Can You Eat Cells? Computer Model Predicts Organisms that Use Phagocytosis

A computer model developed by Museum researchers may provide new insight into the origins of phagocytosis, the process by which single-celled organisms “eat” other cells as a means of absorbing nutrients or eliminating pathogens.

Phagocytosis is thought by some to be the mechanism behind a very early step in the evolution of complex life, when two simple single-celled organisms merged, giving rise to mitochondria—energy-generating organelles that are a key feature of complex cells, including our own.

“Phagocytosis is a major mechanism of nutritional uptake in many single-celled organisms and it’s vital to immune defenses in a number of living things, including humans,” said Eunsoo Kim, associate curator in the Museum’s Division of Invertebrate Zoology. “It dates back some 2 to 3 billion years and played a role in those symbiotic associations that likely started the cascading evolution toward the more diverse and complex life we see on the planet today.”

But pinpointing the ancestral microbes from which mitochondria evolved has been difficult, since no single-celled bacteria or archaea are capable of phagocytosis today. The new model, which uses machine learning based on the genetic patterns of phagocytic cells, can help scientists to quickly predict which cells could be “eaters.” 

“There’s no single set of genes that are strongly predictive of phagocytosis,” said John Burns, a research scientist in the Museum’s Sackler Institute for Comparative Genomics and lead author of a study describing the model that was published today in Nature Ecology & Evolution. “But as we started looking at the genomes of more and more eukaryotes, a genetic pattern emerged, and it exists across diversity, even though it’s slightly different in each species.”

Using the new computer model, researchers have been able to more closely examine the genetic lines of microbes like Asgard archaea, which some recent studies have suggested could be descendants of the first phagocytic cells. However, the findings showed that Asgard microbes lack the genetic traits capable of phagocytosis. Although the new work eliminates one scenario for the birth of mitrochondria—that Asgard archaea engulfed a bacteria—many other options remain.

“When you tease apart the components of these predictive genes, some have roots in archaea, some have roots in bacteria, and some are only unique to eukaryotes,” said Kim, who is co-author of the study with Alexandros Pitti, a former postdoctoral researcher at the Museum. “Our data are consistent with the hypothesis that our cells are a chimera of archaeal and bacterial components, and that the process of phagocytosis arose only after that combination took place. We still have a lot of work to do in this field.”

This article has been republished from materials provided by the American Museum of Natural History. Note: material may have been edited for length and content. For further information, please contact the cited source.

Reference
Gene-based predictive models of trophic modes suggest Asgard archaea are not phagocytotic. John A. Burns, Alexandros A. Pittis & Eunsoo Kim. Nature Ecology & Evolution (2018), doi:10.1038/s41559-018-0477-7.