Just as children smelling fresh baked cookies find their way to the kitchen, ulcer-causing bacteria follow their "noses" to the stomach lining, causing pain and inflammation. Now, an extensive analysis of microbial genomes suggests that more than half of bacteria home in on chemical cues to reach a target, an ability called chemotaxis. That's more than researchers expected, says Igor Zhulin, a computational biologist at Oak Ridge National Laboratory in Tennessee.
The findings should help scientists better sort out what makes some microbes dangerous to human health. "We need to understand the signaling machinery that underlies these behaviors if we hope to manipulate or block them," says John Parkinson, a molecular biologist at the University of Utah in Salt Lake City.
Microbiologists have studied chemotaxis primarily by focusing on a few bacterial species, such as the common gut microbe, Escherichia coli, which is attracted to amino acids and other foods and deterred by toxins. To get a broader perspective, Zhulin and postdoctoral fellow Kristin Wuichet spent the past 7 years analyzing 450 genomes from bacteria and another group of microbes, the archaea.
A surprisingly high number—245—had chemotaxis genes, the duo reports today in Science Signaling. Each chemotactic species shares a core set of proteins, including a receptor for sensing the environment and a response regulator that controls the motor of the flagellum, a tail-like appendage that propels the bacterium in one direction or another. But a variety of auxiliary proteins are involved as well. All together, Zhulin and Wuichet identified 19 types of chemotaxis systems based on the combinations of proteins found, the locations of the genes for these proteins, and other parameters.
The researchers also found clues to the evolution of chemotaxis. It arose in bacteria after they split off from the common ancestor to eukaryotes, organisms (ranging from amoeba to people) whose cells have nuclei, as Zhulin and Wuichet found no chemotaxis proteins in those genomes. And it appears that archaea acquired chemotactic abilities by borrowing those genes from bacteria.
In addition, the analysis provided some hints about how chemotaxis evolved from a simple signaling network that responds slowly to environmental cues—primarily by turning on genes—to a multiprotein system that can quickly alter a cell's course. A few bacteria in the study appear to be intermediates in this transition as they lack core chemotaxis genes but have a few quick-response proteins that are typically part of chemotaxis pathways. The researchers don't know what these proteins do, but they found them in a variety of microbes, including plant and human pathogens, as well as in cellulose-degrading and bioremediation organisms. "It will be exciting to see what the functions of some of these systems are," says microbiologist Caroline Harwood of the University of Washington, Seattle.
"This is an impressive and insightful study," says Victor Sourjik, a molecular microbiologist at the University of Heidelberg in Germany. "It will raise much interest not only in a broad community of bacterial signaling research but also of everyone interested in the evolution of protein networks."