Bacteria and Bacterial Viruses Share Needlelike Structure for Infection

A sleek racing bike flies over pavement but would crumple on an off-road trail. A mountain bike clambers over roots and ruts but cannot compare to the lounge chair comfort of a European touring bike. Yet despite their differences, it is evident that these cycles originated from the same early two-wheeler.

The same principle can be applied in biology. Over time and generations, genetic codes for proteins and the molecular machines they form begin to diverge. But the basic structures of those early machines remain. Eventually, the only way to tell whether two protein structures found in different organisms have the same evolutionary origin is to look at their shapes.

The lab of John Mekalanos is doing exactly that. The team recently found that a syringelike structure that lends virulence to many infectious bacteria, including cholera, resembles a tail structure found in bacterial viruses called bacteriophages. The discovery suggests that these molecular machines have common evolutionary origins, according to a paper published online Feb. 27 in Proceedings of the National Academy of Sciences.

The Mekalanos team also found that in the case of cholera bacteria, the syringe has a poison tip that can kill the human cells that eat them. This work is described in the March Cell Host and Microbe. Together, these two studies might ultimately lead to the design of novel drugs or vaccines that jam up the workings of the machine and shut down virulence.

When looking at evolutionary origins, scientists typically look to genetics for clues about common ancestry. But the genetic codes for the proteins that form these syringelike machines have very little in common. The tube of the syringe, formed by a bacterial protein called Hcp1, has only eight percent similarity to its homolog in the phage. The needle, formed by a bacterial protein called VgrG, only 13 percent.

“They are more diverged than going from a human to a worm,” said biochemist Alan Davidson of the University of Toronto, who published a companion paper in PNAS. “Way more diverged.”

Yet genes are not the last word on evolutionary origins. Rather, said Mekalanos, “The structure says it all.” Like Treks and Bianchis, for example, two molecular machines that have the same form and function but differing underlying sequences likely evolved from a common ancestor.

The work of discovering that the syringelike structures in the bacteria and the phage are very similar began in 2006. Mekalanos, the Adele Lehman professor of microbiology and molecular genetics at HMS, and others recognized the novel structure for bacterial secretion and dubbed it the type VI secretion system. Mekalanos then analyzed a crystallized form of the Hcp1 protein and determined that it forms a tube.

To get a better sense of the shape of the whole system, in 2007, the Mekalanos group turned to bioinformatics tools. These methods predict the atomic structure of a protein using computer software. ­Mekalanos’s team fed amino acid sequences into online computer algorithms that, in turn, accessed a database of known protein structures to predict how these sequences will likely fold as protein molecules.

The results suggested that the protein VgrG, which is located near Hcp1 in the gene cluster for the secretion system, would form a three-dimensional shape very similar to the cell-puncturing tail needle of a bacteriophage, an organism that itself resembles a lunar lander with a stinger at its base.

The prediction grabbed the attention of Petr Leiman, then at Purdue University and now head of the structural biology lab at the École Polytechnique Fédérale de Lausanne (Switzerland). Leiman teamed with Marek Basler, a postdoctoral fellow in the Mekalanos lab, to analyze a crystallized form of VgrG from Escherichia coli. They found the crystal in a public database populated by collaborators at Albert Einstein College of Medicine. Leiman analyzed the crystal to determine if the in silico predictions would match reality. “Once we saw the structure—wow. It’s exactly the same thing,” said Leiman, a co–first author with Basler on Mekalanos’s recent PNAS paper.

“The predictive powers of the algorithms that people are writing are getting so that you can really do a lot of biology before you’ve even done a wet bench lab experiment,” said Mekalanos. In addition to these two proteins that likely form the tube and needle of the secretion syringe, the bioinformatics suggest that a third, smaller bacterial protein is also a phage tail relative.

As the evidence mounts that these two molecular machines evolved from a common origin, Mekalanos expects that evolutionary biologists will investigate the classic chicken-or-egg quandary: Which syringe came first, that of the bacterium or the phage?

Perhaps more important, however, is the medical relevance of the insights this basic science provides. The type VI secretion system is present in 25 percent of Gram-negative bacteria. It has also been linked to virulence in Salmonella, E. coli, Pseudomonas, and the bacteria that cause tularemia and, according to the Mekalanos group, cholera.

Mekalanos and postdoctoral candidate Amy Ma found that in Vibrio cholerae, the needle of the syringe carries a kind of poison tip. A small section of the VgrG needle protein, when thrust into a cell’s cytoplasm, interrupts the formation of the actin cytoskeleton inside the cell and disables its ability to fight the bacterial assault. The group has identified the poisonous portion of the protein, but has not yet identified the mechanism behind its toxicity.

While the syringe may make bacteria dangerous, it also makes them vulnerable. Human cells do not have these syringelike structures, said Davidson, so drugs that targeted them would be less likely to harm human cells. The proteins that form these nanomachines also seem to be exposed on the cell surface, so they may act as vaccine antigens susceptible to immune system antibodies, said Mekalanos.

Moreover, because the tails of bacteriophages have been studied extensively, that knowledge can now be applied to their distant bacterial cousin, the type VI secretion machine. This transfer of know-how could accelerate the discovery of ways to prevent the bacterial machine from forming and functioning.

Students may contact John Mekalanos at john_mekalanos@hms.harvard.edu for more information.

Conflict Disclosure: The authors declare no conflicts of interest.

Funding Sources: The National Institutes of Health, the National Science Foundation, the Department of Energy, the European Molecular Biology Organization, and SGX Pharmaceuticals, Inc.