Office of Biological and Environmental Research Weekly Report

July 3, 2006

Mass Spectrometry Capabilities at the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) Enable Users to Identify a Potential Biomarker for Neurodegenerative Diseases. Users of the William R. Wiley Environmental Molecular Sciences Laboratory (EMSL) at the Pacific Northwest National Laboratory (PNNL) in Richland, Washington, in collaboration with scientists from the David Geffen School of Medicine at the University of California, Los Angeles (UCLA), are researching the precise connection between oxidative stress—cell damage caused during metabolism when the oxygen in the body assumes ever more chemically reactive forms—and neurodegenerative diseases such as Parkinson’s, Alzheimer’s, and Lou Gehrig’s. Through the use of EMSL’s state-of-the-art mass spectrometry capabilities that allow protein identification and separation with unprecedented precision, researchers were able to conduct this important study from the largest and most detailed proteomic analysis of a mammalian brain generated to date—nearly 8,000 different, detectable proteins in the brain of a mouse. Results of the study suggested that many neurodegenerative diseases leave the biomarker, nitrotyrosine, which could be used to predict the earliest stage of brain impairment and perhaps lead to detection of disease states before symptoms occur. The researchers, who are funded by the National Institutes of Health and PNNL, will continue their study using tissues with neurodegenerative diseases. A feature article in Science Daily briefly describes the research findings (http://www.sciencedaily.com/releases/2006/06/060628085601.htm). Details of the research are in Biochemistry [45(26):8009-8022], and details concerning the characterization of the mouse brain proteome are in the Journal of Proteome Research [5(2):361-369].

Media Interest: No

Contact: Paul Bayer, SC-23.4, (301) 903-5324

Structural Studies by LBNL Researcher Provides Insights into Regulation of Bacterial Gene Expression. Many microbes use two component signal transduction as a method of information processing to control their adaptive behaviors in response to changes in the environment. The ‘transmitter’ component receives the initial signal and modifies the ‘receiver’ domain of the second component, called a response regulator; the signal pathway is then turned on or off by the status of the response regulator. Microbial nitrogen assimilation and metabolism is regulated by this type of two-component signal relay, with the NtrC response regulator controlling nitrogen scavenging pathways and nitrogen fixation. Featured on the cover of the June 1, 2006, issue of Genes and Development, LBNL investigator Professor Eva Nogales and colleagues report x-ray and electron microscopy structural biology studies of NtrC that provide new insights into the mechanism of regulation of bacterial transcription and gene expression. When activated by phosphorylation of its receiver domain, NtrC assembles into a donut-like hexameric ring that encloses and binds to regulatory promoter DNA sequences. The resulting conformational change in the molecular machine that produces mRNA, s⁵⁴-RNA polymerase, thereby activates the entire polymerase machinery to initiate transcription of the required nitrogen assimilation genes, to produce a metabolic response to the original signal about the cells nutrient status. This new model suggests that conformational dynamics are crucial for understanding how a transcriptional activator interacts with RNA polymerase to regulate gene expression.

Reference: Sacha De Carlo, Baoyu Chen, Timothy R. Hoover, Elena Kondrashkina, Eva Nogales, and B. Tracy Nixon (2006) The Structural Basis for Regulated Assembly and Function of the Transcriptional Activator NtrC, Genes & Dev 20 (11):1485–1495.

Media Interest: No

Contact: Arthur Katz, SC-23.2, (301) 903-4932