It is my pleasure to announce the seminar by Dr. Donghyuk Kim, who is currently with the University of California, San Diego.

For detailed information, please see the following: 

SIC Seminar

Host:Prof. Hojung Nam / Language: English

Tuesday, May 20, 2014, 16:00-17:00, #203, SIC-B Bldg. 2nd Floor

Elucidating tranxss-scriptional regulation of nitrogen metabolism with systems approaches

Donghyuk Kim, Ph.D.

University of California, San Diego

Abstract

Deciding experimental conditions for TF activation has been frequently based on information from the literature. However, development of cellular network models enabled exploration in unexperimented solution spaces in virtually every imaginable conditions, which could be used to determine activation conditions of TFs of interest. This model-based experimental design was applied to two major TFs in nitrogen metabolism, NtrC and Nac. Genome-wide measurements with ChIP-exo and RNA-seq were performed under the predicted conditions, ammonia and three alternative nitrogen sources. From experimental measurements, 19 and 249 bindings for NtrC and Nac were identified in the regulatory regions, which resulted in 19 and 223 genes in their regulons. Functional analysis on two regulons showed that NtrC regulon is responsible for primary respon se to nitrogen limitation by regulating most of components in Ntr regulatory cascade, and up-regulating glutamine synthetase and transporters of nitrogen sources. Nac, however, regulates metabolic enzymes of carbon metabolism in glycolysis and TCA cycle to re-balance fluxes through carbon metabolism that were fluctuated from nitrogen source shift. Simulated flux states of E. coli metabolism under the experimented conditions further gave insights on how differently bacterial metabolic network could respond to different nitrogen sources. Thus, reconstruction of NtrC and Nac regulons extended the current knowledge of nitrogen regulation in bacteria, and model-based experimental design and interpretation is proven it potential in elucidation of tranxss-scription regulation.