Genome-wide data (ChIP-seq) enabled identification of cell wall-related and aquaporin genes as targets of tomato ASR1, a drought stress-responsive transcription factor

BackgroundIdentifying the target genes of transcription factors is important for unraveling regulatory networks in all types of organisms. Our interest was precisely to uncover the spectrum of loci regulated by a widespread plant transcription factor involved in physiological adaptation to drought, a type of stress that plants have encountered since the colonization of land habitats 400 MYA. The regulator under study, named ASR1, is exclusive to the plant kingdom (albeit absent in Arabidopsis) and known to alleviate the stress caused by restricted water availability. As its target genes are still unknown despite the original cloning of Asr1 cDNA 20 years ago, we examined the tomato genome for specific loci interacting in vivo with this conspicuous protein.ResultsWe performed ChIP followed by high throughput DNA sequencing (ChIP-seq) on leaves from stressed tomato plants, using a high-quality anti-ASR1 antibody. In this way, we unraveled a novel repertoire of target genes, some of which are clearly involved in the response to drought stress. Many of the ASR1-enriched genomic loci we found encode enzymes involved in cell wall synthesis and remodeling as well as channels implicated in water and solute flux, such as aquaporins. In addition, we were able to determine a robust consensus ASR1-binding DNA motif.ConclusionsThe finding of cell wall synthesis and aquaporin genes as targets of ASR1 is consistent with their suggested role in the physiological adaptation of plants to water loss. The results gain insight into the environmental stress-sensing pathways leading to plant tolerance of drought.

[1]  G. Galau,et al.  Developmental biochemistry of cottonseed embryogenesis and germination: changing messenger ribonucleic acid populations as shown by in vitro and in vivo protein synthesis. , 1981, Biochemistry.

[2]  N. Iusem,et al.  Tomato (Lycopersicon esculentum) Transcript Induced by Water Deficit and Ripening , 1993, Plant physiology.

[3]  K. Ferrare,et al.  Two TIP-like genes encoding aquaporins are expressed in sunflower guard cells. , 1997, The Plant journal : for cell and molecular biology.

[4]  M. Loewen,et al.  (+)-Abscisic acid 8'-hydroxylase is a cytochrome P450 monooxygenase , 1998, Plant physiology.

[5]  Palmer,et al.  Phylogeny of early land plants: insights from genes and genomes. , 1999, Trends in plant science.

[6]  D J Cosgrove,et al.  Adaptation of roots to low water potentials by changes in cell wall extensibility and cell wall proteins. , 2000, Journal of experimental botany.

[7]  J Stevens,et al.  ABI PRISM 7700 Sequence Detection Systemを用いたInvaderアッセイによるSNP解析 , 2000 .

[8]  R. Jung,et al.  Aquaporins Constitute a Large and Highly Divergent Protein Family in Maize , 2001, Plant physiology.

[9]  A. Weig,et al.  The complete set of genes encoding major intrinsic proteins in Arabidopsis provides a framework for a new nomenclature for major intrinsic proteins in plants. , 2001, Plant physiology.

[10]  K. Akiyama,et al.  Monitoring the expression profiles of 7000 Arabidopsis genes under drought, cold and high-salinity stresses using a full-length cDNA microarray. , 2002, The Plant journal : for cell and molecular biology.

[11]  W. Pearson,et al.  Current Protocols in Bioinformatics , 2002 .

[12]  F. Carrari,et al.  Reduced Expression of Aconitase Results in an Enhanced Rate of Photosynthesis and Marked Shifts in Carbon Partitioning in Illuminated Leaves of Wild Species Tomato1 , 2003, Plant Physiology.

[13]  N. Iusem,et al.  Adaptive evolution of the water stress-induced gene Asr2 in Lycopersicon species dwelling in arid habitats. , 2003, Molecular biology and evolution.

[14]  C. Gaillard,et al.  A Grape ASR Protein Involved in Sugar and Abscisic Acid Signaling Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.013854. , 2003, The Plant Cell Online.

[15]  W. Frommer,et al.  Cis regulatory elements directing tuber-specific and sucrose-inducible expression of a chimeric class I patatin promoter/GUS-gene fusion , 1990, Molecular and General Genetics MGG.

[16]  S. Rhee,et al.  MAPMAN: a user-driven tool to display genomics data sets onto diagrams of metabolic pathways and other biological processes. , 2004, The Plant journal : for cell and molecular biology.

[17]  Ayelet Gilad,et al.  The water- and salt-stress-regulated Asr1 (abscisic acid stress ripening) gene encodes a zinc-dependent DNA-binding protein. , 2004, The Biochemical journal.

[18]  Hunseung Kang,et al.  An Expression Analysis of a Gene Family Encoding Plasma Membrane Aquaporins in Response to Abiotic Stresses in Arabidopsis Thaliana , 2004, Plant Molecular Biology.

[19]  S. Delrot,et al.  VvHT1 encodes a monosaccharide transporter expressed in the conducting complex of the grape berry phloem. , 2005, Journal of experimental botany.

[20]  Erik Alexandersson,et al.  Whole Gene Family Expression and Drought Stress Regulation of Aquaporins , 2005, Plant Molecular Biology.

[21]  D. Gonzalez,et al.  Differential Expression of the Arabidopsis Cytochrome c Genes Cytc-1 and Cytc-2. Evidence for the Involvement of TCP-Domain Protein-Binding Elements in Anther- and Meristem-Specific Expression of the Cytc-1 Gene1 , 2005, Plant Physiology.

[22]  V. Citovsky,et al.  Identification of an interactor of cadmium ion-induced glycine-rich protein involved in regulation of callose levels in plant vasculature. , 2005, Proceedings of the National Academy of Sciences of the United States of America.

[23]  F. Carrari,et al.  ci21A/Asr1 expression influences glucose accumulation in potato tubers , 2007, Plant Molecular Biology.

[24]  Xin-Yao Yu,et al.  Upland rice and lowland rice exhibited different PIP expression under water deficit and ABA treatment , 2006, Cell Research.

[25]  D. DellaPenna,et al.  Tocopherols Play a Crucial Role in Low-Temperature Adaptation and Phloem Loading in Arabidopsis[W] , 2006, The Plant Cell Online.

[26]  C. Lovisolo,et al.  Isolation and functional characterization of three aquaporins from olive (Olea europaea L.) , 2006, Planta.

[27]  H. Xiao,et al.  Temporal recruitment of CCAAT/enhancer-binding proteins to early and late adipogenic promoters in vivo. , 2006, Journal of molecular endocrinology.

[28]  M. Wise,et al.  The continuing conundrum of the LEA proteins , 2007, Naturwissenschaften.

[29]  N. Iusem,et al.  Dimerization and DNA-binding of ASR1, a small hydrophilic protein abundant in plant tissues suffering from water loss. , 2007, Biochemical and biophysical research communications.

[30]  Panayiotis V. Benos,et al.  STAMP: a web tool for exploring DNA-binding motif similarities , 2007, Nucleic Acids Res..

[31]  B. Epel,et al.  A plasmodesmata-associated β-1,3-glucanase in Arabidopsis , 2007 .

[32]  B. Epel,et al.  A plasmodesmata-associated beta-1,3-glucanase in Arabidopsis. , 2007, The Plant journal : for cell and molecular biology.

[33]  G. Salekdeh,et al.  Proteome response of Elymus elongatum to severe water stress and recovery. , 2006, Journal of experimental botany.

[34]  U. Johanson,et al.  Unexpected complexity of the Aquaporin gene family in the moss Physcomitrella patens , 2008, BMC Plant Biology.

[35]  Jiming Jiang,et al.  Analysis of 90 Mb of the potato genome reveals conservation of gene structures and order with tomato but divergence in repetitive sequence composition , 2008, BMC Genomics.

[36]  Xin-Yao Yu,et al.  Transport functions and expression analysis of vacuolar membrane aquaporins in response to various stresses in rice. , 2008, Journal of plant physiology.

[37]  A. Covarrubias,et al.  The Enigmatic LEA Proteins and Other Hydrophilins1[W] , 2008, Plant Physiology.

[38]  John P. Moore,et al.  Adaptations of higher plant cell walls to water loss: drought vs desiccation. , 2008, Physiologia plantarum.

[39]  Clifford A. Meyer,et al.  Model-based Analysis of ChIP-Seq (MACS) , 2008, Genome Biology.

[40]  D. Bar-Zvi,et al.  Tomato ASR1 abrogates the response to abscisic acid and glucose in Arabidopsis by competing with ABI4 for DNA binding. , 2008, Plant biotechnology journal.

[41]  Christophe Maurel,et al.  Plant aquaporins: membrane channels with multiple integrated functions. , 2008, Annual review of plant biology.

[42]  K. Medzihradszky,et al.  Arabidopsis PPR40 Connects Abiotic Stress Responses to Mitochondrial Electron Transport1[W][OA] , 2008, Plant Physiology.

[43]  N. Iusem,et al.  Nucleotide polymorphism in the drought responsive gene Asr2 in wild populations of tomato , 2009, Genetica.

[44]  A. Jauneau,et al.  In Vivo Interference with AtTCP20 Function Induces Severe Plant Growth Alterations and Deregulates the Expression of Many Genes Important for Development[C][W] , 2008, Plant Physiology.

[45]  J. Bennetzen,et al.  The Physcomitrella Genome Reveals Evolutionary Insights into the Conquest of Land by Plants , 2008, Science.

[46]  Cole Trapnell,et al.  Ultrafast and memory-efficient alignment of short DNA sequences to the human genome , 2009, Genome Biology.

[47]  D. Bar-Zvi,et al.  Synergism between the chaperone-like activity of the stress regulated ASR1 protein and the osmolyte glycine-betaine , 2008, Planta.

[48]  Nozomu Sakurai,et al.  Large-scale analysis of full-length cDNAs from the tomato (Solanum lycopersicum) cultivar Micro-Tom, a reference system for the Solanaceae genomics , 2010, BMC Genomics.

[49]  N. Iusem,et al.  When cells lose water: Lessons from biophysics and molecular biology. , 2009, Progress in biophysics and molecular biology.

[50]  Rodrigo M González,et al.  Protocol: fine-tuning of a Chromatin Immunoprecipitation (ChIP) protocol in tomato , 2010, Plant Methods.

[51]  A. Geitmann,et al.  Mechanics and modeling of plant cell growth. , 2009, Trends in plant science.

[52]  Wing Hung Wong,et al.  Using CisGenome to Analyze ChIP‐chip and ChIP‐seq Data , 2011, Current protocols in bioinformatics.

[53]  Simon J. van Heeringen,et al.  GimmeMotifs: a de novo motif prediction pipeline for ChIP-sequencing experiments , 2010, Bioinform..

[54]  Kerstin Kaufmann,et al.  ChIP-seq Analysis in R (CSAR): An R package for the statistical detection of protein-bound genomic regions , 2011, Plant Methods.

[55]  K. Kaufmann,et al.  Visualizing and characterizing in vivo DNA-binding events and direct target genes of plant transcription factors. , 2011, Methods in molecular biology.

[56]  Marc D. Perry,et al.  ChIP-seq guidelines and practices of the ENCODE and modENCODE consortia , 2012, Genome research.

[57]  Jeffrey H. Chuang,et al.  Transcriptional Enhancers in Protein-Coding Exons of Vertebrate Developmental Genes , 2012, PloS one.

[58]  Yong Zhang,et al.  Identifying ChIP-seq enrichment using MACS , 2012, Nature Protocols.

[59]  Daniel W. A. Buchan,et al.  The tomato genome sequence provides insights into fleshy fruit evolution , 2012, Nature.

[60]  C. Maurel,et al.  Insights into Populus XIP aquaporins: evolutionary expansion, protein functionality, and environmental regulation. , 2012, Journal of experimental botany.

[61]  D. Menke,et al.  Pitx1 broadly associates with limb enhancers and is enriched on hindlimb cis-regulatory elements. , 2013, Developmental biology.

[62]  Jing Zhang,et al.  Unique genome-wide map of TCF4 and STAT3 targets using ChIP-seq reveals their association with new molecular subtypes of glioblastoma. , 2013, Neuro-oncology.

[63]  C. Tonelli,et al.  Challenges and perspectives to improve crop drought and salinity tolerance. , 2013, New biotechnology.

[64]  Helga Thorvaldsdóttir,et al.  Integrative Genomics Viewer (IGV): high-performance genomics data visualization and exploration , 2012, Briefings Bioinform..

[65]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[66]  M. Margis-Pinheiro,et al.  New insights into aluminum tolerance in rice: the ASR5 protein binds the STAR1 promoter and other aluminum-responsive genes. , 2014, Molecular plant.