Bacteria, ‘ecological suicide,’ and the happy little accidents that drive evolution

May 3, 2018

Two recent studies from the lab of Hertz Fellow Jeff Gore at MIT’s Center for the Physics of Living Systems illustrate a pair of compelling principles about the interactions that drive our ecology and evolution.

The first, featured on April 30 in the New York Times, is a study led by Gore lab postdoc Christoph Ratzke, showing how a population of bacteria can pollute themselves into extinction. The research, published in Nature Ecology & Evolution, describes how rapid, unchecked growth of Paenibacillus bacteria can turn their environment so acidic that the population drives itself extinct. “The cells don’t realize what they’re doing in time to stop doing it,” Gore told the Times.

Despite their tendency for what Gore calls “ecological suicide,” Paenibacillus species remain a common and productive part of microbial ecosystems, in part because other microbes have countervailing effects on the environment. In fact, the microbes’ self-destructive tendencies might be an important driver of diversity in microbial communities, where no one species dominates.

When a species environment does change rapidly – whether by its own doing or by outside forces – it must adapt quickly or die. Another recent study from the Gore lab shows how evolution might exploit accidents in the replication of the genome to make that happen.

That study, led by Gore lab postdoc Avihu Yona and published in Nature Communications, examined how likely a given DNA sequence was to function as a promoter – the sequence of DNA near the beginning of a gene where the process of reading the gene off the chromosome. Since promoters have such powerful control over what genes are expressed – and therefore every aspect of an organism’s behavior – one might think that it would be hard for a new promoter to form through accidental mutation.

In fact, exactly the opposite is true. In a randomly generated selection of gene sequences of the right length to serve the role, the team discovered that fully 60% of them were only one mutation away from being a functional promoter.

Why would evolution select for a system where nearly any part of the genome could, at any time, start accidentally being read out as if it were a gene? Yona says a system like this could help quickly turn on new genes – whether latent in the genome or taken in from other species through horizontal gene transfer – when the cell needs to change quickly.

“If you’re far away from accidental expression, you’re also far away from an evolutionary change when you need it badly,” says Yona. “You have to have some mess in order to be able to adapt to new challenges.”

“It’s a balance between the desire to very tightly control how much a gene is expressed, and being able to change that when necessary,” says Gore.

Because the transcription processes that promoters control – and the evolutionary pressures that organisms face – are very similar for organisms from E. coli to humans, Gore says it wouldn’t surprise him if our own transcription system were similarly balanced. “This could have lessons not only for transcription in all life, but also in many other processes” – from cellular metabolism to inter-organism cooperation – “where you want to have this control.”