The genomes of prokaryotes, however, tend to collapse in size in the face of genetic drift, as suggested by work done by Howard Ochman of the University of Texas, Austin and Louis-Marie Bobay, now at North Carolina State University. It’s not clear why, but it may be because gene regulation in prokaryotes is much less complex: All of their genes are transcribed. Deleting DNA could be their way of dealing with less-than-ideal genes taking over under genetic drift, speculated Simpson, who was not involved in the new research. Maybe jettisoning chunks of the genome is a defense against the random effects of drift.
It wasn’t clear if all prokaryotes do this, Ratcliff knew. But if, in a pinch, ancestral prokaryotes got rid of DNA instead of accumulating it, could they have had trouble assembling the toolkit to make a transition to multicellularity?
Ratcliff and Bingham, who is a computational biologist, thought about the ramifications. In effect, the evolution of multicellularity can squeeze what was once many organisms into a smaller population; there might be a lot of cells, but they’re all the same organism. Under this population pressure, prokaryotes and eukaryotes might respond differently — the former in a way that creates barriers to evolving multicellularity, and the latter in a way that accelerates it.
In that case, the transition might have fueled, and been fueled by, eukaryotes’ tendency for genome expansion. In other words, the ability to make the transition to multicellularity might come down to how a population handles its genome in a tight spot. Ratcliff and Bingham wondered if they could find a way to test that idea.
A Toy Model
Ratcliff and Bingham were already aware that multicellularity seems to coincide with increased genome size. “We know from the comparative record that pretty much all multicellular lineages have bigger genomes than their single-celled counterparts,” Ratcliff said. But they wanted to take a closer look.
As a test case, they examined the genomes of cyanobacteria, which have evolved many forms of primitive multicellularity. Ratcliff and Bingham discovered that the more features of multicellularity a given lineage of cyanobacteria had, the larger its genome. This provided support for a link between genome size and multicellularity.
Then, to examine their hypothesis more directly, Ratcliff and Bingham created a highly simplified computational model. In the model, populations of prokaryotes and eukaryotes were under pressure to develop into multicellular organisms of different sizes and accumulate a larger genome. The researchers programmed one group, standing in for eukaryotes, with a tendency to expand its genome; the other, standing in for prokaryotes, shrank it. Even as the organisms grew larger, the eukaryotes were always able to grow their genomes substantially and were rewarded for it. Below a certain size, however, the prokaryotes ran into a wall and couldn’t make their genomes larger, no matter how much they were rewarded.
The model is simple and limited, the researchers state. Still, it suggests that this difference in genomic processes could have significant effects.
Their new hypothesis is striking, Simpson said, because it jibes with other observations about how multicellularity works. Complex multicellular organisms have radiated into many different species. Perhaps that’s a result of additional DNA piling up, providing the raw materials for innovation.
It also connects to the procedures that complex multicellular eukaryotes use to develop different cell types from the same set of genes. They manage to have tissues as different as the liver and the lungs by turning genes on and off in different cells. Perhaps prokaryotic organisms that didn’t start out with the ability to control their DNA that way would have struggled to make the leap.
Crucially, whenever eukaryotes did manage to put together a toolkit to become multicellular, they would not have to fight a genomic process to keep it, Simpson said. “But prokaryotes have to fight it all the time no matter what.”