Illustration by Christoph Niemann

The Paper: Genome Sequence of Yersinia pestis KIM

The Journal: Journal of Bacteriology, August 2002

The Author: Wen Deng, Valerie Burland, Frederick Blattner et al.

The Gist: Nothing holds down world population quite like jumping genes.

Before Translation: There are three regions where multiple inversions appear to have taken place. For each region we calculate the most parsimonious series of inversions that could account for the organizational differences between the two genomes. In most steps, it was possible to identify a sequence homology … that could have given rise to the proposed inversion.

In 1348, wrote Italian poet Giovanni Bocaccio, the bubonic plague struck Europe, for which “neither the advice of physicians nor the power of medicine appeared to have any value.” It “began with swellings in the groin and armpit, in both men and women, some of which were as big as apples and some of which were shaped like eggs . . . certain indications of coming death.” Worst of all, “whenever the disease mixed with healthy people, like a fire through dry grass or oil, it would rush upon the healthy.” A third of Europe’s population was struck down by the Black Death. The unassuming culprit: a safety-pin-shaped bacterium named Yersinia pestis.

Today, scientists around the world are keenly interested in better understanding the bug. Not only because it still breaks out periodically, but also because of the unpredictable manner in which it evolves. With this in mind, Frederick Blattner and his colleagues at the University of Wisconsin’s Genome Center decided to sequence the organism’s DNA. By learning more about how it evolved in the past, they believe, perhaps scientists can better judge how the deadly bacterium might behave in the future.

Y. pestis has three major strains. Blattner’s group focused on Mediaevalis, which is believed to be much the same as the variety that caused the Black Death.

Mediaevalis is similar to its two sister strains, with which it shares 95 percent of its genes. But Blattner was astonished to discover how many of Y. pestis’ genes come from other sources. Scientists can recognize these emigrant genes by examining how they are arranged and comparing them with genes from other bacteria. Genes that look odd-that is, rearranged or inverted-could have become so in several ways. In some cases, genes called transposable elements excise themselves from one position in a bacterium’s DNA and insert themselves somewhere else. These “jumping genes” can also hop all the way into another bacterium. In other cases, bacteriophages-viruses that infect bacteria-pick up genes from one species and deposit them into another.

All this swapping and moving about forces the organism to evolve. When bacteria reproduce, each new bacterium is virtually identical to its parent (though it’s not always an exact copy, because cells can make mistakes when they replicate their DNA). Genes mutate on their own, but without genes from other sources, bacterial evolution would slow to a crawl.

In fact, the Y. pestis genome reveals that, as recently as 1,500 years ago, the organism could have evolved from a less harmful bacterium that infects people’s innards. Over time, Y. pestis acquired genes from other bacteria and viruses that allowed it to live in an animal’s blood rather than its intestine. At that point, it was able to jump from animals into people via the bite of an infected flea.

Today, about a dozen Americans are infected with plague each year, mostly in the rural West and Southwest. Worldwide, plague infects some 3,000 people annually. Could there be another pandemic as devastating as the Black Death?

Well, first the good news. Blattner says that Y. pestis evolves relatively slowly. Unlike viruses that mutate constantly, bacteria are, in general, much more stable. Now the bad news: Bacteria do indeed pick up new genes, as we have seen. A strain of plague found in Madagascar in the late 1990s, for example, was resistant to five antibiotics. The bacillus apparently picked up the genes that gave it hardiness from another bacterial species. Yes, another huge, catastrophic outbreak is possible. But no one can predict when or where.