Bacterial Biophysics

Bacteria are microorganisms that have evolved over 3.5 billion years and are responsible for a wide range of phenomena in the world around us, ranging from causing diseases to helping to digest food to shaping the surface and sub-surface of the Earth. To survive in a broad range of environmental conditions and changes to these conditions, they have developed an amazing range of fascinating and unique biomaterials and mechanisms.

We have developed new techniques and refined existing techniques for the study of different important properties of bacterial cells. Current Dutcher Lab projects on the physics of bacteria are:

Viscoelastic properties of bacterial cells & biofilms

We have developed a simple, AFM-based experiment to measure the time dependent mechanical response of individual bacterial cells to a constant force applied by an AFM tip. Measuring the time-dependent deformation of a material in response to a constant force is referred to as creep deformation. Our experiment on bacterial cells is the nanoscale equivalent of standard engineering measurements on bulk materials to evaluate the stability of the materials under load. We can interpret the results of the nanocreep experiment in terms of simple viscoelastic models. In addition to measuring the mechanical properties of different kinds of bacterial cells, we have also used this experiment to study the mechanical properties and cohesiveness of bacterial biofilms. We are now using this experiment to evaluate the action of different antimicrobial compounds on the mechanical integrity of the bacterial cells.

Fluorescence measurements of protein oscillations & patterns in bacterial cells

Self-assembly of proteins within bacterial cells creates many different structural elements for the cell that perform key functions such as locomotion (flagella and pili), reinforcing the mechanical integrity of the cells (cytoskeleton), and ensuring the proper occlusion of nucleoids and formation of the division septum during cell division. In the rod-shaped bacterium Escherichia coli, an important part of the cell division process is the oscillation of Min proteins along the major axis of the cell. This system has been the focus of much experimental and theoretical work during the past decade, since it can be studied using fluorescence microscopy by tagging the Min system with fluorescent proteins, and using coupled reaction-diffusion models that can reproduce many aspects of the system dynamics. By oscillating from pole to pole of the bacterial cell, a family of Min proteins (MinC, MinD and MinE) prevent the FtsZ protein division septum from forming anywhere except for the midpoint of the cell. This ensures that an equal amount of genetic material is transferred to the two daughter cells. We use a strain of E. coli in which the MinD proteins are tagged with green fluorescent protein (GFP), allowing fluorescence visualization of the MinD oscillation. We use high-resolution total internal reflection fluorescence (TIRF) microscopy and a custom, temperature controlled flow cell to observe the effect of exposure to antimicrobial agents on the MinD oscillation period and, more generally, to analyze spatio-temporal patterns of the MinD proteins within the cells. These measurements provide insight into the mechanisms of antimicrobial action.

Bacterial biomaterials

There are a large number of unique biomaterials in bacterial cells that self-assemble to perform key functions for the cell. One particularly striking example is the outer bag of the cell, which is called the peptidoglycan sacculus. This is one of Nature's largest and strongest biopolymers with fascinating structure and properties. It is needed to withstand the internal cytoplasmic turgor (osmotic) pressure while allowing the bacteria to grow and expand. The intricate nature of its structure and biosynthesis pathway make peptidoglycan a marvel of nanotechnology but also allow it to be the principal target of many antibiotics1 and one of the main microbial products recognized by the immune system. It is a covalent macromolecular structure of stiff glycan chains that are crosslinked by flexible peptide bridges. Although the peptidoglycan has been the subject of decades of investigation, its construction and higher-order structure are still debated. Two models have been proposed for the architecture of the peptidoglycan network (orientation of the glycan strands parallel or perpendicular to the cytoplasmic membrane), but it has not been possible to date to determine unambiguously which model is correct. We use atomic force microscopy (AFM) imaging and the collection of force-distance curves on purified intact Escherichia coli K12 sacculi, as well as computer modeling of the force-distance curves in terms of the polymer network, to learn about the architecture of the peptidoglycan network and the effect of amidases on the network.

Surface motility of bacteria

The most commonly known form of bacterial motion or motility is swimming in liquid, which is facilitated by the flagellum, a self-assembled protein filament that is anchored in the bacterial cell envelope. Bacteria have a strong tendency to adsorb to almost any surface, ultimately leading to the colonization of the surface as bacterial biofilms. Some bacteria have evolved mechanisms to move on surfaces, such as Type IV pili which leads to twitching motility. We are quantifying the twitching motility of Pseudomonas aeruginosa bacteria on agar films under different enviromental conditions.

cells on surface