How are chloroplasts communicating with the nucleus?

For plants, light is an important environmental factor not only as a source of energy for photosynthesis but also as a signal for capturing environmental information. Light signals are sensed by photoreceptor proteins called phytochrome. The amino acids that make up proteins are transparent and cannot absorb visible light. Therefore, pigments are essential for photoreceptor proteins to sense light, and these are called chromophores. The phytochrome chromophore, phytochromobilin (PFB), is synthesized from heme, a blood pigment. Thus, PΦB, a metabolite of heme, plays an important role in light signaling, but heme itself has also been proposed to function as a signaling molecule that transmits the functional state of chloroplasts to the nucleus. However, because PΦB is synthesized from heme, it has been impossible to separate and analyze heme signaling from phytochrome signaling until now.

By utilizing bacterial enzymes that cleave heme molecules at different sites, a research group led by Professor Tatsuru Masuda of the University of Tokyo and Associate Professor Takayuki Shimizu of Nara Women's University developed a method to dissect phytochrome-dependent light and heme retrograde signaling pathways, which have previously been difficult to discuss separately.

The research team introduced either of two bacterial heme oxygenases (HOs) that cleave different sites on the heme molecule into plants (Arabidopsis thaliana) that had lost their major HO activity. One type of HO (derived from Neisseria meningitidis) (NmHO) cleaves the same site as in plants and can synthesize PΦB, but the other type of HO (derived from Pseudomonas aeruginosa) (PaHO) cleaves a different site and cannot synthesize PΦB. This allowed them to create plants that could metabolize heme and synthesize PΦB to form active phytochrome, and plants that could not. As a result, even in plants where phytochrome was non-functional, changes in the expression of photosynthesis-related genes in the nucleus were observed. This revealed that heme molecules function as plastid-derived signaling molecules. Furthermore, the research team compared plants in which bacterial-derived HO functions within plastids with plants in which it functions within the cytoplasm. It became clear that degrading heme not only in plastids but also in the cytoplasm alters the expression of photosynthesis-related genes in the nucleus. From these findings, it became clear that heme produced in chloroplasts is transmitted as a signal to the nucleus via the cytoplasm, regulating the expression of photosynthesis-related genes in the nucleus involved in chloroplast formation. This study also revealed that some photosynthesis-related genes are regulated by light signals, while others are not.

The results of this research were published online in Plant Physiology on 23 May 2026.

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