Vertical systems biology: from DNA to flux and back

Systems biology has witnessed exponential growth since its inception early this century, when genomics combined with mathematical biology. Much of systems biology has remained tightly linked with a single genomics methodology and with the observation of patterns at a single level of cell function, that is, the genome, the transcriptome, the proteome or the metabolome. In this chapter we shall describe a novel methodology that is orthogonal to these approaches. It analyses practically how functions in living organisms are being regulated at the same time at all these various levels of the cellular regulation hierarchy. The principles behind the methodology are reviewed and extended. This underpins complete time-dependent hierarchical regulation analysis from flux through metabolites, enzyme, mRNA, gene and back. An important part of the methodology, discriminating between metabolic and gene-expression regulation, is then illustrated in detail experimentally. It is shown how yeast regulates its capacity to produce ethanol when it is confronted with a lack of nitrogen source. It regulates the flux through alcohol dehydrogenase first by reducing the gene expression of the corresponding enzyme. As time proceeds, the close to 100% gene-expression regulation, is replaced with virtually entirely metabolic regulation. How a gene-expression regulatory coefficient may come about is then illustrated in an in silico model for yeast glycolysis. The expression level of the glucose transporter is supposed to be regulated at the level of protein synthesis by the pyruvate concentration. This leads to regulation of glucose uptake partly through gene-expression, partly through direct metabolic interactions.