The structural characteristics and properties that have been observed in various circular bacterial chromosomes have become increasingly clear based on the decipherment of the complete genome sequences of approximately three thousand bacteria. A consideration of chromosome structure includes various symmetries at many scales, ranging from base composition to the gene strand bias, which are based on the replication origin and a terminal axis, and the supercoiling involved in the nucleoid structure. In this study, I focused on the chromosome structure and attempted to shed light on the mechanisms related to the formation and preservation of the chromosomes. First, I performed a comprehensive prediction of replication termination sites based on sequence, and I determined that the sequence is widely conserved in almost all bacteria. Based on this result, I proposed a model of replication termination from the standpoint of bioinformatics. The use of this newly defined symmetric structure made it possible to investigate how strongly symmetric structures have been maintained, and I analyzed the relationship between symmetric structures and insertion events. Furthermore, I found that the association of nucleoid binding sites with protein was controlled by cod on usage in the host bacterial genomes. Finally, I designed and implemented a versatile browser to facilitate the visualization of symmetric structures that cannot be fully captured by purely numeric information, allowing an intuitive grasp of these structures. Throughout this dissertation, I performed comprehensive analyses of the genomic functionality, characteristics, and structural evolution of bacterial chromosome, which serves as a medium of living systems. Based on these analyses, I discuss the means by which chromosome composition and structure have adapted to biological mechanisms in the course of evolution.

先端生命科学プロジェクト 冨田勝研究会2011年度