Comparing Slime

Figure 1. Slime molds are frikin cool. (Source)

Social amoebae (sometimes referred to as slime molds, though they are not true members of the slime mold group) are a diverse group of unicellular organisms that congregate into “multicellular” forms for the purpose of reproduction. They have been widely studied because of the implications of their lifestyle to the establishment of multicellularity. Why? Because in order for an organism to become multicellular, different cells have to take on different functions. A consequence of this is that only some cells make up the germline and some cells do not reproduce. Convincing cells to be all work and no play is a major barrier to establishing multicellularity.

Social amoebae appear to be at the evolutionary cusp of multicellularity. Whereas they generally persist as unicellular beasts, asexual reproduction occurs as a group. The cells congregate and form the fruiting body (Fig. 2), but in doing so, only about 80% of the cells end up in the spore and others in the support structure. There is competition to be in the 80%, so cell types that make up the support structure reproduce at times, otherwise the population would only consist of spore formers and that wouldn’t work. But, the system is complex and certain cell types are more aggressive at getting into the spore than others (Strassmann, Zhu & Queller, 2000).

Figure. 2. Stages of D. discoideum reproduction.

Because of the heavy scientific interest in social amoebae, and in particular the thoroughly studied Dictyostelium discoideum, the genome of this organism was sequenced in 2005 (Eichinger et al. 2005). Since then, however, no other genome from this group has been sequenced, despite their small size (~33 Mb). In the early addition of Genome Biology, however, we finally have a second social amoebae genome from Dictyostelium purpureum (Sucgang et al. 2011).

Don’t be fooled by the fact that these two organisms are in the same genus. Divergence estimates, based on sequence data, put the split between them at roughly 400 MYA. For reference, the origin of animals is believed to have occurred around 600 MYA. Let’s just say that taxonomy can be subjective based on the characters we deem important rather than actual divergence between two organisms and leave it at that, but the two social amoebae being compared share a very distant common ancestor.

An important difference between D. discoideum and D. purpureum is that the latter has a greater tendency to favor the formation of the multicellular “slug” with kin groups than the former. When the D. discoideum genome was sequenced there were several protein families that were identified as potentially involved in multicellular stage formation, including subfamilies of ABC transporters, aspects of an innate immune system, and cell surface proteins. Nearly all of the genes implicated in social behavior in D. discoideum were found in D. purpureum, which was not surprising, but provided some independent confirmation of their function.

Most interestingly, to me anyway, was the finding that genes involved in the amoeba sociality do not have significantly different copy number between the two species, but have increased rates of evolution. Additionally, the “socialome” was determined to have a reduced ortholog number and higher rates of non-synonomous change, compared with other gene families The authors suggest that this is the result of reproductive competition and that the mechanism follows almost a “Red Queen” like adaptation. In other words, competition between different strains to be a reproducing member of the spore stage drives the evolution of genes related to sociality.

As the cost of genome sequencing continues to drop and the breadth of taxa we sample increases, comparative studies of related species that have different lifestyles will become more and more prevalent. These comparisons stand to elucidate some of the critical genomic factors that result in lifestyle changes and delve deeper into the nitty gritty of evolution at the genomic level.

Eichinger, L., Pachebat, J., Glöckner, G., Rajandream, M., Sucgang, R., Berriman, M., Song, J., Olsen, R., Szafranski, K., Xu, Q., Tunggal, B., Kummerfeld, S., Madera, M., Konfortov, B., Rivero, F., Bankier, A., Lehmann, R., Hamlin, N., Davies, R., Gaudet, P., Fey, P., Pilcher, K., Chen, G., Saunders, D., Sodergren, E., Davis, P., Kerhornou, A., Nie, X., Hall, N., Anjard, C., Hemphill, L., Bason, N., Farbrother, P., Desany, B., Just, E., Morio, T., Rost, R., Churcher, C., Cooper, J., Haydock, S., van Driessche, N., Cronin, A., Goodhead, I., Muzny, D., Mourier, T., Pain, A., Lu, M., Harper, D., Lindsay, R., Hauser, H., James, K., Quiles, M., Madan Babu, M., Saito, T., Buchrieser, C., Wardroper, A., Felder, M., Thangavelu, M., Johnson, D., Knights, A., Loulseged, H., Mungall, K., Oliver, K., Price, C., Quail, M., Urushihara, H., Hernandez, J., Rabbinowitsch, E., Steffen, D., Sanders, M., Ma, J., Kohara, Y., Sharp, S., Simmonds, M., Spiegler, S., Tivey, A., Sugano, S., White, B., Walker, D., Woodward, J., Winckler, T., Tanaka, Y., Shaulsky, G., Schleicher, M., Weinstock, G., Rosenthal, A., Cox, E., Chisholm, R., Gibbs, R., Loomis, W., Platzer, M., Kay, R., Williams, J., Dear, P., Noegel, A., Barrell, B., & Kuspa, A. (2005). The genome of the social amoeba Dictyostelium discoideum Nature, 435 (7038), 43-57 DOI: 10.1038/nature03481

Strassmann JE, Zhu Y, & Queller DC (2000). Altruism and social cheating in the social amoeba Dictyostelium discoideum. Nature, 408 (6815), 965-7 PMID: 11140681

Sucgang, R., Kuo, A., Tian, X., Salerno, W., Parikh, A., Feasley, C., Dalin, E., Tu, H., Huang, E., Barry, K., Lindquist, E., Shapiro, H., Bruce, D., Schmutz, J., Salamov, A., Fey, P., Gaudet, P., Anjard, C., Babu, M., Basu, S., Bushmanova, Y., van der Wel, H., Katoh-Kurasawa, M., Dinh, C., Coutinho, P., Saito, T., Elias, M., Schaap, P., Kay, R., Henrissat, B., Eichinger, L., Rivero, F., Putnam, N., West, C., Loomis, W., Chisholm, R., Shaulsky, G., Strassmann, J., Queller, D., Kuspa, A., & Grigoriev, I. (2011). Comparative genomics of the social amoebae Dictyostelium discoideum and Dictyostelium purpureum Genome Biology, 12 (2) DOI: 10.1186/gb-2011-12-2-r20

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