A procedure for the simultaneous isolation of mitochondrial and plastid nucleoids was first established in BY-2 cells. Biochemical analysis suggested the presence of nucleosome-like repetitive structural units in both of the plant organelle nucleoids. The isolated organelle nucleoids were also used for establishment of in vitro transcription/DNA synthesis systems, with which regulation of organelle genomes during proliferation and differentiation was investigated. The results revealed that transient and synchronous activation of DNA synthesis occurred in mitochondria and plastids in the initial phase of cell proliferation, which was caused by a transient activation of dually-targeted organelle DNA polymerase genes. Another series of investigations revealed a drastic difference in the transcription activity between BY-2 proplastids and leaf chloroplasts, which was brought about by differential use of bacterial- and phage-type plastid RNA polymerases. To investigate regulation of plastid gene expression further, a procedure to induce amyloplast formation in BY-2 cells was established. Various changes observed during this process were collectively similar to those observed during root cap cell differentiation. BY-2 cells were also used to develop a novel model system for programmed cell death during hypersensitive reaction (HR), in which we have succeeded in inducing programmed cell death with 100% efficiency by application of an elicitor. This system revealed that the HR cells activated anti-microbial defense mechanism by themselves and transmitted signal(s) to establish acquired resistance in neighboring cells, while executing cell-death program. Thus, BY-2 cells have taught us a lot about proliferation, differentiation, and death of plant cells.