SUBA: the Arabidopsis Subcellular Database

Abstract

Knowledge of protein localisation contributes towards our understanding of protein function and of biological inter-relationships. A variety of experimental methods are currently being used to produce localisation data that need to be made accessible in an integrated manner. Chimeric fluorescent fusion proteins have been used to define subcellular localisations with at least 1100 related experiments completed in Arabidopsis. More recently, many studies have employed mass spectrometry to undertake proteomic surveys of subcellular components in Arabidopsis yielding localisation information for ∼2600 proteins. Further protein localisation information may be obtained from other literature references to analysis of locations (AmiGO: ∼900 proteins), location information from Swiss-Prot annotations (∼2000 proteins); and location inferred from gene descriptions (∼2700 proteins). Additionally, an increasing volume of available software provides location prediction information for proteins based on amino acid sequence. We have undertaken to bring these various data sources together to build SUBA, a SUBcellular location database for Arabidopsis proteins. The localisation data in SUBA encompasses 10 distinct subcellular locations, >6743 non-redundant proteins and represents the proteins encoded in the transcripts responsible for 51% of Arabidopsis expressed sequence tags. The SUBA database provides a powerful means by which to assess protein subcellular localisation in Arabidopsis ().

Remodeled Respiration in ndufs4 with Low Phosphorylation Efficiency Suppresses Arabidopsis Germination and Growth and Alters Control of Metabolism at Night

“…Data from in-gel digestions of the spots were matched using Mascot (Matrix Sciences) to a database of Arabidopsis proteins (The Arabidopsis Information Resource 8). AGI, Arabidopsis Genome Initiative accession number; MOWSE, Molecular Weight Search score derived by Mascot from the MS/MS search; Peptide, number of matching peptides; Coverage, percentage of protein sequence covered by the peptides identified; Localization, subcellular compartment where the protein is located based on MS, GFP, and predictor data according to the SUBA database (Heazlewood et al, 2007 ndufs4 mutant and the complemented line under three different stresses: cold, salt, and osmotic stress. The root length was measured and compared with control plants grown under nonstressed conditions.…”

Proteomic Analysis of Chloroplast-to-Chromoplast Transition in Tomato Reveals Metabolic Shifts Coupled with Disrupted Thylakoid Biogenesis Machinery and Elevated Energy-Production Components

“…The protein list was compared with five plastidial databases either specific to plastids (AT-CHLORO: Ferro et al, 2010; http://www.grenoble.prabi.fr/proteome/ grenoble-plant-proteomics/; plprot: Kleffmann et al, 2006; http://www. plprot.ethz.ch) or general databases comprising subcellular subsets (PPDB: Sun et al, 2009; http://ppdb.tc.cornell.edu; SUBA: Heazlewood et al, 2007; http://www.suba.bcs.uwa.edu.au; Uniprot: The Uniprot Consortium, 2010: http://www.uniprot.org). Predictions of subcellular localization were undertaken using three predictors (TargetP: Emanuelsson et al, 2000; http:// www.cbs.dtu.dk/services/TargetP/; iPSORT: Bannai et al, 2002; http:// hypothesiscreator.net/iPSORT/; Predotar: Small et al, 2004; http://genoplanteinfo.infobiogen.fr/predotar/).…”

Arabidopsis Photorespiratory Serine Hydroxymethyltransferase Activity Requires the Mitochondrial Accumulation of Ferredoxin-Dependent Glutamate Synthase

“…Such a physical interaction would require common localization of Fd-GOGAT and SHMT1, which seemed unlikely as photorespiratory SHMT activity is known to be mitochondrial (Somerville and Ogren, 1981), whereas photorespiratory Fd-GOGAT activity is chloroplastic (Somerville and Ogren, 1980). At this time, the Subcellular Proteomics Database does not provide proteomic data to support a mitochondrial localization of Fd-GOGAT (Heazlewood et al, 2007). Therefore, to verify these localizations, we performed microscopy analyses and biochemical fractionation experiments.…”