In Research In Brief: The What, Why, and How, we explore new research from the UW–Madison Department of Biochemistry to learn more about the world around us — and inside us. In this edition: Cellular function requires proteins and other molecules to be organized and distributed to the right place at the right time. Researchers can engineer cells to express new genes and produce specific proteins, giving the cells new parts to work with. But it has been difficult to provide cells with instructions on how to organize and use the parts to induce a desired function. New tools now offer scientists an innovative way around this problem by harnessing patterns of movement produced by bacterial proteins.
WHAT you need to know
Inside our cells — all cells — proteins and other molecules undergo organization and reorganization to carry out cellular function. Like a fleet of commuter trains moving along at scheduled intervals along their different routes, proteins within a cell are organized in time and space to carry out complex but predictable functions. Everything cells do depends on how molecules are organized within the cell.
Bacteria such as E. coli, for example, identify the cellular midpoint in anticipation of cell division thanks to the interplay of a set of molecules known as Min proteins. Two of these proteins — MinD and MinE, known collectively as MinDE — interact with each other along the cell membrane. Their movement produces a wave-like pattern which helps to distribute other proteins, thereby inhibiting cellular division anywhere except the midpoint. The ratio of MinD to MinE proteins impacts the size and oscillations of the waves, allowing for nearly endless variations of patterns of movement. As proteins and other molecules interact with MinDE proteins, they are organized and distributed inside of the cell so that they are in the right place at the right time.
On the other hand, when molecules fail to organize properly within the cell, it can have serious consequences, including cells dividing unevenly and improper communication within and among cells, both of which are associated with developmental disorders and diseases such as cancer.
For decades, researchers have been engineering cells to express new genes and produce specific proteins. But, for scientists looking to engineer cells with new or altered function, inducing molecules to organize themselves in time and space has been an ongoing challenge. In short, we know how to give cells some new parts, but it’s much harder to provide the instructions on how to organize and use them.
WHY it matters
Programming a cell to distribute and use a protein in a prescribed manner is a complex problem that’s challenging to solve. One reason it is so hard is because the mechanisms by which molecules organize and interact with each other have been fine-tuned over millennia of evolution. Manipulating a cell’s ability to distribute a single molecule of interest might require de-programming modes of interaction that are innate to a cell.
New tools developed by researchers in the Department of Biochemistry at UW–Madison offer scientists an innovative way around this problem for mammalian cells. By harnessing the waves and oscillations derived from interactions between MinDE proteins, mammalian cells can be induced to organize proteins in prescribed ways. Because MinDE proteins are found only in bacteria, they do not interfere with mammalian cellular functions, allowing researchers to control the movement and organization of specific proteins while leaving others alone.
HOW our scientists made progress
Using different ratios of MinDE proteins, researchers in the Coyle Lab have developed tools for researchers to design wave and oscillatory patters of movements in mammalian cells. This innovative new tool, which appears as a cover story in the journal Cell, has multiple potential uses for scientists interested in engineering specific cellular activity or studying cellular activity in situ.
By engineering interactions between the MinDE proteins and proteins of interest, scientists can create highly specified patterns to organize molecules within a cell to induce cellular behaviors and functions. Because patterns of movement are themselves controlled by ratios of MinD and MinE, the tool allows researchers to tweak and alter the patterns in response to stimuli, essentially programming molecules to move around a cell to specific locations over time. This could be used to control many cellular functions, such as localizing signaling receptors in specific regions or redirecting where cells move.
The variation in movement patterns resulting from differing ratios of MinD and MinE can also be used to study cellular activity. As each ratio emits a unique oscillatory pattern, the proteins can be inserted into a group of cells to give each cell its own pattern of movement — an individual beacon for each cell. These unique patterns can be used to study signaling pathways within individual cells by engineering an interaction between MinDE proteins and a signaling molecule. The signals can then be analyzed to reveal information about the shape, location, and signaling activity of each individual cell. The researchers liken the tool to an FM radio dial: they can tune to the unique data that each cell emits in a multicellular system.
The MinDE tool opens the door for scientists to explore and engineer cellular function in new ways. The Coyle Lab plans to continue exploring its applications, including studying the dynamics of signaling pathways in tumors.
Written by Renata Solan.
The image at the top of the article is an artistic rendering of a spatiotemporal protein pattern in a human cell based on the programmable MinDE system described in this article. The image was generated algorithmically as a representation of the tool’s capability. The image appears in full on the cover of the January 18, 2024 issue of Cell.
This edition of Research in Brief: The What, Why, and How is based on the following publication:
Rajasekaran, Chang, Weix, Galateo, and Coyle. A programmable reaction-diffusion system for spatiotemporal cell signaling circuit design, Cell, 2024 Jan 18, 1-15(187).
This research was funded in part by David and Lucille Packard Fellowship for Science and Engineering (2020-71385), NIH New Innovator Award (1DP2GM154329-01), and National Institute of General Medical Sciences NIH Chemistry-Biology Interface Training Program (T32GM008505). A pending patent has been filed through WARF.