.de INTRODUCTION There are three important NO-dependent modifications: metal Nitric oxide (NO) is a small, highly reactive gaseous radical. nitrosylation, tyrosine nitration, and cysteine S-nitrosylation. Although it is cytotoxic in high concentrations, NO plays a key In a direct reaction termed metal nitrosylation, NO (Lewis base) role as a biological messenger in all kingdoms. In plants, it is binds to the transition metal (Lewis acid) of metalloproteins yield- implicated in various physiological processes like flowering, stom- ing a metal–nitrosyl complex. One example from mammals is the atal closure, germination, root development, gravitropism, and binding of NO to the heme center of soluble guanylate cyclase responses to abiotic and biotic stresses (Delledonne et al., 1998; which activates this enzyme by inducing conformational changes Durner et al., 1998; Garcia-Mata and Lamattina, 2002; Pagnussat and this in turn leads to the production of cyclic GMP (Russwurm et al., 2002; He et al., 2004; Hu et al., 2005; Lombardo et al., 2006; and Koesling, 2004). De Michele et al., 2009; Sirova et al., 2011; Tanou et al., 2012). Reactive nitrogen species can modify the activity of proteins Due to its instable nature, NO has a very rich chemistry. by covalently binding to tyrosine and cysteine residues. Tyrosine Besides direct dative binding to metal ions NO can further react nitration refers to the addition of a nitro group to susceptible with superoxide and molecular oxygen, resulting in the forma- tyrosine residues in ortho position to the hydroxyl group thus tion of peroxynitrite and dinitrogen trioxide N2O3 (or higher leading to 3-nitrotyrosine. The main nitrating species is peroxyni- oxides like NO2), respectively. Moreover, adding or removing trite which is produced in a diffusion controlled reaction between one electron from the antibonding highest occupied molecular NO and superoxide (Ferrer-Sueta and Radi, 2009). Tyrosine nitra- orbital by reducing or oxidizing chemicals yields nitroxyl anion tion was originally considered to be indicative for oxidative and (NO−) and nitrosonium cation (NO+). Collectively, these species nitrosative stress but evidence accumulates that this modification are referred to as reactive nitrogen species (RNS) each having also has a signaling function in plant cells (Cecconi et al., 2009; distinct chemical properties leading to numerous reactions with Gaupels et al., 2011). biological molecules like lipids, carbohydrates, nucleic acids, and S-nitrosylation of protein cysteine residues is believed to be proteins. Although most of these reactions were assumed to be the most important mechanism for transduction of bioactivity of indicative for nitrosative stress in the past, it has become clear that NO in plants. The formation of nitrosothiols is still debated. The some of these RNS also function as important redox-signaling direct reaction of thiol groups with NO is too slow to occur in vivo, molecules in the cell by binding covalently to target proteins instead it is assumed that N2O3 is the main nitrosylating species in (Suzuki et al., 2012; Yun et al., 2012). This as redox-signaling aerobic conditions although the formation of dinitrogen trioxide termed mechanism should not be considered as a discrete set of is controversially discussed (Folkes and Wardman, 2004; Ridnour signaling cascades. Rather, the cell should be seen as set of com- et al., 2004). Other RNS described to mediate S-nitrosothiol for- partments each having distinct redox-sensitive proteins as well as mation are nitrosonium and nitroxyl ions (Ridnour et al., 2004). redox buffering capacities. Changes in the redox potential of these Nitroso groups can also be transferred between thiols in a process compartments could then influence other signaling pathways by termed as transnitrosylation. Transnitrosylation occurs between modifying redox-sensitive proteins (Foyer and Noctor, 2013). proteins and between proteins and low molecular weight SNOs www.frontiersin.org August 2013 | Volume 4 | Article 293 | 1 “fpls-04-00293” — 2013/7/30 — 17:42 — page1—#1 Mengel et al. S-nitrosylation of nuclear proteins (e.g., S-nitrosylated glutathione GSNO) in animals; in plants, post-translational modifications like oxidation to sulfinic acid, however, evidence for this mechanism is lacking (Hogg, 2002; S-glutathionylation, or S-nitrosylation. Each of these modifica- Nakamura and Lipton, 2013). Enzymatic denitrosylation is medi- tions affects binding affinity and specificity of OxyR to DNA ated by GSNO reductase (GSNOR) and thioredoxins (Trx), both thus resulting in distinct transcriptional responses (Marshall et al., proteins are crucial for maintaining SNO-homeostasis (Sakamoto 2000). Besides regulation of DNA-binding, S-nitrosylation of et al., 2002; Feechan et al., 2005; Sengupta and Holmgren, 2013). nuclear proteins could also affect their subcellular localization or Initial proteomic screens for S-nitrosylated proteins in regulate the association with binding partners thereby modulating A. thaliana revealed 53 mainly cytoplasmic proteins but this num- transcription and/or general nuclear metabolism. In animals, for ber increased drastically over the last years (Lindermayr et al., instance, S-nitrosylation of the nuclear export receptor CRM1 2005). Up to date several screens targeting the proteomes of differ- (karyopherin chromosomal region maintenance 1) leads to a ent organelles like mitochondria and peroxisomes identified more decrease in the export rate and a subsequent nuclear accumula- than 250 candidate proteins to be S-nitrosylated involved in a wide tion of its target protein Nrf2, an antioxidant transcription factor range of physiological processes ranging from stress response to (Wang et al., 2009). The possible modes of action of NO on gene metabolism (Kovacs and Lindermayr, 2013; Lounifi et al., 2013). transcription are shown in Figure 1. Interestingly, microarray analysis and amplified fragment-length In this review, we will summarize the current knowledge about polymorphism (AFLP) transcript profiling of plants treated with S-nitrosylated nuclear plant proteins. What is the impact and func- gaseous NO and sodium nitroprusside, respectively, showed that tion of this post-translational modification? Comparisons to the NO leads to changes in the transcriptome of Arabidopsis (Huang animal system will be drawn in which much more is known about et al., 2002; Polverari et al., 2003). Promoter analysis of the genes the effect of S-nitrosylation on transcription. co-expressed after NO treatment revealed the accumulation of cer- tain transcription factor binding sites, like octopine synthase gene S-NITROSYLATED NUCLEAR PROTEINS (ocs) elements and WRKY-sites (Palmieri et al., 2008). This raised GLYCERALDEHYDE 3-PHOSPHATE DEHYDROGENASE AND CYTOSOLIC the question whether NO affects transcription directly by nitro- ALDOLASE sylating transcription factors or other transcriptional regulators. It is well-known that glyceraldehyde 3-phosphate dehydrogenase In some bacteria, for instance, redox-sensitive cysteine residues of (GAPDH) not only plays an important role in glycolysis but also the transcriptional activator OxyR can undergo redox-dependent participates in nuclear events like regulation of gene transcription, FIGURE 1 | S-nitrosylation can affect gene transcription in several 2007; Lindermayr et al., 2010; Sha and Marshall, 2012). Additionally, ways. Upon S-nitrosylation proteins can change their subcellular localization SNO-formation can lead to association/dissociation of macromolecular which
Load more

Recommended publications
  • Hypothetical Cytokinin-Binding Riboswitches in Arabidopsis Thaliana Jeremy Grojean1, Brian Downes2*
    Grojean and Downes Biology Direct 2010, 5:60 http://www.biology-direct.com/content/5/1/60 HYPOTHESIS Open Access Riboswitches as hormone receptors: hypothetical cytokinin-binding riboswitches in Arabidopsis thaliana Jeremy Grojean1, Brian Downes2* Abstract Background: Riboswitches are mRNA elements that change conformation when bound to small molecules. They are known to be key regulators of biosynthetic pathways in both prokaryotes and eukaryotes. Presentation of the Hypothesis: The hypothesis presented here is that riboswitches function as receptors in hormone perception. We propose that riboswitches initiate or integrate signaling cascades upon binding to classic signaling molecules. The molecular interactions for ligand binding and gene expression control would be the same as for biosynthetic pathways, but the context and the cadre of ligands to consider is dramatically different. The hypothesis arose from the observation that a compound used to identify adenine binding RNA sequences is chemically similar to the classic plant hormone, or growth regulator, cytokinin. A general tenet of the hypothesis is that riboswitch-binding metabolites can be used to make predictions about chemically related signaling molecules. In fact, all cell permeable signaling compounds can be considered as potential riboswitch ligands. The hypothesis is plausible, as demonstrated by a cursory review of the transcriptome and genome of the model plant Arabidopsis thaliana for transcripts that i) contain an adenine aptamer motif, and ii) are also predicted to be cytokinin- regulated. Here, one gene, CRK10 (for Cysteine-rich Receptor-like Kinase 10, At4g23180), contains an adenine aptamer-related sequence and is down-regulated by cytokinin approximately three-fold in public gene expression data.
    [Show full text]
  • The WRKY Transcription Factor Family in Model Plants and Crops
    Critical Reviews in Plant Sciences ISSN: 0735-2689 (Print) 1549-7836 (Online) Journal homepage: http://www.tandfonline.com/loi/bpts20 The WRKY Transcription Factor Family in Model Plants and Crops Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang Cai, Yuan Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang To cite this article: Fei Chen, Yue Hu, Alessandro Vannozzi, Kangcheng Wu, Hanyang Cai, Yuan Qin, Alison Mullis, Zhenguo Lin & Liangsheng Zhang (2018): The WRKY Transcription Factor Family in Model Plants and Crops, Critical Reviews in Plant Sciences, DOI: 10.1080/07352689.2018.1441103 To link to this article: https://doi.org/10.1080/07352689.2018.1441103 Published online: 05 Mar 2018. Submit your article to this journal View related articles View Crossmark data Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=bpts20 CRITICAL REVIEWS IN PLANT SCIENCES https://doi.org/10.1080/07352689.2018.1441103 The WRKY Transcription Factor Family in Model Plants and Crops Fei Chena, Yue Hua, Alessandro Vannozzib, Kangcheng Wua, Hanyang Caia, Yuan Qina, Alison Mullisc, Zhenguo Linc, and Liangsheng Zhanga aState Key Laboratory of Ecological Pest Control for Fujian and Taiwan Crops; Key Laboratory of Ministry of Education for Genetics, Breeding and Multiple Utilization of Crops; Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology; Fujian Agriculture and Forestry University, Fuzhou, China; bDepartment of Agronomy, Food, Natural Resources, Animals, and Environment (DAFNAE), University of Padova, Legnaro, Italy; cDepartment of Biology, Saint Louis University, St Louis, Missouri, USA ABSTRACT KEYWORDS The WRKY gene family in flowering plants encodes a large group of transcription factors (TFs) that environmental stress; gene play essential roles in diverse stress responses, developmental, and physiological processes.
    [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]
  • Natively Unstructured in Transcription Factors
    Intrinsic Disorder in Transcription Factors Jiangang (Al) Liu Submitted to the faculty of the Indiana University School of Informatics Graduate School in partial fulfillment of the requirements for the degree Master of Sciences in Bioinformatics, August 2005 TABLE OF CONTENTS TOPIC PAGE NUMBER I. ACKNOWLEDGEMENTS 4 II. ABSTRACT 5 III. INTRODUCTION 7 III.A TRANSCRIPTION FACTORS 7 III.A.1 DNA Binding Domains 10 III.A.2 TF activation domain 16 III.B INTRINSIC DISORDER AND PROTEIN FUNCTION 16 III.B.1 Experimental Approaches 17 III.B.2 Computational Approaches 20 IV. BACKGROUND 24 IV.A RELATED RESEARCH 24 IV.B PROSOSED HYPOTHESIS 26 IV.C INTENDED PROJECT 27 V. MATERIALS AND METHODS 28 V.A DATASETS 28 V.A.1 Dataset sources and sequence retrieving methods 28 V.A.2 Non-redundant representative dataset preparation 30 V.B DISORDER PREDICTIONS 31 V.B.1 PONDR VL-XT 31 2 TABLE OF CONTENTS (continued) TOPIC PAGE NUMBER V.B.2 Cumulative Distribution Functions (CDFs) 33 V.B.3 Charge-Hydropathy Plots 33 V.C TF DOMAIN INFORMATION 34 V.D AMINO ACID COMPOSITION PLOTS 35 VI. RESULTS AND DISCUSSION 37 VI.A DATASET CHARACTERIZATION 37 VI.B DISORDER PREDICTION ON TFS 40 VI.C TF COMPOSITIONAL SPECIFICITY 47 VI.D DISORDER IN TF DOMAIN AND SUBDOMAIN 49 VI.E TOP 15 PREDICTIONS OF DISORDERED TFS 56 VI.F TF DISORDER IN DIFFERENT SPECIES 60 VII. CONCLUSIONS 63 VIII. REFERENCES 65 IX. APPENDIX 72 3 I. ACKNOWLEDGEMENTS Committee members: Dr. Narayanan B Perumal Dr. Vladimir Uversky Dr. A Keith Dunker Eli Lilly and Company: Dr.
    [Show full text]
  • Polyploidization Events Shaped the Transcription Factor Repertoires in Legumes (Fabaceae)
    Polyploidization events shaped the transcription factor repertoires in legumes (Fabaceae) Kanhu C. Moharana and Thiago M. Venancio* Laboratório de Química e Função de Proteínas e Peptídeos, Centro de Biociências e Biotecnologia, Universidade Estadual do Norte Fluminense Darcy Ribeiro; Campos dos Goytacazes, Brazil. * Corresponding author Av. Alberto Lamego 2000 / P5 / 217; Parque Califórnia Campos dos Goytacazes, RJ Brazil CEP: 28013-602 [email protected] Supplementary figures Supplementary Figure S1: Number of Arabidopsis thaliana transcription factors predicted using our pipeline in comparison with that available in PlantTFDB. Supplementary Figure S2: Ks distribution of collinear paralogous pairs in Vitis vinifera and legumes. Ks peaks from each species likely represent whole-genome duplications. The time scale at the top was used to estimate the age of the duplication event and was estimated as T=Ks/2λ, where λ is number of synonymous substitutions per synonymous substitutions sites per year. We estimated T using λ =6.1*1e-9, as previously described (Lynch and Conery, 2003). Supplementary Figure S3: Schematic representation of collinear regions in Aquilegia coerulea and Amborella trichopoda, showing the expansion of GRAS TFs in the latter. In both panels (A and B), the upper and lower bars represent pseudo-chromosomes/contigs from Aq. coerulea and Am. trichopoda, respectively. Genes are represented by yellow arrows. Green shades connect homologous genes in the two species. Locally duplicated genes are shown as red arrows. GRAS genes are labeled with gene names and have red borders. A. Aq. coerulea (Ac05:38.45Mb-38.73Mb) versus Am. trichopoda (Sf00166:0.16Mb-0.52Mb), B. Aq. coerulea (Ac02:32.95Mb-33.18Mb) versus.
    [Show full text]
  • (12) Patent Application Publication (10) Pub. No.: US 2002/0177218 A1 Fang Et Al
    US 2002O177218A1 (19) United States (12) Patent Application Publication (10) Pub. No.: US 2002/0177218 A1 Fang et al. (43) Pub. Date: Nov. 28, 2002 (54) METHODS OF DETECTING MULTIPLE DNA Publication Classification BINDING PROTEIN AND DNA INTERACTIONS IN A SAMPLE, AND (51) Int. Cl." ....................................................... C12N 1/20 DEVICES, SYSTEMS AND KITS FOR (52) U.S. Cl. .......................................................... 435/252.3 PRACTICING THE SAME (57) ABSTRACT (76) Inventors: Yu Fang, Fremont, CA (US); Methods for detecting the presence of at least one, usually Xiao-Yang Wang, Mountain View, CA a plurality of, DNA binding proteins, e.g., transcription (US); Pierre Turpin, San Francisco, factors, in a Sample, both qualitatively and quantitatively, are CA (US) provided. In the Subject methods, a Substrate having one or Correspondence Address: more DNA probes immobilized on a surface thereof, one for each DNA binding protein of interest, is contacted with a BOZICEVIC, FIELD & FRANCIS LLP Sample under conditions Sufficient for binding complexes of 200 MIDDLEFIELD RID the probes and their respective DNA binding proteins to be SUTE 200 produced. The Sample may be purified with respect to one or MENLO PARK, CA 94025 (US) more DNA binding proteins or be a cellular/nuclear extract. (21) Appl. No.: 10/113,877 Resultant binding complexes on the Surface of the Substrate are then detected and related to the presence of the DNA (22) Filed: Mar. 29, 2002 binding protein-DAN interations of interest in the Sample. Also provided are devices and Systems for use in practicing Related U.S. Application Data the subject methods. The subject methods find use in a variety of different applications, e.g., detecting the presence (60) Provisional application No.
    [Show full text]
  • The WRKY Superfamily of Plant Transcription Factors Thomas Eulgem, Paul J
    trends in plant science Reviews The WRKY superfamily of plant transcription factors Thomas Eulgem, Paul J. Rushton, Silke Robatzek and Imre E. Somssich The WRKY proteins are a superfamily of transcription factors with up to 100 representatives in Arabidopsis. Family members appear to be involved in the regulation of various physio- logical programs that are unique to plants, including pathogen defense, senescence and trichome development. In spite of the strong conservation of their DNA-binding domain, the overall structures of WRKY proteins are highly divergent and can be categorized into distinct groups, which might reflect their different functions. ne of the apparent fundamental principles of biological The name of the WRKY family is derived from the most promi- evolution is that the progression from ancient to advanced nent feature of these proteins, the WRKY domain, a 60 amino acid Olife forms is inseparably connected to an increase in regu- region that is highly conserved amongst family members. The latory capacity. Genome-sequencing efforts have provided evi- emerging picture is that these proteins are regulatory transcription dence for a positive correlation between the proportion of genes factors with a binding preference for the W box, but with the involved in information processing and the complexity of organ- potential to differentially regulate the expression of a variety of isms. More than 20% of the genes within the sequence available target genes. Consistent with a role as transcription factors, for the Arabidopsis thaliana genome appear to encode proteins PcWRKY1 and WIZZ (from tobacco) have been shown to be tar- that play a role in signal transduction or transcription1, whereas geted to the nucleus11,12.
    [Show full text]
  • Table S2. List of Arabidopsis Transcription Factors Encoding Genes Cloned in the Per8gw Binary Vector Used in This Work. AGI
    Table S2. List of Arabidopsis transcription factors encoding genes cloned in the pER8GW binary vector used in this work. AGI code Annotation AT3G16770.1 ATEBP_EBP_ERF72_RAP2.3__ethylene-responsive element binding protein AT5G18270.1 ANAC087__Arabidopsis NAC domain containing protein 87 AT4G14550.1 IAA14_SLR__indole-3-acetic acid inducible 14 AT4G36540.1 BEE2__BR enhanced expression 2 AT2G18300.1 basic helix-loop-helix (bHLH) DNA-binding superfamily protein AT4G11880.1 AGL14__AGAMOUS-like 14 AT5G13790.1 AGL15__AGAMOUS-like 15 AT3G57230.1 AGL16__AGAMOUS-like 16 AT2G22630.1 AGL17__AGAMOUS-like 17 AT3G04730.1 IAA16__indoleacetic acid-induced protein 16 AT1G51950.1 IAA18__indole-3-acetic acid inducible 18 AT3G23050.1 AXR2_IAA7__indole-3-acetic acid 7 AT5G10140.1 AGL25_FLC_FLC_FLF__K-box region and MADS-box transcription factor family protein AT5G65050.1 AGL31_MAF2__AGAMOUS-like 31 AT5G23260.1 ABS_AGL32_TT16__K-box region and MADS-box transcription factor family protein AT5G55690.1 MADS-box transcription factor family protein AT5G51870.1 AGL71__AGAMOUS-like 71 AT4G17490.1 ATERF6_ERF-6-6_ERF6__ethylene responsive element binding factor 6 AT3G12890.1 ASML2__activator of spomin::LUC2 AT2G46790.1 APRR9_PRR9_TL1__pseudo-response regulator 9 AT4G09100.1 RING/U-box superfamily protein AT3G61550.1 RING/U-box superfamily protein AT1G51070.1 bHLH115__basic helix-loop-helix (bHLH) DNA-binding superfamily protein AT4G35550.1 ATWOX13_HB-4_WOX13__WUSCHEL related homeobox 13 AT2G01500.1 HOS9_PFS2_WOX6__Homeodomain-like superfamily protein AT5G45980.1 STPL_WOX8__WUSCHEL
    [Show full text]
  • Transcriptional Regulation: a Genomic Overview
    The Arabidopsis Book ©2002 American Society of Plant Biologists Transcriptional Regulation: a Genomic Overview José Luis Riechmann Mendel Biotechnology, 21375 Cabot Blvd., Hayward, CA 94545, USA e-mail: [email protected] and California Institute of Technology, Division of Biology 156-29, Pasadena, CA 91125 e-mail: [email protected] Abstract The availability of the Arabidopsis thaliana genome sequence allows a comprehensive analysis of transcriptional regulation in plants using novel genomic approaches and methodologies. Such a genomic view of transcription first necessitates the compilation of lists of elements. Transcription factors are the most numerous of the different types of proteins involved in transcription in eukaryotes, and the Arabidopsis genome codes for more than 1,500 of them, or approximately 6% of its total number of genes. A genome-wide comparison of transcription factors across the three eukaryotic kingdoms reveals the evolutionary generation of diversity in the components of the regulatory machinery of transcription. However, as illustrated by Arabidopsis, transcription in plants follows similar basic prin- ciples and logic to those in animals and fungi. A global view and understanding of transcription at a cellular and organismal level requires the characterization of the Arabidopsis transcriptome and promoterome, as well as of the interactome, the localizome, and the phenome of the proteins involved in transcription. Introduction. Many of the biological processes in a plant are regulated mutations in transcription factors (Peng et al., 1999), at the level of transcription. Changes in gene expression alterations in their expression (Doebley et al., 1997; Wang have been shown to underlie the response to et al., 1999b), or changes in the expression of other types environmental cues and stresses (such as light, of regulatory proteins (Frary et al., 2000).
    [Show full text]
  • Mitogen-Activated Protein Kinase Cascades in Plants
    Opinion TRENDS in Plant Science Vol.7 No.7 July 2002 301 18 Blazquez, M.A. and Weigel, D. (2000) Integration substrate change and catalytic simplification. of genomes. Proc. Natl. Acad. Sci. U. S. A. of floral inductive signals in Arabidopsis. Proc. Natl. Acad. Sci. U. S. A. 93, 9033–9038 99, 1405–1409 Nature 404, 889–892 27 Nowak, M.A. et al. (1997) Evolution of genetic 36 Shu, G. et al. (2000) LEAFY and the evolution of 19 Blazquez, M.A. et al. (1997) LEAFY expression redundancy. Nature 388, 167–171 rosette flowering in violet cress (Jonopsidium and flower initiation in Arabidopsis. Development 28 Lynch, M. et al. (2001) The probability of acaule, Brassicaceae). Am. J. Bot. 87, 634–641 124, 3835–3844 preservation of a newly arisen gene duplicate. 37 Ahearn, K.P. et al. (2001) NFL1, a Nicotiana 20 Parcy, F. et al. (1998) A genetic framework for Genetics 159, 1789–1804 tabacum LEAFY-like gene, controls meristem floral patterning. Nature 395, 561–566 29 Wagner, G.P. and Altenberg, L. (1996) Complex initiation and floral structure. Plant Cell Physiol. 21 Lohmann, J.U. et al. (2001) A molecular link adaptations and the evolution of evolvability. 42, 1130–1139 between stem cell regulation and floral patterning Evolution 50, 967–976 38 Gourlay, C.W. et al. (2000) Pea compound leaf in Arabidopsis. Cell 105, 793–803 30 Coen, E.S. and Meyerowitz, E.M. (1991) The war architecture is regulated by interactions among 22 Weigel, D. et al. (1992) LEAFY controls of the whorls: genetic interactions controlling the genes UNIFOLIATA, COCHLEATA, AFILA, floral meristem identity in Arabidopsis.
    [Show full text]
  • Transcriptome Profiling Reveals Transcriptional Regulation by DNA
    International Journal of Molecular Sciences Article Transcriptome Profiling Reveals Transcriptional Regulation by DNA Methyltransferase Inhibitor 5-Aza-20-Deoxycytidine Enhancing Red Pigmentation in Bagged “Granny Smith” Apples (Malus domestica) Changqing Ma 1,2, Bowen Liang 1, Bo Chang 1,2, Li Liu 1,2, Jiuying Yan 1,2, Yazhou Yang 1,2 and Zhengyang Zhao 1,2,* 1 State Key Laboratory of Crop Stress Biology for Arid Areas, College of Horticulture, Northwest A & F University, Yangling 712100, China; [email protected] (C.M.); [email protected] (B.L.); [email protected] (B.C.); [email protected] (L.L.); [email protected] (J.Y.); [email protected] (Y.Y.) 2 Shaanxi Research Center of Apple Engineering and Technology, Yangling 712100, China * Correspondence: [email protected] or [email protected]; Tel.: +86-029-8708-2922 Received: 10 August 2018; Accepted: 9 October 2018; Published: 12 October 2018 Abstract: The red color of apples (Malus domestica) is an attractive trait for consumers. The green skinned “Granny Smith” cultivar develops red pigmentation after bagging treatment. DNA methylation plays an important role in various developmental processes in plants. To explore the possible functions of DNA methylation in the pigmentation of bagged “Granny Smith” apples, we first analyzed the anthocyanin content of fruit skin following treatment with the DNA methyltransferase inhibitor 5-aza-20-deoxycytidine (5-aza-dC). The results revealed an increase in anthocyanin content in bagged fruits following 5-aza-dC treatment, while no anthocyanins were detected in unbagged fruits. In addition, 8482 differentially expressed genes between 5-aza-dC-treated and control groups were identified in bagged fruits by RNA sequencing, including genes encoding transcription factors, enzymes related to anthocyanin accumulation, and methylases.
    [Show full text]
  • BIOINFORMATICS of GENOME REGULATION and STRUCTURE\SYSTEMS BIOLOGY (BGRS\SB-2018) the Eleventh International Conference
    Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences Novosibirsk State University BIOINFORMATICS OF GENOME REGULATION AND STRUCTURE\SYSTEMS BIOLOGY (BGRS\SB-2018) The Eleventh International Conference Abstracts 20–25 August, 2018 Novosibirsk, Russia Novosibirsk ICG SB RAS 2018 УДК 575 B60 Bioinformatics of Genome Regulation and Structure\Systems Biology (BGRS\SB-2018) : The Eleventh International Conference (20–25 Aug. 2018, Novosibirsk, Russia); Abstracts / Institute of Cytology and Genetics, Siberian Branch of Russian Academy of Sciences; Novosibirsk State University. – Novosibirsk: ICG SB RAS, 2018. – 267 pp. – ISBN 978-5-91291-036-4. ISBN 978-5-91291-036-4 © ICG SB RAS, 2018 International program committee • Nikolai Kolchanov, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia (Conference Chair) • Ralf Hofestädt, University of Bielefeld, Germany • Mikhail Fedoruk, Novosibirsk State University, Novosibirsk, Russia • Lubomir Aftanas, State Scientific-Research Institute of Physiology & Basic Medicine, Novosibirsk, Russia • Ivo Grosse, Halle-Wittenberg University, Halle, Germany • Olga Lavrik, Institute of Chemical Biology and Fundamental Medicine of SB RAS, Novosibirsk, Russia • Dmitry Afonnikov, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia • Andrey Lisitsa, IBMC, Moscow, Russia • Mikhail Voevoda, Institute of Internal Medicine and Preventive Medicine – ICG SB RAS, Russia • Vladimir Ivanisenko, Institute of Cytology and Genetics of SB RAS, Novosibirsk, Russia • Sergey
    [Show full text]