Mapping transcription factor interactome networks using HaloTag protein arrays

Significance Using a newly developed technology, HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we increase the capacity of in situ protein microarray technology several-fold, such that proteome-scale screening becomes feasible. Many examples of novel protein–protein interactions (PPIs) among plant signaling pathways were observed. With few exceptions, nearly all of these connections are undocumented in the existing literature. This study has resulted in an important new resource for the plant biology community—a plant transcription factor-anchored protein–protein interaction network map. Such transcription factor- and transcriptional regulator-based PPI networks may help in the identification of novel genes for use in the improvement of agronomic traits such as grain quality, disease resistance, and stress tolerance. Protein microarrays enable investigation of diverse biochemical properties for thousands of proteins in a single experiment, an unparalleled capacity. Using a high-density system called HaloTag nucleic acid programmable protein array (HaloTag-NAPPA), we created high-density protein arrays comprising 12,000 Arabidopsis ORFs. We used these arrays to query protein–protein interactions for a set of 38 transcription factors and transcriptional regulators (TFs) that function in diverse plant hormone regulatory pathways. The resulting transcription factor interactome network, TF-NAPPA, contains thousands of novel interactions. Validation in a benchmarked in vitro pull-down assay revealed that a random subset of TF-NAPPA validated at the same rate of 64% as a positive reference set of literature-curated interactions. Moreover, using a bimolecular fluorescence complementation (BiFC) assay, we confirmed in planta several interactions of biological interest and determined the interaction localizations for seven pairs. The application of HaloTag-NAPPA technology to plant hormone signaling pathways allowed the identification of many novel transcription factor–protein interactions and led to the development of a proteome-wide plant hormone TF interactome network.

[1]  Joseph R. Ecker,et al.  An ABA-increased interaction of the PYL6 ABA receptor with MYC2 Transcription Factor: A putative link of ABA and JA signaling , 2016, Scientific Reports.

[2]  M. Diekhans,et al.  The ORFeome Collaboration: a genome-scale human ORF-clone resource , 2016, Nature Methods.

[3]  L. Kurepin,et al.  Light signaling and the phytohormonal regulation of shoot growth. , 2014, Plant science : an international journal of experimental plant biology.

[4]  Felipe F. Aceituno,et al.  Systems approach identifies TGA1 and TGA4 transcription factors as important regulatory components of the nitrate response of Arabidopsis thaliana roots. , 2014, The Plant journal : for cell and molecular biology.

[5]  Kate B. Cook,et al.  Determination and Inference of Eukaryotic Transcription Factor Sequence Specificity , 2014, Cell.

[6]  J. LaBaer,et al.  Copper-catalyzed azide-alkyne cycloaddition (click chemistry)-based Detection of Global Pathogen-host AMPylation on Self-assembled Human Protein Microarrays* , 2014, Molecular & Cellular Proteomics.

[7]  G. Wallstrom,et al.  A versatile protein microarray platform enabling antibody profiling against denatured proteins , 2013, Proteomics. Clinical applications.

[8]  Ying-Bo Mao,et al.  Arabidopsis MYC2 Interacts with DELLA Proteins in Regulating Sesquiterpene Synthase Gene Expression[W][OA] , 2012, Plant Cell.

[9]  Y. Kamiya,et al.  Identification of an abscisic acid transporter by functional screening using the receptor complex as a sensor , 2012, Proceedings of the National Academy of Sciences.

[10]  P. Braun.  Interactome mapping for analysis of complex phenotypes: Insights from benchmarking binary interaction assays , 2012, Proteomics.

[11]  Hongwei Guo,et al.  Coordinated regulation of apical hook development by gibberellins and ethylene in etiolated Arabidopsis seedlings , 2012, Cell Research.

[12]  Shoji Mano,et al.  Gateway Vectors for Plant Genetic Engineering: Overview of Plant Vectors, Application for Bimolecular Fluorescence Complementation (BiFC) and Multigene Construction , 2012 .

[13]  Miguel A Blázquez,et al.  Hierarchy of hormone action controlling apical hook development in Arabidopsis. , 2011, The Plant journal : for cell and molecular biology.

[14]  Jonathan D. G. Jones,et al.  Evidence for Network Evolution in an Arabidopsis Interactome Map , 2011, Science.

[15]  J. Schroeder,et al.  Evolution of Abscisic Acid Synthesis and Signaling Mechanisms , 2011, Current Biology.

[16]  A. Gavin,et al.  SnapShot: Protein-Protein Interaction Networks , 2011, Cell.

[17]  A. Barabasi,et al.  Interactome Networks and Human Disease , 2011, Cell.

[18]  J. Franco-Zorrilla,et al.  The Arabidopsis bHLH Transcription Factors MYC3 and MYC4 Are Targets of JAZ Repressors and Act Additively with MYC2 in the Activation of Jasmonate Responses[C][W] , 2011, Plant Cell.

[19]  Heng Zhu,et al.  Functional protein microarray technology , 2010, Wiley interdisciplinary reviews. Systems biology and medicine.

[20]  P. Quail,et al.  PIFs: pivotal components in a cellular signaling hub. , 2011, Trends in plant science.

[21]  Xingliang Hou,et al.  DELLAs modulate jasmonate signaling via competitive binding to JAZs. , 2010, Developmental cell.

[22]  S. Cutler,et al.  Abscisic acid: emergence of a core signaling network. , 2010, Annual review of plant biology.

[23]  J. Yates,et al.  PYR/PYL/RCAR family members are major in-vivo ABI1 protein phosphatase 2C-interacting proteins in Arabidopsis , 2009, The Plant journal : for cell and molecular biology.

[24]  David E Hill,et al.  High-quality binary interactome mapping. , 2010, Methods in enzymology.

[25]  Hongwei Guo,et al.  EIN3/EIL1 cooperate with PIF1 to prevent photo-oxidation and to promote greening of Arabidopsis seedlings , 2009, Proceedings of the National Academy of Sciences.

[26]  P. Bork,et al.  Proteome Organization in a Genome-Reduced Bacterium , 2009, Science.

[27]  S. Cutler,et al.  Modulation of drought resistance by the abscisic acid receptor PYL5 through inhibition of clade A PP2Cs. , 2009, The Plant journal : for cell and molecular biology.

[28]  Y. Tsay,et al.  CHL1 Functions as a Nitrate Sensor in Plants , 2009, Cell.

[29]  Nobutaka Mitsuda,et al.  Functional analysis of transcription factors in Arabidopsis. , 2009, Plant & cell physiology.

[30]  M. Estelle,et al.  Recent advances and emerging trends in plant hormone signalling , 2009, Nature.

[31]  E. Grill,et al.  Regulators of PP2C Phosphatase Activity Function as Abscisic Acid Sensors , 2009, Science.

[32]  P. McCourt,et al.  Abscisic Acid Inhibits Type 2C Protein Phosphatases via the PYR/PYL Family of START Proteins , 2009, Science.

[33]  Jun Wan,et al.  Protein Acetylation Microarray Reveals that NuA4 Controls Key Metabolic Target Regulating Gluconeogenesis , 2009, Cell.

[34]  Julie M. Sahalie,et al.  An experimentally derived confidence score for binary protein-protein interactions , 2008, Nature Methods.

[35]  A. Barabasi,et al.  An empirical framework for binary interactome mapping , 2008, Nature Methods.

[36]  M. Vidal,et al.  Literature-curated protein interaction datasets , 2009, Nature Methods.

[37]  A. Barabasi,et al.  High-Quality Binary Protein Interaction Map of the Yeast Interactome Network , 2008, Science.

[38]  Caren Chang,et al.  Ethylene signaling: new levels of complexity and regulation. , 2008, Current opinion in plant biology.

[39]  T. Demura,et al.  Vascular-related NAC-DOMAIN7 is involved in the differentiation of all types of xylem vessels in Arabidopsis roots and shoots. , 2008, The Plant journal : for cell and molecular biology.

[40]  Marjeta Urh,et al.  HaloTag: a novel protein labeling technology for cell imaging and protein analysis. , 2008, ACS chemical biology.

[41]  Yanhui Hu,et al.  Next generation high density self assembling functional protein arrays , 2008, Nature Methods.

[42]  Jonathan D. G. Jones,et al.  DELLAs Control Plant Immune Responses by Modulating the Balance of Jasmonic Acid and Salicylic Acid Signaling , 2008, Current Biology.

[43]  C. Fankhauser,et al.  A molecular framework for light and gibberellin control of cell elongation , 2008, Nature.

[44]  Michael J Taussig,et al.  Printing protein arrays from DNA arrays , 2008, Nature Methods.

[45]  Xing Wang Deng,et al.  The development of protein microarrays and their applications in DNA-protein and protein-protein interaction analyses of Arabidopsis transcription factors. , 2008, Molecular plant.

[46]  Yuji Kamiya,et al.  Global Analysis of DELLA Direct Targets in Early Gibberellin Signaling in Arabidopsis[W] , 2007, The Plant Cell Online.

[47]  Sorina C. Popescu,et al.  Differential binding of calmodulin-related proteins to their targets revealed through high-density Arabidopsis protein microarrays , 2007, Proceedings of the National Academy of Sciences.

[48]  Sean R. Collins,et al.  Toward a Comprehensive Atlas of the Physical Interactome of Saccharomyces cerevisiae*S , 2007, Molecular & Cellular Proteomics.

[49]  P. Benfey,et al.  Transcription factors and hormones: new insights into plant cell differentiation. , 2006, Current opinion in cell biology.

[50]  Jennifer L. Nemhauser,et al.  Different Plant Hormones Regulate Similar Processes through Largely Nonoverlapping Transcriptional Responses , 2006, Cell.

[51]  M. Gerstein,et al.  Global analysis of protein phosphorylation in yeast , 2005, Nature.

[52]  Joshua LaBaer,et al.  Protein microarrays as tools for functional proteomics. , 2005, Current opinion in chemical biology.

[53]  Bhupinder Bhullar,et al.  Self-Assembling Protein Microarrays , 2004, Science.

[54]  Joseph M. Dale,et al.  Empirical Analysis of Transcriptional Activity in the Arabidopsis Genome , 2003, Science.

[55]  J. Kawai,et al.  Genomics approach to abscisic acid- and gibberellin-responsive genes in rice. , 2003, DNA research : an international journal for rapid publication of reports on genes and genomes.

[56]  E. Huq,et al.  PIF4, a phytochrome‐interacting bHLH factor, functions as a negative regulator of phytochrome B signaling in Arabidopsis , 2002, The EMBO journal.

[57]  R. Finkelstein,et al.  Abscisic Acid Signaling in Seeds and Seedlings , 2002 .

[58]  C. Foyer,et al.  ABA plays a central role in mediating the regulatory effects of nitrate on root branching in Arabidopsis. , 2002, The Plant journal : for cell and molecular biology.

[59]  M. Taussig,et al.  Single step generation of protein arrays from DNA by cell-free expression and in situ immobilisation (PISA method). , 2001, Nucleic acids research.

[60]  M. Gerstein,et al.  Global Analysis of Protein Activities Using Proteome Chips , 2001, Science.

[61]  T. Sasaki,et al.  Embarking on rice functional genomics via cDNA microarray: use of 3' UTR probes for specific gene expression analysis. , 2000, DNA research : an international journal for rapid publication of reports on genes and genomes.

[62]  E. Meyerowitz.  2 Structure and Organization of the Arabidopsis thaliana Nuclear Genome , 1994 .

[63]  S. Fields,et al.  A novel genetic system to detect protein–protein interactions , 1989, Nature.