1001 Proteomes: a functional proteomics portal for the analysis of Arabidopsis thaliana accessions

• Published in: Bioinformatics (Oxford, England) Vol. 28; no. 10; pp. 1303 - 1306
• Main Authors: JOSHI, Hiren J, CHRISTIANSEN, Katy M, HEAZLEWOOD, Joshua L, FITZ, Joffrey, JUN CAO, LIPZEN, Anna, MARTIN, Joel, SMITH-MORITZ, A. Michelle, PENNACCHIO, Len A, SCHACKWITZ, Wendy S, WEIGEL, Detlef
• Format: Journal Article
• Language: English
• Published: Oxford Oxford University Press 15-05-2012
• Subjects: Amino Acid Substitution; Arabidopsis - genetics; Arabidopsis Proteins - genetics; Biological and medical sciences; Databases, Protein; DNA, Plant; Fundamental and applied biological sciences. Psychology; General aspects; Mathematics in biology. Statistical analysis. Models. Metrology. Data processing in biology (general aspects); Phosphorylation; Polymorphism, Single Nucleotide; Protein Processing, Post-Translational; Proteome - genetics; Proteomics; Sequence Analysis, DNA; Arabidopsis thaliana; Cruciferae; Dicotyledones; Angiospermae; Proteomics; Proteome; Spermatophyta; Functional analysis
• ISSN: 1367-4803; 1367-4811
• DOI: 10.1093/bioinformatics/bts133

The sequencing of over a thousand natural strains of the model plant Arabidopsis thaliana is producing unparalleled information at the genetic level for plant researchers. To enable the rapid exploitation of these data for functional proteomics studies, we have created a resource for the visualization of protein information and proteomic datasets for sequenced natural strains of A. thaliana.
The 1001 Proteomes portal can be used to visualize amino acid substitutions or non-synonymous single-nucleotide polymorphisms in individual proteins of A. thaliana based on the reference genome Col-0. We have used the available processed sequence information to analyze the conservation of known residues subject to protein phosphorylation among these natural strains. The substitution of amino acids in A. thaliana natural strains is heavily constrained and is likely a result of the conservation of functional attributes within proteins. At a practical level, we demonstrate that this information can be used to clarify ambiguously defined phosphorylation sites from phosphoproteomic studies. Protein sets of available natural variants are available for download to enable proteomic studies on these accessions. Together this information can be used to uncover the possible roles of specific amino acids in determining the structure and function of proteins in the model plant A. thaliana. An online portal to enable the community to exploit these data can be accessed at http://1001proteomes.masc-proteomics.org/