Missing genes may help explain why plague bacteria are so deadly

What makes the germ that causes plague so fearsomely lethal, while a close relative only produces digestive disorders and is rarely fatal?

The answer may be in its genes – or rather, its lack of them.

By comparing the genome of the plague bacillus, Yersinia pestis, with the almost-identical DNA sequence of Yersinia pseudotuberculosis, an international team led by researchers at Lawrence Livermore National Laboratory (LLNL) has found that several hundred genes that apparently were inactivated as the plague bacterium evolved may be largely responsible for its virulence.

In a report published on September 9th in the online edition of the Proceedings of the National Academy of Sciences, the researchers said the “massive gene loss” and DNA rearrangements that occurred as Y. pestis evolved “provide a sobering example of how a highly virulent epidemic (pathogen) can suddenly emerge from a less virulent, closely related progenitor.”

“This work is seminal because it has enabled us for the first time to follow the precise molecular events that led to the emergence of this highly virulent bacterium,” said LLNL biologist Emilio Garcia, who headed the research team.

Knowledge of the genetic factors that contribute to the plague bacteria’s virulence could aid researchers in developing better ways to detect, prevent, and treat the deadly disease.

The LLNL research, conducted in conjunction with the Yersinia Research Unit of the Institut Pasteur in Paris and several other organizations, suggests that natural selection may have led to the inactivation of genes in Y. pestis that tended to suppress its lethality, possibly giving it an evolutionary leg up on its more benign cousins.

Evolutionary pressures may have also made the bacterium better adapted to colonize the flea, its preferred vector (means of transmission), and thus facilitate the flea-borne spread of the disease.

Perhaps the most infectious of all bacteria in humans, Y. pestis was responsible for the bubonic plague, or “Black Death,” that killed millions of people in Asia and Europe in the Middle Ages.

Most Y. pestis strains are treatable with antibiotics. If left untreated, however, bubonic plague is lethal in 70 percent of the cases, usually with a week; while pulmonary plague, acquired by breathing the bacteria, is almost always fatal within two to three days.

The last urban plague epidemic in the United States occurred in Los Angeles in 1924-25. An average of 10 to 15 cases in the United States, and between 1,000 and 3,000 cases worldwide, are reported every year. The disease has long been considered a prime candidate for bioterrorism because of its extreme virulence and its potential to be spread through the air as well as by infected fleas.

To get at the genetic basis for the deadly nature of Y. pestis, the Livermore-led researchers first sequenced the complete genome of Y. pseudotuberculosis, an animal and human pathogen that can cause fever and appendicitis-like pain if ingested in water or food. They then compared the Y. pseudotuberculosis genome with the DNA sequences of two Y. pestis strains previously sequenced by the Sanger Institute in Cambridge, England.

While the comparison revealed a number of genes in the plague bacterium that are not present in its relative, Garcia said the more important finding was the extent and apparent cause of gene inactivation in Y. pestis.

“As many as 13 percent of Y. pseudotuberculosis genes no longer function in Y. pestis,” he said. “We found that the number of insertion sequence (IS) elements (DNA sequences capable of interfering with gene expression) has dramatically expanded in Y. pestis, delineating the probable role of IS expansion in the elimination and modification of preexisting gene expression pathways.”

Sequencing of the Y. pseudotuberculosis genome was part of a “Bio-foundation Initiative” funded by the U.S. Department of Energy’s Chemical and Biological Nonproliferation Program, in collaboration with Elisabeth Carniel of the Institut Pasteur. Also participating in the project were researchers from the Life Sciences Division at Oak Ridge National Laboratory, Oak Ridge, Tenn.; the Department of Microbiology and Molecular Genetics at Michigan State University, East Lansing; Rocky Mountain Laboratories in Hamilton, Mont.; the Institut National de la Sante et de la Recherche Medicale at the Universite de Lille in France; and Genoscope and the Centre National de la Recherche Scientifique-Unite Mixte de Recherche in Evry Cedex, France.