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Dictyostelium ecology
- The genome of the social amoeba Dictyostelium discoideum

Dictyostelium ecology

Dictyostelium faces many complex ecological challenges in the soil. Amoebae, fungi and bacteria compete for limited resources in the soil while defending themselves against predation and toxins. For instance, the nematode C. elegans is a competitor for bacterial food and a predator of Dictyostelium amoebae, but also a potential dispersal agent for Dictyostelium spores46. Dictyostelium has expanded its repertoire of several protein classes that are likely to be crucial for such inter-species interactions and for survival and motility in this complex ecosystem.

Polyketide synthases
A small number of natural products have already been identified from Dictyostelium, but the gene content suggests it is a prolific producer of such molecules. Some of them may act as signals during development, such as the dichloro-hexanophenone DIF-1, but others are likely to mediate currently unknown ecological interactions47. Many antibiotics and secondary metabolites destined for export are produced by polyketide synthases, modular proteins of around 3,000 amino acids48. We identified 43 putative polyketide synthases in Dictyostelium (see Supplementary Information). By contrast, S. cerevisiae completely lacks polyketide synthases and Neurospora crassa has only seven. In addition, two of the Dictyostelium proteins have an additional chalcone synthase domain, representing a type of polyketide synthase most typical of higher plants and found to be exclusively shared by Dictyostelium, fungi and plants. In addition to polyketide synthases, the predicted proteome has chlorinating and dechlorinating enzymes as well as O-methyl transferases, which could increase the diversity of natural products made. Thus, Dictyostelium appears to have a large secondary metabolism which warrants further investigation.

ABC transporters
ATP-binding cassette (ABC) transporters are prevalent in the proteomes of soil microorganisms and are thought to provide resistance to xenobiotics through their ability to translocate small molecule substrates across membranes against a substantial concentration gradient4952. There are 66 ABC transporters encoded by the genome, which can be classified according to the subfamilies defined in humans, ABCA-ABCG, based on domain arrangement and signature sequences53. At least twenty of them are expressed during growth and are probably involved in detoxification and the export of endogenous secondary metabolites.

Cellulose degradation
Curiously, many of the predicted cellulose degrading enzymes in the proteome (see Supplementary Information) that have secretion signals are expressed in growing cells that do not produce cellulose54. The proteome also has one xylanase enzyme that can degrade the xylan polymers that are often found associated with the cellulose of higher plants. Perhaps Dictyostelium uses these enzymes to degrade plant tissue into particles that are then taken up by cells. These enzymes may also aid in the breakdown of cellulose-containing microorganisms upon which Dictyostelium feeds. Alternatively, these enzymes may promote the growth of bacteria that can serve as food, since Dictyostelium’s habitat also contains cellulose-degrading bacteria.

Specializations for cell motility
During both growth and development, Dictyostelium amoebae display motility that is characteristic of human leukocytes55. As a consequence, studies of Dictyostelium have contributed significantly to cytoskeleton research56. Dictyostelium’s survival depends on an ability to efficiently sense, track and consume soil bacteria using sophisticated systems for chemotaxis and phagocytosis. Its multicellular development depends on chemotactic aggregation of individual amoebae and the coordinated movement of thousands of cells during fruiting body morphogenesis. The proteome reveals an astonishing assortment of proteins that are used for robust, dynamic control of the cytoskeleton during these processes. As suggested from the functional parallels to human cells, these proteins are most similar to metazoan proteins in their variety and domain arrangements (Fig. 7; Table SI 11). Surprisingly, although the actin cytoskeleton has been studied for over twenty-five years, 71 putative actin-binding proteins apparently escaped classical methods of discovery. For example, actobindins had not been previously recognized in Dictyostelium. Curiously, the actin depolymerisation factor (ADF) and calponin homology (CH) domain proteins appear to have diversified by domain shuffling, a substantial fraction having domain combinations unique to Dictyostelium (Fig. SI 13; Table SI 12). In addition to 30 actin genes, there are also orthologues of all actin-related protein (ARP) classes present in mammals, as well as three founding members of a new class (Fig. SI 14).
Cytoskeletal remodelling during chemotaxis and phagocytosis is regulated by a considerable number of upstream signaling components. Of the 15 Rho family GTPases in Dictyostelium, some are clear Rac orthologues and one belongs to the RhoBTB subfamily57. However, the Cdc42 and Rho subfamilies characteristic of metazoa and fungi are absent, as are the Rho subfamily effector proteins. The activities of these GTPases are regulated by two members of the RhoGDI family, by components of ELMO1/DOCK180 complexes and by a surprisingly large number of proteins carrying RhoGEF and RhoGAP domains (>40 of each), most of which show domain compositions not found in other organisms. Remarkably, Dictyostelium appears to be the only lower eukaryote that possesses class I PI 3-kinases, which are at the crossroad of several critical signalling pathways (for details of the regulators and their effectors, see Table SI 13)58. The diverse array of these regulators and the discovery of many additional actin-binding proteins suggests that there are many aspects of cytoskeletal regulation that have yet to be explored.

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