Cryo-Electron Microscopy Study Allows Researchers to Visualize Structural Changes in E. coli Enzyme Synthesizing Ribosomal RNA That Shift It Between Turbo- and Slow-Modes Depending on Bacteria’s Growth Rate

The enzyme that makes RNA from a DNA template is altered to slow the production of ribosomal RNA (rRNA), the most abundant type of RNA within cells, when resources are scarce and the bacteria Escherichia coli needs to slow its growth. Researchers used cryo-electron microscopy (cryo-EM) to capture the structures of the RNA polymerase (see image left and below) while in complex with DNA and showed how its activity is changed in response to poor-growth conditions. A paper describing this research, led by Penn State scientists, was published online on January 22, 2020 in the journal Nature Communications. The open-access article is titled “Structural Basis of Ribosomal RNA Transcription Regulation.” "RNA polymerase is an enzyme that produces a variety of RNAs using information encoded in DNA," said Katsuhiko Murakami, Professor of Biochemistry and Molecular Biology at Penn State and leader of the research team. "This is one of the key steps in the central dogma of molecular biology: transferring genetic information from DNA to RNA, which in turn often codes for protein. It's required for life and the process is basically shared from bacteria to humans. We are interested in understanding how the structure of RNA polymerase is changed for modulating its activity and function, but it's been difficult to capture using traditional methods like X-ray crystallography, which requires crystallizing a sample to determine its structure." RNA polymerase functions by binding to specific DNA sequences called "promoters" found near the beginning of genes that are going to be made into RNA. To understand the structure and function of the polymerase during this interaction, researchers need to capture the polymerase while it is bound to the promoter DNA, but the interaction can be very unstable at some promoters.
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