SUBA3: a database for integrating experimentation and prediction to define the SUBcellular location of proteins in Arabidopsis

Abstract

The subcellular location database for Arabidopsis proteins (SUBA3, http://suba.plantenergy.uwa.edu.au) combines manual literature curation of large-scale subcellular proteomics, fluorescent protein visualization and protein–protein interaction (PPI) datasets with subcellular targeting calls from 22 prediction programs. More than 14 500 new experimental locations have been added since its first release in 2007. Overall, nearly 650 000 new calls of subcellular location for 35 388 non-redundant Arabidopsis proteins are included (almost six times the information in the previous SUBA version). A re-designed interface makes the SUBA3 site more intuitive and easier to use than earlier versions and provides powerful options to search for PPIs within the context of cell compartmentation. SUBA3 also includes detailed localization information for reference organelle datasets and incorporates green fluorescent protein (GFP) images for many proteins. To determine as objectively as possible where a particular protein is located, we have developed SUBAcon, a Bayesian approach that incorporates experimental localization and targeting prediction data to best estimate a protein’s location in the cell. The probabilities of subcellular location for each protein are provided and displayed as a pictographic heat map of a plant cell in SUBA3.

Two Distinct Families of Protein Kinases Are Required for Plant Growth under High External Mg2+ Concentrations in Arabidopsis

“…We further screened the proteins to narrow down the candidate SRK2D-interacting proteins using the following criteria: (1) the protein should contain more than two unique peptides (with confidence . 95%), (2) the peptides should be specifically detected in the SRK2D-sGFP samples but not the sGFP samples (in at least two of three independent analyses), and (3) the protein should be predicted to localize in the cytoplasm, nucleus, or plasma membrane by the Subcellular Localization Database for Arabidopsis Proteins, version 3 program (Tanz et al, 2013) based on the fact that SRK2D-sGFP localizes in both the cytoplasm and the nucleus Supplemental Fig. S2B).…”

Sucrose-induced Receptor Kinase SIRK1 Regulates a Plasma Membrane Aquaporin in Arabidopsis

“…Information about subcellular location was derived from the consensus location available from SUBA3 (66). For data not derived from mass spectrometry studies, statistical analyses were carried out using Sigma Plot (Jandel Scientific, San Rafael, CA) and Excel (Microsoft, Redmond, WA).…”

“…These protein classes are known to be particularly "sticky" and often occur as nonspecific interactors in pull-downs. Therefore, only proteins with plasma membrane or extracellular locations based on the consensus location from SUBA3 were considered (66). A total of 36 proteins remained as significant sucrose-induced interaction partners for all SIRK1 constructs (Fig.…”

Widespread dual targeting of proteins in land plants: When, where, how and why

“…In fact as little as 15 percent of the known dual targeted protein in Arabidopsis have been identified in proteomic studies of both target organelles (24 out of 162 proteins, Table 1). 39 It is possible that the use of split tags (e.g., self assembling GFP 40 or alpha complementation using GUS 41 ) may prove more useful as they only require the attachment of small tags to target proteins. The development of new fluorescent tags which only require one amino acid may also help in this regard.…”