Phytochrome as a Transcription Factor

Phytochrome causes long-lasting changes in the plant, such as greening, by changing which genes are expressed.P_r is found in the cytoplasm. When it absorbs red light and is converted to P_fr, the molecule changes shape. This exposes a signal that lets P_fr move through the nuclear pores into the nucleus.In the nucleus, P_fr binds to proteins called phytochrome-interacting factors (PIFs). PIFs are transcription factors: they bind to the promoter regions of target genes and control whether RNA polymerase can transcribe them. In the dark, PIFs keep the seedling etiolated. When P_fr binds to them, the PIFs are tagged for breakdown, so the genes they were controlling are switched on or off.In this way phytochrome regulates transcription. Hundreds of genes respond to red light, including genes for:• enzymes of chlorophyll synthesis
• the chlorophyll a/b binding protein of the light-harvesting complex
• the small subunit of rubiscoThe new mRNA is translated into proteins, and these proteins bring about de-etiolation. This explains why photomorphogenic responses take hours or days to appear, even though the light signal itself can be a single flash.Far-red light converts P_fr back to P_r, which stays in the cytoplasm, so far-red light reverses these effects on gene expression. Phytochrome's control of flowering also works through changes in gene expression, including the genes for the florigen protein made in the leaves.