Systems analysis of peptide-mediated cell-cell communication in the plant root by in situ sequencing

The cells of multicellular organisms can communicate with each other by allowing small peptides to be exported from a cell and then bind to receptors on the surface of neighboring cells, activating these and thereby changing the expression of genes. This project studies how peptide-based cell-to-cell communication regulates root growth and root architecture under various conditions. The Arabidopsis thaliana (Vårskrinneblom) model plant has been used to identify genes that encodes peptide-receptor pairs in roots. Then, employing genetic, biochemical, and bioinformatics methods, we have used these to identify and describe communication pathways between cells. The root cap, which covers the tip of the roots where the stem cells are situated and also can sense environmental conditions in the surroundings, are periodically sloughed off. The peptide IDA-LIKE1 expressed in the cells being sloughed, signals via the receptor HSL2 and ensures that the sloughing is co-ordinated with production of new cell layers. Thus, a homeostatic balance is maintained in which the loss of the root cap is compensated by adding a new cell layer to the root tip. The result of this research has been published in the prestigious journal Nature Plants (Shi et al., 2018). We are continuing with studies that may reveal whether there is a correlation between stress tolerance and the frequency of root cap sloughing.

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This project aims at studying and describing how peptide mediated cell-cell communication regulate root growth and root system architecture under normal and abiotic stress conditions and thereby contribute knowledge to design interventions to alleviate the adverse effect of abiotic stress on plant development and growth. We propose a systems biology approach using the model plant Arabidopsis thaliana to achieve this task and identify two main goals. First, we aim at defining a minimal set of genes driving peptide-mediated cell-cell communication in the growing root. Second, we will develop integrated experimental and computational technology to perform a targeted analysis of these components and describe their cell-cell communication induced relationships. To achieve the first goal, we will use conventional RNA sequencing approaches to comprehensively map out putative peptide hormones expressed in the Arabidopsis root tip, carry out a phenotypic perturbation screen to map peptides with paracrine activity and perform transcriptomic profiling to identify intercellular downstream signaling targets. Achievement of the second goal requires the development of an enabling technology for detecting and describing intercellular events on the molecular level with single cell resolution in the Arabidopsis root organ. For this we will develop a microfluidic chip platform that will enable the acquisition of spatially resolved single cell transcription profiles of up to thirty targets jointly by in situ RNA sequencing in root tips. In accordance with the call focus, this project investigates regulatory mechanisms of inter- and intracelluar processes. We use conventional genomics techniques to map out the relevant molecular system inventory, as well as by new developed, integrated experimental and computational technology to describe the communication induced relationships among the system components to identify the key responses at the level of peptidemediated cell communication.