Does Evolution Evolve Under Pressure?

In 1996, Susan Rosenberg, then a young professor at the University of Alberta, undertook a risky and laborious experiment. Her team painstakingly screened hundreds of thousands of bacterial colonies grown under different conditions, filling the halls outside her lab with tens of thousands of plates of bacteria. “It stank,” Rosenberg recalled with a laugh. “My colleagues hated me.”

The biologist, now at Baylor College of Medicine in Houston, hoped to resolve a major debate that had rocked biology in different incarnations for more than 100 years. Were organisms capable of altering themselves to meet the needs of their environment, as Jean Baptiste Lamarck had proposed in the early 1800s? Or did mutations occur randomly, creating a mixture of harmful, harmless or beneficial outcomes, which in turn fueled the trial-and-error process of natural selection, as Charles Darwin proposed in “On the Origin of Species”?

Although Darwin’s ideas have clearly triumphed in modern biology, hints of a more Lamarckian style of inheritance have continued to surface. Rosenberg’s experiments were inspired by a controversial study, published in the late 1980s, that suggested that bacteria could somehow direct their evolution, “choosing which mutations will occur,” the authors wrote — a modern molecular biologist’s version of Lamarckian theory.

Rosenberg’s results, published in 1997, disputed those findings, as other’s hadbefore, but with a twist. Rather than targeting specific traits, as Lamarck’s theory would have predicted, the mutations struck random genes, with some good outcomes and some bad. However, the process wasn’t completely random. Rosenberg’s findings suggested that bacteria were capable of increasing their mutation rates, which might in turn produce strains capable of surviving new conditions.

Biologist Susan Rosenberg of Baylor College of Medicine in Houston studies how bacteria mutate when under stress.

“Cells are able to adapt to stress not by knowing exactly what they need to do, but by throwing the dice as a population and making random changes to the genome,” said James Broach, a biologist at Pennsylvania State University’s College of Medicine in Hershey who studies a similarphenomenon in yeast. “That will allow stressed progeny to find an escape route.”

Rosenberg expected the biology community to be relieved. Darwin, after all, had prevailed. But some scientists questioned the findings. Indeed, the research triggereddebates that played out in the pages of scientific journals for several years. Accurately measuring mutation rates can be tricky, and given that most mutations are harmful to the cell, boosting their frequency seemed like a risky evolutionary move.

Over the past decade, however, labs around the world have found similar patterns in bacteria, human cancer cells and plants. And Rosenberg and others have pinpointed the molecular mechanisms underlying the stress-induced mutations, which vary from organism to organism.

Scientists are now beginning to explore how these mechanisms can be targeted for medical treatments, such as new cancer therapies and long-lasting antibiotics. The research provides insight into how both cancer cells and pathogenic bacteria evolve resistance to treatment, a stubborn and deadly problem that has plagued physicians and drug developers.

Bacterial colonies mutate more frequently when put under stress, as shown by the visible mutation in these blue-green colonies.

Last March, for example, Ivan Matic, a research director at the French National Institute of Health and Medical Research in Paris, and collaborators found that very low levels of antibiotics, present in the water supply from human and animal waste, were enough to push bacteria into a stressed state, boosting their mutation rates. “It’s a spectacular example of stress-induced mutation,” said Matic, whose findings were published in Nature Communications last year. Some of these mutations made the bacteria resistant to antibiotics, suggesting that exposure to a low dose of one antibiotic could prime bacteria to evolve resistance to other antibiotics as well.

Most scientists now accept that stress boosts mutation rates in some organisms, although questions remain regarding how much the phenomenon contributes to their evolution. “What’s controversial now is whether cells evolved to do this to create mutations,” said Patricia Foster, a biologist at Indiana University in Bloomington.

Molecular Mistakes

In 1943, Max Delbrück and Salvador Luria, two of the founding fathers of molecular biology, performed a landmark experiment designed to examine the nature of mutation. They showed that mutations in bacteria arise spontaneously, rather than in response to a specific environmental pressure. The work, which ultimately won them a Nobel Prize, was all the more impressive given that scientists did not yet know the structure of DNA.

We now know that mutations arise in a variety of ways, typically when a cell is copying or repairing its DNA. Every so often, the molecular machinery that makes DNA inserts the wrong building block, or the copying machinery jumps elsewhere in the genome and copies the wrong piece. Those changes can have no effect, or they can alter the structure of the protein that the DNA produces, changing its function for better or, more often, for worse.

Under stressful conditions, such as when food is scarce, E. coli bacteria employ an enzyme that tends to make mistakes when copying DNA.

According to Delbrück and Luria’s model, these accidents happen randomly, gradually accruing over time. But scientists have occasionally considered an alternative — that organisms can in some cases control how they mutate, enabling them to more rapidly evolve to adapt to new environments. Indeed, in unpublished correspondence, Delbrück’s one-time adviser, Wolfgang Pauli, questioned whether the mutation process could be truly random. As Rosenberg, who read the letters at a conference in 2007, recalls, Pauli argued that “a simple probabilistic model would not be sufficient to generate the fantastic diversity we see.”

The debate surfaced again in 1988, when the biologist John Cairns and collaborators at Harvard University made a provocative proposal in the journal Nature, that bacteria could somehow choose which genes to mutate. The evidence? Bacteria incapable of digesting a sugar called lactose evolved that ability when given no other alternative food. “The paper was hugely controversial,” recalled Foster, a friend of Cairns’ who collaborated with him on follow-up studies. “Letters flew back and forth.”

The idea that cells can regulate their mutation rates is not as outlandish as it might seem. Certain immune system cells, for example, mutate much more frequently than others, enabling them to produce varieties of antibodies that can subdue novel invaders. But these cells are confined to the immune system and do not pass along their mutations to the next generation.

It was Cairns’ finding that inspired Rosenberg to undertake her experiments. She suspected that his proposal was wrong, but not entirely. “People fought about it for five years in the front pages of major journals,” she said. “It was clear to me that it was a hugely important question.”

Subsequent research from both Rosenberg and Foster showed that mutations were scattered across the E. coli genome, rather than directed to specific genes, as Cairns had proposed. (Cairns abandoned his hypothesis after follow-up experiments with Foster.) They also found that stress, including lack of food, was a crucial factor in boosting the mutation rate.

“It was a surprise for people,” Rosenberg said. “Cells actually decide to turn up their mutation rate when they are poorly adapted to the environment. That’s a different kind of picture from constant random mutation that is blind to the environment the cell is in.”

A network of more than 90 proteins is required to trigger stress-induced mutations in E. coli bacteria.

With a background in molecular biology rather than evolution, Rosenberg felt that the only way to quell remaining skepticism was to figure out how the mutations were forming. She and Foster independently spent the next few years hammering away at the molecular mechanism underlying the change in mutation frequency in E. coli. Under normal conditions, the bacteria employ an enzyme that carefully copies DNA. But Rosenberg and Foster found that when bacteria are under stress, a mistake-prone enzyme takes over, bumping up the frequency of mutations.

Some scientists are still skeptical, if not about the phenomenon itself, then about how significant it is for an organism’s survival and evolution. At the heart of the debate is a paradox. Most random mutations will be harmful to the organism, knocking out vital proteins, for example. Therefore, more frequent mutations would be likely to generate a less-fit population. “People have still been doubting the phenomenon because they believe that it would be maladaptive,” said Foster. “Increasing the mutation rate would increase deleterious mutations as well as advantageous ones.” Some scientists think that evolution would not select such a mechanism, she said.

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