Overview

Metabolomics is the scientific study of chemical processes involving metabolites. Specifically, metabolomics is the "systematic study of the unique chemical fingerprints that specific cellular processes leave behind", the study of their small-molecule metabolite profiles. The metabolome represents the collection of all metabolites in a biological cell, tissue, organ or organism, which are the end products of cellular processes. (Jordan, Nordenstam et al. 2009) Thus, while mRNA gene expression data and proteomic analyses do not tell the whole story of what might be happening in a cell, metabolic profiling can give an instantaneous snapshot of the physiology of that cell.

In our project, we investigate the origin of formaldehyde metabolism using computer simulation of biochemical networks in tobacco. By utilizing the genetic engineering, threepathways of formaldehyde metabolism in tobacco were taken into account and three models of regulatory mechanism were established for these pathways. There are photosynthetic HCHO assimilation pathway (gene PHS and PHI), folate-independent pathway (gene FALDH and FDH) and the pathway of formaldehydeinto the stoma (H+-ATPase).Below, let us describeall the procedures one by one.

Mathematical Principles

Almost all chemical reactions obey the law of constant proportion:
(1)
where vi(l) is the constant proportion of reaction componentAiin the l-threaction. The components with vi(l)>0 are the resultants. On the contrary, they are reagents. Let ?l represents the extent of l-th reaction which means the relevant components increase vi(l) mol when ?l=1. Thus, the equation between ?l and vi(l) can be given by:
(2)
ni(l) is the quantity ofi-th component. Then reaction rateJl can be defined by:
(3)
V is the reaction volume. Assume thatthe quantity of component Ai changes merely due to the chemical reaction and the exchange of outside and inside. Base on the assumption, the law of conservation of matter can be established for ni of every componentAi:
(4)
Xi is the concentration of i-th component. or stands for the exchange of outside and inside.Due to the changes of reaction system volume is very slight, the relative growth rate shall be thought equal to zero. Let for the concentration of Ai in environment, the principle of dynamics of can be expressed by:
(5)
Finally, we obtain dynamic equation group of the reaction system:
(6)

Photosynthetic HCHO assimilation pathway

The metabolism of photosynthetic HCHO assimilation was shown on Fig.1. Since the substrate (Ru5P) and product (F6P) ofthe sequential reactions catalyzed by HPS and PHI are intermediates of the Calvin cycle in plants, photosynthesis could provide sufficient substrates for the reactions catalyzed by HPS and PHI if the two enzymes were expressed in plant(Song, Orita et al. 2010).It has been proved that over-expressing the HPS/PHI fusion protein can enhance the ability of the plants to absorb and assimilate exogenous HCHO(Chen, Yurimoto et al. 2010).In this case, we utilize the mathematical principles described above to analyze the metabolism.

Fig.1 Schematic diagram of photosynthetic HCHO assimilation pathway. Ru5P, D-ribulose 5-phosphate; Hu6P, D-arabino-3-hexulose 6-phosphate; F6P, fructose 6-phosphate; Xu5P, xylulose 5-phosphate; RuBP, ribulose 1,5-bisphosphate; 3-PGA, glycerate 3-phosphate; FBP, fructose-1,6-bisphosphatase;

Simplify the system (Fig.2), consist of the input of HCHO and CO2, the recycle of Ru5P and the output of F6P:

Fig.2 A simplified version of photosynthetic HCHO assimilation pathway