Joint BioEnergy Institute and Physical Biosciences Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Bioinformatics. 2012 May 15;28(10):1303-6. doi: 10.1093/bioinformatics/bts133. Epub 2012 Mar 25.
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/
对模式植物拟南芥的上千个自然品系进行测序，为植物研究人员提供了前所未有的遗传水平信息。为了能够快速利用这些数据进行功能蛋白质组学研究，我们创建了一个用于可视化测序的拟南芥自然品系的蛋白质信息和蛋白质组数据集的资源。
1001 个蛋白质组门户可用于根据参考基因组 Col-0 可视化拟南芥个体蛋白质中的氨基酸替换或非同义单核苷酸多态性。我们利用可用的处理序列信息来分析这些自然品系中已知残基受蛋白磷酸化影响的保守性。拟南芥自然品系中的氨基酸替换受到严格限制，这可能是蛋白质内功能属性保守的结果。在实际水平上，我们证明该信息可用于澄清磷酸化蛋白质组学研究中定义不明确的磷酸化位点。可用于下载这些自然变体的蛋白质组集，以支持对这些品系的蛋白质组学研究。这些信息可用于揭示特定氨基酸在确定模式植物拟南芥中蛋白质结构和功能方面的可能作用。一个可供社区利用这些数据的在线门户可在 http://1001proteomes.masc-proteomics.org/ 访问。
