Chloroplasts, mitochondria, and peroxisomes form clusters in mesophyll cells of rice ( <i>Oryza sativa</i> )

Chloroplasts, mitochondria, and peroxisomes are consistently positioned in close proximity with physical contact in mesophyll cells, as shown by two-dimensional transmission electron microscopy observations. However, the three-dimensional arrangement of these organelles has not yet been investigated in rice. In this study, we investigated the positions and proximity of the chloroplasts, mitochondria, and peroxisomes in rice mesophyll cells three-dimensionally. Chloroplasts aligned along the cell walls, and mitochondria and peroxisomes were located on the intracellular side of the cell rather than in the peripheral chloroplasts. In total, 345 mitochondria were included in nine replicated cells, and 89.4% of the mitochondria formed binary complexes with peroxisomes. Binary complexes were located between the chloroplasts, forming clusters in the three organelles. Among the 134 chloroplasts and 210 peroxisomes detected in the nine mesophyll cells, only one chloroplast and one peroxisome were not included in the clusters. The clustering of chloroplasts, mitochondria, and peroxisomes at a high frequency has not been observed in other plants; therefore, this arrangement is considered to be unique to rice mesophyll cells, likely due to the smaller and denser cells than those of other plants. In the clusters, the three organelles were in contact with each other and in close membrane proximity. Considering the high correlation between the total volumes of mitochondria and peroxisomes and the area of membrane proximity among the three organelles, it is suggested that the proximity areas in rice mesophyll cells are determined by the size of the binary complexes within the clusters.