On both procaryotic and eucaryotic genomes, there are specific sites at which progress of DNA replication is impeded. Analysis of the fork-blocking systems in E.coli and yeast has revealed their molecular mechanisms. During the course of experiments in E.coli, we found out that a DNA region close to the fork-blocking site is recombinationally activated. Analysis of this phenomenon revealed that organisms have a system, which has ability to destroy the arrested fork and to reconstruct a new replication fork to overcome the obstacle. This rescue system of the fork is really a homologous recombination system in itself. Surprisingly, in yeast the fork-blocking system plays a central role in increase and decrease in copy number of the ribosomal RNA gene through efficient recombination. Suggesting that fork blockage may contribute to various structural changes of genomes more than expected.
F1-ATPase (F1) is a part of the ATP synthase. We have shown that F1 is a rotary motor by visualizing the rotation of a large marker attached to the putative rotator of this protein. Driven by three catalytic subunits, the rotator rotates with discrete 120° steps. Thermodynamic efficiency of F1 is almost 100%
The behavior of a simple coupled oscillator model for a reaction-diffusion-chemotaxis system is examined wish respect to the morphogenesis of the cellular slime mold Dictyostelium discoideum. We explain how the intrinsic difference in the oscillation frequency of secreted chemoattractant gives rise to an anterior-posterior polarity which could drive the migration of a pseudoplasmodium. The phase locking and migration of oscillators and their implication to a phenomenological soft-interface are discussed.
In Drosophila, the factors with sufficient ability to establish germ line are localized in a histologically remarkable region in egg cytoplasm, of germ plasm. Mitochondrial large ribosomal RNA (mtlrRNA) has been indentified as a factor which can rescue embryos from uvcaused inability to form pole cells, or the germline progeniter. MtlrRNA is transported out of mitochondria only in germ plasm. The extra-mitochomdrial mtlrRNA is tightly associated with polar granules, a distinctive organelle of germ plasm. We have recently found that the injection of targeted ribozymes against the extra-mitochondrial mtlrRNA into early embryos results in their failure to form pole cells. These results clearly show that mtlrRNA functions as a factor to form pole cells.
Gene expression in eukatyotic cells involves the interaction of proteins with DNA packaged into nucleosomes: the primary structural units of chromatin. Recent sutudies show that transcription is regulated by multiple-steps of chromatin alteration, and that chromatin remodeling complexes are mainly responsible for the chromatin alteration from inactive state to destabilized state. Destabilization of nucleosomes was also found to occur in vivo at specific DNA sequences which can adopt non-B DNA structures. Hence, the nucleosome destabilizing sequences could be involved in the establishment of promoters that preset chromatin structure accessible for trans-acting factors prior to activation. Finally, organization of repressive chromatin structure by repressors in conjunction with global transcriptional regulators is described.
Inference of gene regulation nechanism from time series of gene expression patterns, which can be determined by recently developed DNA microarray technology, is getting important. We have been studying algorithms for inferring genetic network architecture from gene expression patterns, using the Boolean network model. In the Boolean network model, each gene is assumed to take 0 (not-expressed) or 1 (expressed) as its state value, and each regulation rule is given as a Boolean function. We developed algorithms for inferring Boolean networks from gene expression patterns. We also developed algorithms for inferring network architecture under more realistic models.