Harvard University Office of Technology Development Collaborative Research Opportunity Finder

Current Research Interests

•  The mechanics of the flagellar rotary motors in E. coli; how the directions of rotation of flagellar filaments are controlled during responses to chemical stimuli (chemotaxis); and the different modes of flagellar propulsion.
• The chemotactic sensory network by which a cell detects, amplifies, integrates, and adapts to the signal produced by changes in the concentration of chemical stimuli in the bacterium’s environment.
• The ways in which groups of cells coordinate their motion when swimming in packs over moist surfaces, a process known as swarming which enables cells to invade tissues.

Tools and Assays

The Berg lab has developed a new way of doing darkfield microscopy in an upright microscope, in which laser light entering from below is totally internally reflected at the glass/air interface at the top of a flow cell.  Light scattered by gold nanobeads is collected by a 40x objective viewing the cell from above.  The system also uses phase contrast, so that cells can be located prior to laser illumination.  See Fig. 1 of  Yuan, J., Fahrner, K.A., and Berg, H.C., Switching of the bacterial flagellar motor near zero load, J. Mol. Biol. 390, 394-400 (2009). doi: 10.1016/j.jmb.2009.05.039.

The Berg lab developed assays based on fluorescence resonance energy transfer (FRET) and bioluminescence resonance energy transfer (BRET) that enabled us to monitor activity-dependent protein interactions in real time directly in living cells. For more information, see Sourjik, V., Vaknin, A., Shimizu, T.S. and Berg, H.C. In vivo measurement by FRET of pathway activity in bacterial chemotaxis. Meth. Enzymol. 423, 365-391 (2007). doi:10.1016/S0076-6879(07)23017-4

Research Expertise

The Berg lab has studied flagellar propulsion in bacteria extensively in the model organism Escherichia coli. Research focuses on three main areas: the physical and mechanical workings of the flagellar motor, the signaling pathway that controls the direction and type of motion in response to chemical gradients, and the social behavior of cells that swarm together over nutrient-rich surfaces.

The flagellar motor has been studied via a variety of innovative research techniques. In addition to tethering, in which the bacterium is attached to a surface by its flagellum and the motor spins the cell body instead of the flagellum, the Berg lab has also experimented with removing most or all of the flagellar filament from the motor and replacing it with nanosize gold spheres or other types of beads. Using this system, the motor’s rate of rotation and other mechanical properties can be measured by imaging light scattered from the beads. In addition, various components of the motor can be disabled by deleting or mutating genes coding for motor proteins. The mechanical properties of the motor can then be assessed both in the absence of functional copies of these proteins, and in "resurrection" studies in which good copies of the proteins are reintroduced into the cell. These techniques have allowed researchers in the Berg lab to determine the way mechanical force is generated by the motor, the factors affecting the direction of rotation (clockwise or counterclockwise), and the ways in which filaments change their polymorphic forms.

The Berg lab also studies the sensory network of the chemotactic signaling pathway in E. coli and the way this pathway interacts with the flagellar motor to direct the cell’s movement towards or away from chemical attractants or repellents. The pathway is well characterized, and a mathematical model has been developed (in collaboration with Yuhai Tu of IBM) that accurately describes its function. One of the techniques researchers at the Berg lab use in order to examine responses to different types of chemical signals is in vivo fluorescent labeling of various components of the chemotaxis machinery. The components can then be physically localized within this system, and based on their relative positioning, mechanistic details about how the signaling pathway works can be inferred. The flagellar filaments also can be labeled in vivo with fluorescent dyes, permitting their conformations, movements and interactions to be visualized and recorded. Other fluorescence techniques used by the Berg lab to map the chemotactic pathway are FRET (fluorescence resonance energy transfer) and BRET (bioluminescence resonance energy transfer). In FRET, the color-coded fluorescent proteins CFP and YFP (cyan and yellow, respectively) are genetically fused to proteins in the signal transduction pathway, and in vivo interactions between the pathway members affect the strength of the different fluorescent signals. FRET allows the researchers to characterize the amplification and integration of the chemotactic signal, as well as adaptation to the signal. In BRET, the enzyme luciferase is incorporated in the cells being studied and acts as the source of excitation for the fluorescent labels, which eliminates the need for an external light source, and reduces background noise and other problems associated with external excitation. The Berg lab uses BRET to measure the kinase response in the chemotactic pathway upon various perturbations of the system, such as jamming the flagellar motors by cross-linking different flagellar filaments.

The Berg lab also studies other types of motility structures in other bacterial species, such as the tiny cilia-like hairs in the cyanobacterium Synechococcus, pili in Pseudomonas and the structures responsible for gliding in Mycoplasma, which are being characterized.