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Researchers pop bacterial hood, uncover engine that drives cell division
Two proteins work in tandem to power the great divide


What drives bacterial cell division? The answer may be a pair of oscillating master regulator genes -- essentially an engine that powers the process -- discovered by a team of medical school microbiologists.

“This work gives new insight into a core question in microbiology: What makes the engine of cell division go forward?” said Harley McAdams, PhD, associate professor of developmental biology.

Before this work, microbiologists knew only one of the regulator proteins that control the cell cycle in Caulobacter crescentus bacteria. McAdams and Lucy Shapiro, PhD, professor of developmental biology, published a paper that appeared in Friday's issue of Science that identifies a companion protein.

The two proteins work together, forming a genetic circuit so their concentrations in the cell rise and fall rhythmically. The cyclical pattern of the regulatory protein concentrations turns hundreds of other genes on or off at specific times during the cell cycle.

The newly discovered gene, called GcrA, is essential for cell division and growth, Shapiro said, giving it potential as a unique antibiotic target. Although Caulobacter does not cause disease in humans, GcrA is present in related pathogenic bacteria. Examples include Rickettsia, which causes typhus, Brucella, which infects livestock, and Agrobacterium, which infect plants. Shapiro and McAdams founded the Palo Alto research firm Anacor Pharmaceuticals in 2002 with Penn State chemist Stephen Benkovic to discover these new classes of antibiotic molecules.

Prevalent in freshwater streams and lakes, Caulobacter species are adapted to live in wet environments with relatively low nutrients. Caulobacter has even been found living in aquifers contaminated by oil or gasoline, having adapted to consume oil as food. Environmental engineers are also interested in Caulobacter's potential for converting toxic heavy metals such as mercury and cadmium to chemical forms less harmful to people.

Microbiologists like to study Caulobacter because it divides in a relatively orderly way compared with a common intestinal bacterium such as E. coli, which continuously replicates its DNA. Caulobacter, on the other hand, always divides into two different daughter cell types, a stalked cell and a motile swarmer cell.

After division, the stalked cell immediately starts replicating its DNA in preparation for the next division. In contrast, the swarmer daughter delays DNA replication and uses its propeller-like flagellum to swim around searching for food. Eventually it discards its flagellum, grows a stalk in its place and starts DNA replication. Biologists use Caulobacter as a model to study the molecular processes by which a cell divides into two unequal daughter cells, a fundamental problem in developmental biology.

Scientists can easily take advantage of the Caulobacter cell types' different shapes to create synchronized populations of cells that progress together through their cell cycles. Using DNA microarrays, they can monitor the activity of each of Caulobacter's 3,800 genes in synchronized populations providing a powerful tool to study the regulatory network controlling the cell cycle.

The part of the control circuit scientists already knew about, the gene CtrA, partitions unequally between the swarmer and stalked cells. The CtrA protein is active in swarmer cells but gets destroyed in the half of the dividing cell that becomes the newborn stalked cell. In swarmer cells, CtrA binds to the bacterial chromosome where DNA replication begins, preventing the process from starting.

Shapiro and McAdams had been studying how CtrA's activity rises and falls during the cell cycle, publishing an analysis of all the genes that CtrA controls in a 2002 Science paper. Out of the roughly 3,800 genes in Caulobacter, about 550 rhythmically turn on and off, and CtrA controls 26 percent of that group. To account for other groups of genes whose activity rose and fell at different times, they knew there had to be other control genes. Their new research shows how the two proteins each control activity of the other protein's gene, causing GcrA to rise when CtrA is falling and vice versa.

McAdams describes the action of GcrA and CtrA as the spring and ratchet mechanism driving a clock. The GcrA-CtrA genetic circuit acts like a spring providing the force driving the cell cycle forward while the companion ratchet is provided by checkpoint mechanisms. These mechanisms monitor progress of events such as DNA replication and cell division, ensuring that the cell cycle proceeds at the correct pace.

An electrical engineering student from McAdams' lab, Peter Brende, performed the statistical analysis of which genes rise and fall, while lead author Julia Holtzendorff, PhD, and Patrick Viollier, PhD, postdoctoral scholars from Shapiro's lab, with research associate Ann Reisenauer did the microbiological work. Dean Hung, a previous grad student in Shapiro's lab, did the genetic screen that identified the GcrA and CtrA proteins as candidate cell cycle regulatory proteins.

Integrating biological research with computation, engineering (9/27/00)

Stanford scientists to probe inner workings of remarkable microbe (11/9/01)

Medical center researchers pick apart mystery behind asymmetric cell division (8/6/03)