&
Bacteria, rubber duckies,
PopZ
some rubber ducks 1. Get (a LOT of rubber ducks) 2. Toss them in a pool 3. Let them bob around in an organizer named PopZ 4. Toss and you’ll see how order emerges
from chaos, and how living things are organized at the microscopic scale. Grant Bowman Assistant Professor, Department of Molecular Biology acteria are the simplest life forms on planet Earth. They have 1/600th as much DNA as humans, they produce a much smaller variety of proteins and other biomolecules, and their body size is smaller by about a million fold. Being simple provides a great advantage: duplication is fast and easy. One bacterial cell and its progeny can repeatedly divide to produce ten billion cells in less than a day, whereas the human population has required tens of thousands of years to approach that number of individuals. And yet even bacteria can’t be TOO simple. Their survival and proliferation depends upon some complex features they share with their human counterparts (Figure 1). One is anatomical organization. Just as humans have dedicated anatomical features for actions like movement and reproduction, bacterial cells have comparable structures that perform the same types of functions.
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Multicellularity is another feature shared with more complex organisms. For many bacteria, cell division produces two very different daughter cells that play distinct roles in that species’ strategy for survival and proliferation. Even the simplest cells on the planet produce specialized parts placed in discrete locations. My laboratory research asks how such anatomical features are created.
Much Bobbing and Bumping To understand the challenges a bacterial cell faces in constructing discrete structures: Imagine it as a swimming pool that contains about 1.5 million rubber duckies, all floating so closely together they continually bump into each other (as in Figure 2). Each of the ducks represents an individual protein, and their number and density approximates the typical conditions in a bacterial cell. Now imagine there are about 2,500 different kinds of duckies. This represents the number of different types of proteins in a cell. The pool is somewhat wavy, and the duckies are making frequent contact and exchanging positions. This represents the random movement and collisions of particles inside the cell. Without some kind of system for rubber ducky organization, the pool would be a chaotic mixture. Now imagine programming the duckies with rules that determine whether one type of ducky will stick to another. For example, duckies with eye patches will stick to duckies with red hats, and they will remain together for a few seconds before parting and going their separate ways. Other duckies might prefer to stick to the sides of the pool. These rules approximate interactions that occur between proteins in real cells. Anatomical features like those discussed in Figure 1 would include hundreds or thousands of proteins of many different types. The
Figure 1. (Top Panel) The ends of rod-shaped Caulobacter crescentus cells exhibit distinct anatomical features. One end has a flagellum that rotates like a propeller to move the cell through water. The other end has a stalk, which includes an adhesive material that will anchor the cell to a fixed surface. This cell will soon divide through the middle to produce two daughter cells. The behavior of the daughter cells is determined by their external anatomies as well as internal regulatory factors (not shown), which activate distinct patterns of gene expression. (Bottom Panel) Two different cell types are produced in this time-lapse sequence of cell division in Agrobacterium tumefaciens. Here, an anatomical feature is labeled by a red fluorescent indicator, which marks the location of an organizing protein called PopZ.
Figure 2.
molecular biology
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challenge is to devise a system of rules that will produce these multicomponent structures.
PopZ, the Great Organizer Our research is revealing that anatomical features in Caulobacter crescentus, Agrobacterium tumefaciens, and other bacteria are produced with the aid of an organizing protein called PopZ. This protein has a fascinating combination of properties that give it organizing capabilities: it interacts with itself to form a loosely connected network, and it also interacts with certain other “guest” proteins to bring them into the network. Through biochemical experiments and microscopic observation, we are learning the organizing effect of PopZ depends upon the interactions among PopZ molecules being weak. Returning to the ducky analogy, weak interactions among PopZ duckies make temporary gaps that allow other types of duckies to enter the crowd. Those that have no particular affinity for PopZ duckies pass through the crowd relatively quickly, while those that can stick to PopZ duckies pass much more slowly (Figure 3). Even if individual interactions between the “guest” duckies and PopZ duckies are short-lived, the large number of PopZ duckies in the crowd provides a large number of temporary interactions. This has the effect of concentrating sticky “guest” duckies within the PopZ crowd. For contrast, imagine a pool in which interactions between PopZ duckies are strong and long lasting. This would create a tightly packed PopZ crowd and prevent the incorporation of other types of duckies. Alternatively, if interactions between PopZ and other types of duckies were very strong, this would reduce the amount of time for interactions 28
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between PopZ duckies and disrupt the formation of the PopZ crowd.
Strong Organization, Weak Interaction Thus, our model has a surprising implication: that organization occurs most easily when interactions between duckies are weak, not strong. The success of weakness over strength seems counterintuitive until one considers the model, especially considering the chaotic movements of the duckies in the pool. As this is my laboratory’s working model of cell organization, a number of major questions must still be addressed. A meaningful way to advance beyond the rubber ducky model is to understand more about the molecular structure of PopZ, both when interacting with itself and when interacting with other proteins.
Our data suggests PopZ interacts with itself and other proteins through the same interface, and that structural disorder provides the flexibility needed for interactions with multiple partners. An important remaining question is whether increasing structural flexibility has corresponding effects on reducing binding strength and longevity.
Cancer Connections We know structurally disordered binding proteins exist in humans, and it is interesting to note these types of proteins are mutated in most human cancers, and that cancer cells are quite disorganized. While it is unlikely that rubber duckies kissing has ever been used to discuss such serious subject matter, there is a chance this could happen. To contact: Bowman can be reached at (307) 766-2147 or at grant. bowman@uwyo.edu.
PopZ
Figure 3. Weak interactions between PopZ duckies allow temporary gaps that let other types of duckies enter the crowd; duckies with little affinity for PopZ pass through quickly while those that can stick to PopZ pass more slowly.