Evolution in the Air: Studies zoom in on interplay between environment, species, and building blocks of life

December 20, 2006

Joe Caspermeyer, Media Relations Manager & Science Editor
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Claudia Acquisti, a postdoctoral researcher who recently joined the Center for Evolutionary Functional Genomics at the Biodesign Institute at Arizona State University, 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 measuring 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 the 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," said Acquisti, who completed the work at the Max Planck Institute for Plant Breeding Research in K?ln, 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. Oxygen was then 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" said Acquisti.

In the study, Acquisti and colleagues 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 physically 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 both the form and function of these bridge-like proteins. According to Acquisti, 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. ?In contrast, organisms that appeared when oxygen levels were higher have transmembrane proteins that contain more oxygen and have larger extracellular domains.

"Natural selection would have acted against the production of large extracellular domains needed for communication across membranes. When atmospheric oxygen levels rose, this constraint would have been lessened, and the production of communication-related transmembrane proteins would have been much easier," said Acquisti.

Acquisti now joins ASU School of Life Sciences professors Kumar and Elser, who are already linking interdisciplinary studies of proteomes and genomes with ecology. Their goal: to examine the total carbon and nitrogen content of plant and animals proteins. ?"We already knew that plant biomass was very low in nitrogen, as compared to animal biomass," said Elser. "And we just asked: is it possible that these differences in nitrogen investment might actually be seen at a molecular level rather than just the whole organism level?"?

In a recent paper in the journal Molecular Biology and Evolution (Mol. Biol. Evol. 23, 10.1093/molbev/msl068 (2006), which was an Editor’s Choice in the journal Science (25 August 2006:Vol. 313. no. 5790, p. 1020 DOI: 10.1126/science.313.5790.1020c), 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. "Our findings, for the first time, demonstrate the influence of environmental resource availability on proteomes in these species," said Elser.

The ASU team of Kumar, Elser, and Acquisti 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 "Our community resource will enable scientists to develop and test ecological-genomics hypotheses in a wide range of species" said Kumar.

Editor’s note:
-information for this article was also contributed by Margaret Coulombe, of the School of Life Sciences

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