When a normal cell experiences a break in the double strands of DNA that provide its genetic blueprint, it seeks out a normal repair enzyme that guides the repair process along normal lines.

However, the process is different in stressed cells, said Dr. Susan Rosenberg, professor of molecular and human genetics at Baylor College of Medicine and colleagues in a report that appears online today in the journal Cell Reports.

"Under stress, special error-prone DNA copying enzymes (other repair enzymes) get involved," she said. These DNA copying enzymes do not replicate the DNA faithfully, resulting in mutations that can lead to substantive changes in the genetic code. Now it turns out that those DNA breaks spawn mutation hotspots—small local zones of mutations—that can speed the ability of cells to adapt to environments and evolve.

Pinpointing hotspots

Rosenberg has pioneered the concept that Escherichia coli and other cells speed up the rate of mutation when the cells are stressed—as when they are starved. She and her colleagues also were aware of mutation hotspots, but why and how these occurred remained a mystery.

Rosenberg credits the report's first author, Dr. Chandan Shee (a postdoctoral associate in her laboratory) with the painstaking laboratory work that enabled them to show that hotspots occur and pinpoint where the hotspots occurred.

"We found that there was a huge, strong mutation hotspot at the site of the break," she said. "Then a weak hotspot extends up to a megabase away.” (A base is one of the chemicals that make up the DNA molecule—adenine, thymine, cytosine and guanine.)

"When an Escherichia coli (a form of bacteria used as a model organism) chromosome has a hole in it because of a break, it has to find a sister DNA molecule from which to copy the lost DNA, fill the hole and repair itself," said Rosenberg. "These DNA molecules are double-stranded. The ends find space on the sister molecule and copy some DNA."

Two-step process

The repair is a two-step process. First the enzyme erodes part of the remaining DNA on the ends and then new DNA is synthesized to repair the break.

"When we used a mutant that is erosion deficient but can do the repair," said Rosenberg, "the strong local hotspot goes away. The strong local hot spot is caused by the resection of DNA strands and the synthesis of new DNA." The weak distant hotspot remains, she said. That showed that the erosion is an important part of establishing the hotspot.

If the mutation hotspot is limited to a small zone, then the ability to make new proteins is improved, she said.

"These local mutation hotspots are evolution drivers," she said. "It is a pattern that has just been recognized in cancer genomes as mutation showers."

Driving force

While they cannot do the painstaking genetic engineering in human cells that enabled them to prove that the mutation hotspot occurs near a DNA break in E. coli, Rosenberg said the theory demonstrates a molecular mechanism that is likely to be the driving force in these mutation showers seen in tumors.

"The more you know how it works, the more plausible it becomes to intervene," said Rosenberg.

Dr. Janet L. Gibson, an instructor at BCM and a member of Rosenberg’s laboratory also took part in the study.

Funding for this work came from the National Institutes of Health (R01-GM53158).

Rosenberg holds the Ben F. Love Chair in Cancer Research. She is a member of the NCI-designated Dan L. Duncan Cancer Center at BCM and is also a professor in the departments of biochemistry and molecular biology, molecular virology and microbiology, the Interdepartmental programs in Cell and Molecular Biology and Translational Biology and Molecular Medicine.