Comparative Genomics of Social Amoebae

The Science

Found in soils worldwide, slime molds such as Dictyostelium discoideum are perhaps best known by their behavior in the presence or absence of food. When food is plentiful, the social amoeba behave as individuals, but when food is scarce, they come together to form multicellular “fruiting bodies” that look like a flower bud atop a single stalk or foot composed of a fifth of the amoebae that have sacrificed themselves for the group.

Studying social amoebae allows researchers to learn more about multicellularity because these amoebae can exist in both single-cell and multicellular states. From a bioremediation perspective however, slime molds are important candidates in cleaning up sites contaminated with chemicals and radioactive materials.

In a recent paper, researchers from DOE’s Joint Genome Institute and Baylor College offer a second Dictyostelium genome, and compare the 33-million base draft sequence produced using the Sanger platform with the finished genome of the model organism D. discoideum.

Separated by 400 million years of evolution, Dictyostelium purpureum is a close relative of D. discoideum and shares many of the same characteristics. Aside from their food-related behaviors, they also have a highly sophisticated recognition system that allows them to distinguish same-species Dictyostelium from others. The researchers found that the genes involved in sociality evolve more rapidly, probably due to continuous adaptation and counter-adaptation.

Summary

The social amoebae (Dictyostelia) are a diverse group of Amoebozoa that achieve multicellularity by aggregation and undergo morphogenesis into fruiting bodies with terminally differentiated spores and stalk cells. Researchers produced a draft genome sequence of another group dictyostelid, Dictyostelium purpureum, and compare it to the D. discoideum genome. Comparative analyses revealed a core set of orthologous genes that illuminate dictyostelid physiology, as well as differences in gene family content. Interesting patterns of gene conservation and divergence are also evident, suggesting function differences; some protein families, such as the histidine kinases, have undergone little functional change, whereas others, such as the polyketide synthases, have undergone extensive diversification.

BER Program Manager

U.S. Department of Energy, Biological and Environmental Research (SC-33)
Biological Systems Science Division
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References

Sucgang, R., A. Kuo, X. Tian, W. Salerno, A. Parikh, C. L. Feasley, E. Dalin, H. Tu, E. Huang, K. Barry, E. Lindquist, H. Shapiro, D. Bruce, J. Schmutz, A. Salamov, P. Fey, P. Gaudet, C. Anjard, M. Madan Babu, S. Basu, Y. Bushmanova, H. van der Wel, M. Katoh-Kurasawa, C. Dinh, P. M. Coutinho, T. Saito, M. Elias, P. Schaap, R. R. Kay, B. Henrissat, L. Eichinger, F. Rivero, N. H. Putnam, C. M. West, W. F. Loomis, R. L. Chisholm, G. Shaulsky, J. E. Strassmann, D. C. Queller, A. Kuspa, and I. V. Grigoriev. 2011. “Comparative Genomics of the Social Amoebae Dictyostelium discoideum and Dictyostelium purpureum,” Genome Biology 12, R20. DOI:10/1186/gb-2011-12-2-r20.