Cytosolic heme metabolism by alternative localization of heme oxygenase 1 in plant cells

Heme, an organometallic molecule, is widely engaged in oxygen transport, electron delivery, enzymatic reactions, and signal transduction. Additionally, heme serves as a precursor to phytochromobilin, the chromophore of plant phytochrome. Heme oxygenase (HO) initiates the first committed step in heme metabolism. Our transcription start site-sequencing (TSS-seq) revealed that HO1 in Arabidopsis thaliana and Oryza sativa (rice) has two TSSs, producing long (HO1L) and short (HO1S) transcripts, with or without an intact N-terminal plastid transit peptide. HO1L and HO1S products localize in plastids and the cytosol, respectively. In Arabidopsis, HO1L is prevalent in light-exposed shoots, while HO1S is clearly detected in roots and etiolated seedlings. During de-etiolation and early development, HO1L ratio gradually rises and HO1S ratio decreases. Light perception via phytochrome and cryptochrome elevates HO1L ratio and reduces HO1S ratio through the functioning of HY5 and HYH transcription factors, and the suppression of DET1, E3 ubiquitin ligase COP1, and PIFs transcription factors. As expected, HO1L product was able to complement the HO1-deficient mutant gun2 (hy1), but surprisingly, HO1S expression could also restore the short hypocotyl phenotype and high pigment content, and make the mutant recover from the gun phenotype. This indicates the formation of functional holo-phytochrome within these lines. Our work highlights the presence of a cytosolic pathway for heme metabolism, especially during etiolation and early development. Furthermore, it supports the hypothesis that a mobile heme signal is involved in the mediation of retrograde signaling from the chloroplast.