Report of Taikichiro Mori Memorial Research Fund 2008

 

 

 

Introduction

 

My research is based on experimental and computation biology. The Mori grant has given me a good opportunity to improvise my research by equipping the lab with necessary equipments. I have purchased a Mass Flow Controller, which is an essential piece of equipment required for my research. Apart of that, I have upgraded my computers and storage devices to store and process huge amount of data files. My research theme, progress and final goals are given below.

 

Research Project Abstract

Yeast cells respond differently in nitrogen rich and nitrogen deficient environment. When Saccharomyces cerevisiae is grown on nitrogen sources that can readily be utilised, the nitrogen catabolite repression (NCR) genes that code for the proteins involved in the catabolism of poor nitrogen sources are not expressed, whereas during growth on poor nitrogen sources the NCR genes will be activated [1]. This system also acts in concert with general amino acid biosynthesis to form a highly integrated sub-system in yeast that is widely conserved in eukaryotes. Continuously grown cultures of yeast cells show robust oscillations in respiration [2]. The population synchrony is the result of inter-cellular metabolite communication, and is also correlated to the NAD(P)H and ATP oscillations (redox and energy metabolism). Analysis of global gene expression level has shown specific patterns in expression during the oscillation [3]. This further suggests that metabolism related inter-cellular communication influences gene expression. Amino acid biosyntheses are tightly regulated and the system is hyper-sensitive to nM concentrations of Rapamycin (derepressor of NCR genes) during the oscillation. This signifies that both the function of general nitrogen control (regulated by Gcn4p) and NCR regulation systems are linked. However, the temporal regulation involved in the metabolic feedback of metabolites on gene regulation in this system is remain to be elucidated. Therefore, we are studying the functional interactions of nitrogen regulatory control utilising continuously grown synchronous yeast cultures. To clarify the network of transcriptional control of nitrogen, we are constructing an expanded model from various experimental observations, such as stress and perturbation conditions. This model will be experimentally validated using precise culture conditions and perturbations coupled to state-of-the-art experimental procedures. This validated model will further be used to get better understanding of the emergence of coherent behaviour in combined metabolic and transcriptional networks, i.e., self-organisation. This study will eventually help us to obtain a better understanding of the role of metabolic, proteomic controls in transcriptional mechanism.

 

Full Report (PDF format)

 

References

1. T. G. Cooper. Transmitting the signal of excess nitrogen in Saccharomyces cerevisiae from the Tor proteins to the GATA factors: connecting the dots. FEMS Microbiol Rev, 26(3):223-238, Aug 2002.

2. A. D. Satroutdinov, H. Kuriyama, and H. Kobayashi. Oscillatory metabolism of Saccharomyces cerevisiae in continuous culture. FEMS Microbiol Lett, 77(1-3):261-267, Nov 1992.

3. D. B. Murray, M. Beckmann, and H. Kitano. Regulation of yeast oscillatory dynamics. PNAS,104(7):2241-2246, Feb 2007.