Using advanced imaging technology and computational simulations, scientists have, for the first time, glimpsed the action of a cellular machine at work within living cells. The work puts forth a new concept of cellular machines as dynamic protein complexes that are continually building and rebuilding themselves within the cell, rather than the stable structures scientists have traditionally thought them to be. The study was published in the Nov. 22, 2002, issue of Science.
Researchers from the National Cancer Institute (NCI), in collaboration with scientists from three other institutions, investigated a cellular machine known as RNA polymerase I, an enzyme that decodes a specific group of genes in the cell. The polymerase is composed of more than ten protein subunits. By analyzing the time it took the many subunits to arrive at a gene and assemble themselves into a functioning protein complex, researchers discovered that RNA polymerase I is constantly assembling and disassembling itself from a large pool of subunits within the cell.
"These findings challenge the current model of cellular machines," said Tom Misteli, Ph.D., of NCI's Cell Biology of Gene Expression Group, the lead investigator on the study. "No longer can we think of cellular machines as stable, static, and precisely-assembled complexes, akin to man-made machines."
Instead, researchers found that polymerase subunits came together and formed a complex each time a gene was read, on average every 1.4 seconds. Computer simulations suggest that each formation resulted from random, chaotic interactions between protein subunits that eventually came together in the proper configuration. Once a complete polymerase finished reading a gene, the subunits quickly disassembled and scattered throughout the cell. Researchers speculate that the dynamic nature of cellular machines allows components to assemble as needed in response to changing environmental conditions.
"The new method we used here allows us to study a whole new dimension in cellular processes - time," said Miroslav Dundr, Ph.D., also of NCI's Cell Biology of Gene Expression Group. Researchers anticipate this approach will lead to unprecedented insight into many other biological processes in the future.
To visualize the polymerase at work within living cells, researchers marked many of the smaller subunits with a small jellyfish protein that emits fluorescent light that can be detected under a microscope. To track the assembly and disassembly of these subunits, the researchers applied a very short, intense laser pulse to the cell. While most of the tagged subunits throughout the cell continued to emit fluorescent light, the laser bleached the fluorescence out of a defined area within the cell. As tagged polymerase subunits began to move into the bleached area, their movement could then be tracked as an increase in fluorescence.
Using the data they had collected about the time it took the fluorescently tagged polymerase subunits to form a complete RNA polymerase I complex and then redisperse, researchers applied computer simulations to test various models of how the polymerase assembles and reads genes. Combining observations made in living cells with computational methods enabled researchers to measure fundamental biophysical properties in living cells. The approach is considered a first step toward complete computer models of living cells and organisms.
Dundr M, Hoffman-Rohrer U, Hu Q, Grummt I, Rothblum LI, Phair RD, Misteli T. A kinetic framework for a mammalian RNA polymerase in vivo. Science 2002; 298:1623-1626.
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