Construction and analysis of metabolic pathways from the complete genome sequence of mycoplasma pnuemoniae and mannheimia succiniciproducens MBEL55E

Abstract

From the development of genetics and molecular biology, complete genome sequences of organisms including human beings have been obtained in a short time period. A large portion of the cellular characteristics is included in genome sequences. However, there are a few problems and limitations to analyze cellular functions in DNA sequence level. For the meaningful understanding of the essential capabilities of organisms, analysis of proteins and metabolites has to be performed thoroughly. In this study, the procedures for the construction of metabolic pathways in genomic scale were proposed. Metabolic pathways of two microorganisms were constructed from the complete genome sequence. Complete genome sequences were obtained from on-line sequence databases and a sequencing company. The genetic information inherent in the sequence was decoded. Functions were assigned to genes based on sequence homology and phylogenetic information. Metabolic pathways were constructed using top-down method and bottom-up method. Enzymatic reactions and metabolic pathways of the reference data are generally a result of selective accumulation of data obtained from numerous experiments and biochemical analysis. These data can be used as a guideline of generating metabolic pathways. Various graph theories can be used to generate metabolic pathways from the list of reactions. Both methods have advantages and disadvantages. From the analysis of metabolic capabilities, a lot of information were obtained. As an example, Mycoplasma pneumoniae causing atypical pnuemonia does not have most of pathways involved in biosynthesis and TCA cycle. In contrast, Mannheimia succiniciproducens MBEL55E isolated from the rumen of Korean cow shows a capability of producing inorganic acids and succinic acid.