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Open Access Research article

GRASP [Genomic Resource Access for Stoichioproteomics]: comparative explorations of the atomic content of 12 Drosophila proteomes

James D J Gilbert12*, Claudia Acquisti345, Holly M Martinson2, James J Elser5, Sudhir Kumar45 and William F Fagan2

Author Affiliations

1 A08 Heydon-Lawrence Bdg, University of Sydney, Sydney NSW 2006, Australia

2 University of Maryland, College Park, MD 20742, USA

3 WWU Munster, Institute for Evolution and Biodiversity, Hufferstr. 1, Munster 48149, Germany

4 Center for Evolutionary Medicine and Informatics, Biodesign Institute, Arizona State University, Tempe, AZ 85287-5301, USA

5 School of Life Sciences, Arizona State University, Tempe, AZ 85287-4501, USA

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BMC Genomics 2013, 14:599  doi:10.1186/1471-2164-14-599

Published: 4 September 2013

Abstract

Background

“Stoichioproteomics” relates the elemental composition of proteins and proteomes to variation in the physiological and ecological environment. To help harness and explore the wealth of hypotheses made possible under this framework, we introduce GRASP (http://www.graspdb.net webcite), a public bioinformatic knowledgebase containing information on the frequencies of 20 amino acids and atomic composition of their side chains. GRASP integrates comparative protein composition data with annotation data from multiple public databases. Currently, GRASP includes information on proteins of 12 sequenced Drosophila (fruit fly) proteomes, which will be expanded to include increasingly diverse organisms over time. In this paper we illustrate the potential of GRASP for testing stoichioproteomic hypotheses by conducting an exploratory investigation into the composition of 12 Drosophila proteomes, testing the prediction that protein atomic content is associated with species ecology and with protein expression levels.

Results

Elements varied predictably along multivariate axes. Species were broadly similar, with the D. willistoni proteome a clear outlier. As expected, individual protein atomic content within proteomes was influenced by protein function and amino acid biochemistry. Evolution in elemental composition across the phylogeny followed less predictable patterns, but was associated with broad ecological variation in diet. Using expression data available for D. melanogaster, we found evidence consistent with selection for efficient usage of elements within the proteome: as expected, nitrogen content was reduced in highly expressed proteins in most tissues, most strongly in the gut, where nutrients are assimilated, and least strongly in the germline.

Conclusions

The patterns identified here using GRASP provide a foundation on which to base future research into the evolution of atomic composition in Drosophila and other taxa.

Keywords:
Bioinformatics; Comparative-phylogenetic analysis; Ecological stoichiometry; Material costs; Nutrient limitation; Proteomics