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, three pathways 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 HPS 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.

The modeling

Photosynthetic HCHO assimilation pathway (HPS/PHI)
Folate-independent pathway (FALDH/FDH)
Modeling of stoma (AtAHA2)

Reference

Chen, L. M., H. Yurimoto, K. Z. Li, I. Orita, M. Akita, N. Kato, Y. Sakai and K. Izui (2010). "Assimilation of formaldehyde in transgenic plants due to the introduction of the bacterial ribulose monophosphate pathway genes." Biosci Biotechnol Biochem 74(3): 627-635.