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April 2007

Changes in Environmental Conditions Impact Cell Function

Scientists investigate enzyme that makes RNA

Results: Scientists at Pacific Northwest National Laboratory have found the first evidence that, when environmental conditions are right, cells "reprogram" to create faster and more efficient cellular machinery. Their study explained changes in the assembly of a large supramolecular protein complex involving RNA polymerase. Their results appeared in the March 20, 2007 issue of Biochemistry.

Why it matters: RNA polymerase (RNAP) is an enzyme responsible for making RNA from a DNA template (the transcription process) in all cells. In the Biochemistry paper, the results suggest that the coupling between RNAP and identified metabolic enzymes takes place at the membrane enabling faster enzyme growth.

Methods: To identify proteins that modulate transcription, PNNL scientists expressed a tagged alpha-subunit of RNA polymerase in the bacterium Shewanella oneidensis under controlled growth conditions. They isolated the protein complex using newly developed multiuse affinity probes. They used liquid chromatography and tandem mass spectroscopy to identify proteins in the complex. Complementary fluorescence correlation spectroscopy measurements were used to determine the average size of the RNA polymerase complex in cellular lysates. The PNNL scientists found that RNAP exists as a large supramolecular complex whose protein composition substantially changes in response to growth conditions. Enzymes that copurify with RNA polymerase include those associated with transfer RNA (tRNA) processing, nucleotide metabolism, and energy biosynthesis, which the researchers propose are necessary for optimal transcriptional rates.

RNAP metabolic enzymes
Cartoon depicting suggested organization of RNAP in complex with metabolic enzymes. Enlarged View

Next steps: Future measurements will focus on identifying structural changes in the core complex of RNAP that modulate its cellular localization and function. The goal is to clarify underlying mechanisms that could be useful in re-engineering organisms for bioremediation or bioenergy.

Acknowledgments: The research team members are Seema Verma, Yijia Xiong, Uljana Mayer, and Thomas Squier, PNNL. This work was supported by the Genomics: GTL Program of the U.S. Department of Energy Office of Biological and Environmental Research.

Reference: Verma S, Y Xiong, MU Mayer, and TC Squier. 2007 "Remodeling of bacterial RNA polymerase supramolecular complex in response to environmental conditions." Biochemistry 46(11):3023-3035: 10.1021/bi0621157.

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