Zhiyong Wang

  Staff Scientist
  Department of Plant Biology
  Carnegie Institution for Science
  260 Panama Street
  Stanford, CA 94305
  Phone: (650) 739-4205
  Fax: (650) 325-6857 
  Email: zywang24@stanford.edu

Research Interests

Hormone Signaling and growth control

Plant growth and development are regulated by hormones and environmental signals through signal transduction pathways that link signal perception to gene regulation. We are interested in understanding those signal transduction pathways and gene regulation networks that control plant growth and development. We use a wide range of approaches, including molecular genetics, biochemistry, proteomics, genomics, and cell biology, to gain a comprehensive understanding of the regulatory systems in plants. Our current research focuses on the signaling pathway of plant the steroid hormone brassinosteroid (BR), which is the best-understood receptor-kinase signaling pathway in plants. We are particularly interested in the biochemical mechanisms of signal transduction and the downstream transcription network controlling specific development and adaptation processes. One area of future focus is hormonal regulation of photomorphogenesis and photosynthesis.

BR is a major growth-promoting hormone that regulates a wide range of developmental and physiological processes, including seed germination, cell elongation, growth, flowering, light responses, photosynthesis, and stress tolerance. Genetic deficiency in BR synthesis or signaling causes dramatic developmental defects, including dwarfism, male sterility, delayed flowering, reduced apical dominance, and development of light-grown morphology in the dark. In contrast, application of BR or increasing BR biosynthesis can enhance plant growth and biomass production. Research on BR can potentially lead to means of increasing crop yield and help solve the food and energy problems of the world.

BR is perceived by the cell-surface receptor-like kinase BRI1, which contains an extracellular leucine-rich repeat domain, similar to the Toll-like receptors in animals, and a cytoplasmic serine/threonine kinase domain. BR binding to the extracellular domain activates the BRI1 kinase and initiates a signaling cascade leading to regulation of gene expression in the nucleus. This signaling cascade includes the BR-signaling kinases (BSKs), the PP1-like phosphatase BSU1, the GSK3-like kinase BIN2, and protein phosphatase 2A (PP2A), the phosphopeptide-binding 14-3-3 proteins, and the homologous transcription factors BZR1 and BZR2 (also named BES1). When BR level is low, BIN2 phosphorylates BZR1/BZR2 and phospho-BZR1/BZR2 lose DNA binding activity and are retained in the cytoplasm by the 14-3-3 proteins. When BR level is high, BRI1 phosphorylates BSKs and BSKs bind to BSU1, which dephosphorylates and inactivates BIN2, whereas PP2A dephosphorylates BZR1 and BZR2. As such, BR induces rapid dephosphoryaltion and nuclear localization of BZR1 and BZR2. As DNA-binding proteins, BZR1 and BZR2 directly regulates the expression of thousands of genes.

Proteomics is a powerful approach for studying signal transduction. We have successfully identified the last two missing components of the BR pathway using proteomics. Analysis of plasma membrane proteins using two-dimensional difference gel electrophoresis identified the BSKs as BRI1 kinase substrates that are phosphorylated upon BR signaling. Tandem affinity purification of the BZR1 complex identified the PP2A as the BZR1 phosphatase. We continue to use these effective proteomic approaches to study signal transduction mechanisms in the model plant  Arabidopsis and crops such as rice, maize and rye. For example, our quantitative proteomic analysis discovered cold-induced aggregation of metabolic enzymes as a mechanism of rapid response that protects plants from sudden temperature drop below freezing point. Affinity purification continues to reveal new signaling mechanisms based on protein modification and protein-protein interactions.

Modern genomic approaches, such as expression profiling and chromatin-immunoprecipitation followed by microarray or sequencing (ChIP-chip or ChIP-Seq), are powerful tools in identifying all target genes of a signaling pathway. Using these approaches, we have identified over two thousands BZR1 binding sites and one thousands BR-regulated BZR1 target (BRBT) genes in the Arabidopsis genome. These BZR1 target genes represent diverse cellular and developmental functions controlled by BR signaling. The BR targets include over a hundred transcription factors as well as components of other signaling pathways, such as the light, gibberellin (GA) and auxin (IAA) pathways. For example, BZR1 represses the GATA2 gene, which encodes a light-regulated transcription factor controlling light-responsive genes. Our research reveals a complex network that integrates multiple signaling and developmental pathways for growth regulation in plants. We continue to use genetic approaches to dissect this molecular network.

Our studies using molecular genetic, genomic, and proteomic approaches have yielded a detailed understanding of how BR signal is transduced from the cell surface receptor kinase to nuclear transcription factors and thousands of target genes. Our current research focuses on how the BR pathway integrates with other signaling pathways and developmental programs to control complex processes in the context of growth, development, and adaptation. Examples of ongoing research projects include: (1) proteomic identification and functional study of proteins that interact with known BR signaling proteins; (2) functional study of BZR1 target genes; (3) mapping the transcription network underlying BR and light responses using chromatin immunoprecipitation-sequencing (ChIP-seq) and computation biology; (4) BR regulation of organ boundary and root development; (5) crosstalk between BR signaling pathway and other receptor kinase pathways; (6) proteomic studies of other signaling pathways and processes that regulate plant growth and adaptation; (8) proteomic and genomic studies of regulatory pathways in rice and C4 plants such as maize.