Plant SECRETome

Photo by Iswanto Arif on Unsplash

NSF PGRP Project - 1546879, 1810468, 1936492

Project Objectives

The goal of this project is to provide a foundation for the identification of components determining different secretory cell types in plants, their biological functions and regulatory mechanisms in the context of development and environmental stimuli. We will provide data sets, genetic material and gene editing technologies that will advance the studies on cell-specific gene regulation and cellular secretory functions. We will address a major resource gap: the lack of secretory cell-specific promoters (e.g., to control genes for defense against the pathogens, manage cell-specific processes during abiotic stress, or enhance the flux of nutrients towards seeds to improve yield). We will train high school, community college and four-year college undergraduate, graduate students and postdocs in cell biology, genomic-editing, genomics, bioinformatics and collaborative interdisciplinary research.


During the evolution of multicellular eukaryotes, cells specialized in different tasks. In plants, some cells serve as primary producers whereas others fully depend on nutrient supply and are ‘receivers’. Prominent examples of producers are photosynthetic cells. Embryo cells exemplify receivers that depend on external nutrient and energy supply. Certain situations are, however, more complex. For example, roots are generally receivers, but can serve secretory functions (e.g., epidermal cells exude chelators and sugars and vascular cells transport essential nutrients to shoots). Transport processes bridge producer and receiver cells. Specifically, phloem and xylem parenchyma facilitate phloem and xylem translocation; root pericycle cells load the xylem with ions. Secretory activities are critical for cuticle production of the leaf epidermis as well as suberization and lignification of the root hypodermis to reduce water loss in dry soil or oxygen loss in water-saturated soil. Pollen and embryos depend on maternal supply with nutrients. Maturing pollen is fed and coated by the anther tapetum; and small molecule transfer between cells is key to embryo development and germination. Certain organs, i.e., hydathodes and nectaries, specialize in secretory activities. Moreover, secretory activities can be influenced by the environment: symbionts or pathogens tap into the host’s nutrient resources by modulating the expression profiles of host cells and abiotic stresses perturb the ability to produce photosynthate and limit resource availability for growth. Under these circumstances, movement of nutrients can be dramatically altered. Here, we define ‘secretory cells’ as those having important functions in the secretion of solutes and macromolecules. This project will explore the key mechanistic features of secretory cells, taking advantage of the ability to monitor cell-type specific mRNA translation using TRAP (Translating Ribosome Affinity Purification) that enables profiling of mRNAs and non-coding RNAs associated with ribosomes (translatome) and CRISPR/Cas9-aided genomic-editing.

Expected Deliverables

Deliverables: (1) Translatome atlas (the entirety of ribosome-associated mRNAs and non-coding RNAs) of secretory cells and their activities of two plant species; (2) Cross- species characterization of secretory cells through non-invasive gene profiling and physiological assays; (3) Genetic resources for functional analyses, i.e. cell-specific promoters, CRISPR/Cas9-aided gene knock-out and reporter gene knock-in strategies; (4) Detailing of novel processes: pathways, circuits and functions of secretory cells; (5) SECRETome web-based resources; and (6) Public education on genomic editing technologies through forums and multimedia resources.


Oryza sativa, Arabidopsis thaliana, secretory cells, cell-specific gene expression, translatome, RNA-seq, TRAP-seq, CRISPR/Cas9, genomic editing, transporters, transcription factors, bioinformatics