The plant endoplasmic reticulum UPRome: A repository and pathway browser for genes involved in signaling networks linked to the endoplasmic reticulum

Abstract

The endoplasmic reticulum (ER) houses sensors that respond to environmental stress and underly plants' adaptative responses. These sensors transduce signals that lead to changes in nuclear gene expression. The ER to nuclear signaling pathways are primarily attributed to the unfolded protein response (UPR) and are also integrated with a wide range of development, hormone, immune, and stress signaling pathways. Understanding the role of the UPR in signaling network mechanisms that associate with particular phenotypes is crucially important. While UPR-associated genes are the subject of ongoing investigations in a few model plant systems, most remain poorly annotated, hindering the identification of candidates across plant species. This open-source curated database provides a centralized resource of peer reviewed knowledge of ER to nuclear signaling pathways for the plant community. We provide a UPRome interactive viewer for users to navigate through the pathways and to access annotated information. The plant ER UPRome website is located at http://uprome.tamu.edu. We welcome contributions from the researchers studying the ER UPR to incorporate additional genes into the database through the "contact us" page.

Keywords: curated database; plant protein interaction maps; plant signal transduction; unfolded protein response.

FIGURE 1

Plant endoplasmic reticulum (ER) UPRome. The panels of information that the readers will see on the front page of the database.

FIGURE 2

Plant UPRome workflow. The database was constructed based on the reported unfolded protein response (UPR) associated genes in model plant species esp. Arabidopsis thaliana . Homology based gene retrieval was carried out against major plant genome databases as indicated in the second panel. The retrieved genes were manually curated after careful inspection of their sequences, domains, and motifs as shown in the top third panel. We also incorporated a feed aggregator so the users can obtain up to date references related to the six plant species included in our database. We used Microsoft ASP.net, C#, Bootstrapper, and Microsoft SQL Server for the implementation of the Plant UPRome.

FIGURE 3

Interactive viewer. (a) A screenshot of the interactive viewer. All the unfolded protein response (UPR) components are hotlinked so the users can obtain their information by clicking on each component. (b) A use case illustrating the retrieval of IRE1 information. When users click on IRE1a or IRE1b, it will open the relevant gene information pages. Users can select one of the six species by clicking on the species name logo. It will bring weblinks for major databases.