FIG. 1.

Organization of the various -omes in a hierarchical fashion. The comprehensive DNA sequence in a cell is the genome, which consists of coding regions, shown as gray bars. The coding process begins with the expression of DNA to the respective RNA species, which consists of the transcriptome. The transcription process is dictated by several factors, including the interaction of proteins and metabolites with DNA and the presence/absence of the required cellular machinery. The mRNA species are translated to form proteins (proteome). As shown in the figure, there may not exist a one-to-one correspondence between proteins and genes. The various interactions between proteins, DNA, and metabolites, called the interactome, is the key determinant of any cellular process. The solid arrows represent the flow of biological information, while the dashed lines show possible interactions between various cellular components. Proteins are the functional entities that carry out the actual metabolic process by interconverting metabolites (metabolome). Any observed phenotype such as growth and product formation is the net result of all these cellular events. Therefore, capturing information at just one stage of the process (transcription, translation, etc.) will not reveal the cause and effect relationships between cellular components. It is necessary for the metabolic engineer to understand these relationships in order to accurately design and control biological systems.