"This is the first amoeba genome to be completely sequenced," said Dr. Adam Kuspa, professor of biochemistry and molecular biology at BCM and senior author of the report on the sequencing that appears in the current issue of the journal Nature. The report outlines the unusual features of the organism itself.
Kuspa said the sequencing effort has, over the past five years, clarified the place this unusual organism occupies in the hierarchy of existence. "It is more closely related to fungi and animals than we had previously thought," he said.
Dictyostelium is used as a model organism for studying cell polarity, how amoeba move and the differentiation of tissues. It usually exists as a single cell organism that inhabits forest soil, consuming bacteria and yeast. When starved, however, the single cells come together, differentiate into tissues and become a true multicellular organism with a fruiting body composed of a stalk with spores poised on top. This increases its utility in a variety of studies.
"An organism's relationship to humans depends on related proteins that are found in the two cell types," said Kuspa. "You can make direct analogies, or you could learn general principles about how cells regulate their behavior. Both things will apply in the studies we do."
In the sequencing, he and his international collaborators found that there are more protein coding genes in the organism than they had thought - and nearly twice as many as there are in fungi. Their research also led to the conclusion that amoebozoa, the group to which Dictyostelium belongs, evolved from the common ancestor of eukaryotes (the group of organisms that contain all animals, plants, algae, protozoa, slime mold and fungi) before fungi. It has about 12,000 genes that produce a greater variety of proteins than the approximately 6,000 found in fungi.
"That really speaks to how much we will relate the gene function information we find to humans," he said. It makes Dictyostelium a better model for looking for targets against which drugs can act.
Kuspa said key collaborators in the project at BCM include Dr. Richard Gibbs, director of the BCM Human Genome Sequencing Center; Dr. George Weinstock, co-director of the sequencing center; and Dr. Richard Sucgang, an assistant professor of biochemistry at BCM, among many others. The effort was international, involving investigators from around the world, he said. BCM did approximately half of the sequencing work.