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MBE Advance Access published online on July 26, 2006
Molecular Biology and Evolution, doi:10.1093/molbev/msl068
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© The Author 2006. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution. All rights reserved. For permissions, please e-mail: journals.permissions@oxfordjournals.org
Accepted July 12, 2006

Research Article

Signatures of Ecological Resource Availability in the Animal and Plant Proteomes

James J. Elser 1, William F. Fagan 2, Sankar Subramanian 3, and Sudhir Kumar 3 *

1 School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe AZ, 85287 USA
2 Department of Biology, University of Maryland, College Park, MD 20742 USA
3 School of Life Sciences, The Biodesign Institute, Arizona State University, Tempe AZ, 85287 USA; Center for Evolutionary Functional Genomics, The Biodesign Institute, Arizona State University, Tempe AZ, 85287 USA

* To whom correspondence should be addressed.
Sudhir Kumar, E-mail: s.kumar{at}asu.edu


  Abstract

Although substantial and ecologically significant differences in elemental composition are well-documented for whole organisms, little is known about whether such differences extend to lower levels of biological organization, such as the elemental composition of major molecules. In a proteome-scale investigation of nine plant genomes and nine animal genomes, we find that the nitrogen (N)-content of plant proteins is lower than that in animal proteins. Furthermore, protein N-content declines with the intensity of gene expression for plants, whereas the N content of animal proteins shows no consistent pattern with expression. Additional analyses indicate that the differences in N-content between plant and animal proteomes and in plant proteins as a function of gene expression cannot be attributed to protein size, GC content, gene function, or amino acid properties. These patterns suggest that ecophysiological selection has operated to conserve N in plants via decreased reliance on N-rich amino acids. This inference was supported by an analysis of conserved and variable sites indicating that the N-content of plant amino acids coded by variable sites is similar to that of the sites conserved between plant and animal genomes and shows no association with expression level. In contrast, in animals the N content of amino acids coded by variable sites is significantly higher than that for conserved sites, suggesting relaxation of selective constraints for N-usage in the animal lineage. This constitutes the first evidence for an influence of environmental resource availability on proteomes of multi-cellular organisms.

Keywords: proteome; nitrogen; animal; plant; stoichiometry.
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