Bioinformatic analysis and application of genomic and metabolic information of various organisms

Abstract

Development of integrated system and novel approach for the effective analysis of large-scale genomic and metabolic information, i.e. complete genome sequences of microorganism, was carried out in Part I. In Chapter 2, the integrated metabolic database system was developed for the query and comparison of the heterogeneous metabolic information obtained from the public databases. Users can obtain the relevant information on the enzymes, biochemical reactions and metabolic reactions from the system. In Chapter 3, a novel analytical approach using the concept of KEGG orthology was introduced to identify the genome-scale characteristics by applying two-step clustering methods. The clustering results were consistent with various phenotypic characteristics of the analyzed organisms and showed different aspect of relationship among the genomes which have been established through rRNA-based comparisons. Subsequently, bioinformatic computation and analysis of the genomic and metabolic information of various microorganisms were performed to identify the global characteristics and possible in silico targets for the experimental and industrial applications in Part II. In Chapter 4, the complete genome sequence of a rumen bacterium, Mannheimia succiniciproducens MBEL55E was analyzed to identify the genomic and metabolic characteristics as well as the relationships among the organisms. Further application of the analysis revealed that the organism is an efficient succinic acid producer. In Chapter 5, the complete genome sequence of a hyperthermophilic bacterium, Thermotoga neapolitana was analyzed to identify the characteristics as well as the applicable targets. Several candidates for the industrial application, i.e. amylases, xylases etc., were identified from the comparative analyses. In Chapter 6, various genomic characteristics of three pseudomonads were compared. The genomic similarities and differences were compared between the genomes. Comparison of the genomic seque...