Scaled-down genome may power up E. coli’s ability in lab, industry

By stripping the E. coli genome of vast tracts of its genetic material — hundreds of apparently inconsequential genes — a team of Wisconsin researchers has created a leaner and meaner version of the bacterium that is a workhorse of modern biology and industry.

The feat, reported this week (April 28) in the journal Science, demonstrates that scientists can make precise, large-scale genetic alterations to organisms without compromising their basic functions. It represents some of the first hard results in a new field of science known as synthetic biology, where researchers are able to mold the entire genomes of bacteria and viruses in unprecedented ways.

The work promises to make E. coli far more malleable for research and industrial use than it already is. It may permit, for example, the mass production of useful proteins and drugs that were previously unattainable in systems dependent on run-of-the-mill laboratory strains of the microbe.

“We’re getting down to the essence of Escherichia coli,” says Frederick Blattner, a University of Wisconsin–Madison professor of genetics and the senior author of the new Science report.

According to Blattner, in a progressive series of experiments, slightly more than 15 percent of the E. coli genome was removed with scientists subtracting up to 82,000 base pairs at a time. Despite having such large segments of DNA removed from their genomes, the resulting E. coli cells retained all of their normal biological functions.

Excising such large amounts of DNA without any impact on the health of the organism is, apparently, a reflection of the tendency of bacteria to readily exchange and accumulate large blocks of genetic material over time from other organisms.

The phenomenon, known as horizontal transfer, occurs when bacteria acquire DNA from other sources, such as viruses that might infect the bacterium and confer genetic material not native to the organism.

That the E. coli genome harbored large amounts of apparently borrowed genetic material became evident when researchers compared the genomes of two types of E. coli previously sequenced in Blattner’s lab, the lab strain and E. coli O157:H7, the strain that sometimes occurs in food and sickens people.

“It was obvious that the different strains had a lot in common,” explains Guy Plunkett III, a UW–Madison scientist and a co-author of the new Science report. “But there were also these big stretches (of DNA) unique to each organism.”

Says Blattner: “It was really clear that these were from a horizontal transfer source. There are tremendous differences between the benign strain and the pathogenic strain.”

Even the genome of the lab strain itself, notes Plunkett, has undergone genetic change since 1924 when it was selected by scientists as a model organism.

Blattner estimates that the E. coli genome contains as many as 1,000 unnecessary genes. “These genes use energy, and they make it harder to do things in the lab.”

E. coli is routinely manipulated at the genetic level in the lab. It is also manipulated genetically in much greater volumes in industry to mass-produce drugs and useful proteins. But some attempts to clone genes of interest or utility in E. coli to make those products were routinely thwarted. The results of the Wisconsin study suggest that some of the superfluous DNA in the microbe’s genome interfered with those efforts to harness E. coli to make some products.

The leaner E. coli genome, the Wisconsin scientists note, yields bacteria that require no additional care and feeding in the laboratory, an important feature for any model organism or organism used to mass produce biological products.

According to Blattner, the changes made to the E. coli genome were accomplished with surgical precision. New tools, he says, made it possible to make wholesale changes to the genome in a rational way. “We know, by design, what’s been done to it. This is the first example of a genome that has precise, large-scale changes.”

In addition to Blattner and Plunkett, authors of the Science paper include Gyorgy Posfai, Tamas Feher, Kinga Umenhoffer and Vitaliy Kolisnychenko of the Institute of Biochemistry, Szeged, Hungary; Gunther M. Keil of the Friedrich-Loeffler Institutes, Germany; Shamik S. Sharma and Sarah W. Harcum of Clemson University; Buffy Stahl and Monika de Arruda of Scarab Genomics, Madison; and David Frisch and Valerie Burland of UW–Madison.

The Wisconsin study was funded in part by a grant from the National Institutes of Health.