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Researchers study interplay between environment, evolution

January 23, 2007

Claudia Acquisti, a postdoctoral researcher who recently joined the Center for Evolutionary Functional Genomics at the Biodesign Institute at ASU, is providing new perspectives on environmental nutrient availability and the evolution of life.

She joins the group led by ASU professors Sudhir Kumar and James Elser, who are using methods to zoom deep within the constellation of proteins in our cells and measure the balance of elements such as nitrogen, carbon and hydrogen found in the chemical backbones of these building blocks of life.

Acquisti's latest results, published in the advanced online edition of Nature (, stretch across a large-scale species comparison and vast epochs in earth's geological history to find common evolutionary threads. Her conclusions suggest that changes in Earth's atmospheric oxygen may have played a significant role on the evolution of proteins and compartments necessary for cell communication in higher organisms.

“We have used the correlation between protein oxygen content, atmospheric oxygen levels and the evolutionary age of organisms to propose the novel hypothesis that oxygen limitation contributed to the timing of the evolution of cellular communication in eukaryotic cells,” says Acquisti, who completed the work at the Max Planck Institute for Plant Breeding Research in Köln , Germany .

One of the most intriguing evolutionary leaps was the jump from bacteria cells that lacked a nucleus (prokaryotes) to the appearance of compartmentalized cells with a nucleus (eukaryotes), thought to have occurred between 2.1 and 1.8 billion years ago.

“One explanation is that atmospheric oxygen of earth was very low until about 3 billion years ago,” Acquisti says. “Oxygen then was introduced quickly into the atmosphere, which led to the formation of eukaryotic cells, and has remained between 15 percent and 25 percent for the past billion years.”

In the study, Acquisti calculated the oxygen content for the complete set of protein information, or proteome, for 19 different species, a compilation that represents thousands of proteins. She discovered that the difference in oxygen content found in each proteome went from low (bacteria) to high (plants and animals).

The evolutionary pressure also arose to communicate across impermeable membranes that act as a physical barrier to keep the contents of the fluid-filled compartments separate from one another. This important communication role is fulfilled by two classes of transmembrane proteins, which act as a bridge to shuttle information across membranes: channel proteins, which allow small charged molecules in and out of the cell; and receptor proteins, which trigger a cascade of intracellular communication events such as signaling in the brain.

Next, Acquisti divided the proteins into the two classes and repeated the oxygen measurements.

Acquisti proposes that the atmospheric oxygen limited the form and function of these bridge-like proteins. She says the evolution of transmembrane proteins with large extracellular domains needed for communication (receptors) may have been selected against in an ancient reducing atmosphere, which is evidenced by the low oxygen content and small size of these domains in organisms that evolved under low-oxygen conditions.

Acquisti now joins ASU School of Life Sciences professors Kumar and Elser, who already are linking interdisciplinary studies of proteomes and genomes with ecology. Their goal: to examine the carbon and nitrogen content of plant and animal proteins.

In a recent paper in the journal Molecular Biology and Evolution, which was an Editor's Choice in the journal Science, Elser and colleagues compared several animal and plant proteomes and found that plant proteins have lower nitrogen content than animal proteins. The difference was the largest for proteins that are used the most in plants, indicating that nature avoids building blocks that are in short supply in plants.

The ASU team of Acquisti, Elser and Kumar will partner with their collaborator, William Fagan (University of Maryland), to build an electronic catalog of the frequency of nitrogen, carbon, sulfur, and other elements in animal and other proteins, which will be accessible through the Web. This effort is supported by a $1 million grant from the National Science Foundation.

Margaret Coulombe,
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Joe Caspermeyer,
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