The following is my summary of a paper (Hornitschek et al., 2012) published on The Plant Journal. It revealed that PIF4 and PIF5 regulate stem growth through control of auxin biosynthesis and signaling genes.

By Qingwu (William) Meng

Plants growing in lower canopies or shadowed by other neighboring plants have adapted to compete for light and exhibit shade avoidance syndrome (SAS). Common responses of SAS include hypocotyl elongation, leaf expansion, and upward leaf orientation. Phytohormones such as gibberellins, auxin, and brassinosteroids, and cytokinins are all involved in SAS. Shade is sensed as a decreased ratio of red (R) to far-red (FR) radiation or enriched green radiation. The primary photoreceptor for sensing changes in R/FR and mediating the shade-induced adaptive responses is phytochrome B (phyB), which accumulates in R radiation. The active form of phyB controls PHYTOCHROME-INTERACTING FACTORS (PIFs), which induce target-gene expression to promote stem growth.

PIF4 and PIF5 are two members of PIFs and are controlled by R/FR to influence SAS. Other target genes of PIFs are also of significance for regulating SAS. Auxin is needed to promote extension growth; however, the relationship between the biosynthesis, signaling network, and transport of auxin and light-regulated PIF activity remains to be elucidated. This paper set out to uncover the mechanisms of how PIF4 and PIF5 mediate elongation growth in consideration of the biological function of auxin.

The authors employed chromatin immunoprecipitation (ChIP) and sequencing (ChIP-seq) and identified PIF5 binding sites in the plant genome. PIF5-HA bound to E- and G-box containing promoters of a set of genes, which depended on PIF4 and PIF5 for regulation of gene expression. Therefore, PIF4 and PIF5 may directly target these genes.

77 genes were then identified to show changes in pif4pif5 double mutants. Two major groups of these genes were classified depending on whether their expression was reduced in high R/FR (group 1) or low R/FR (group 2, including HFR1 and PIL1). Gene Ontology (GO) enrichment analysis revealed that PIF4 and PIF5 were important in mediating auxin responses. In addition, most genes in group 2 were direct target genes of PIF4 and PIF5. These PIFs were essential for proper expression of the genes regulated by shade. These genes included those that coded for auxin biosynthesis (YUC8, which regulates the rate-limiting step) and auxin signal transduction.

At last, PIF4 and PIF5 bound to target genes more favorably at a low photosynthetic photon flux density. Auxin sensitivity was reduced at a low photosynthetic photon flux density. The gene expression, ChIP, and physiological studies together showed that PIF4 and PIF5 directly controlled auxin biosynthesis and signaling components to ultimately regulate stem growth of plants.

Source: Hornitschek, P., Kohnen, M.V., Lorrain, S., Rougemont, J., Ljung, K., López‐Vidriero, I., Franco‐Zorrilla, J.M., Solano, R., Trevisan, M., Pradervand, S. and Xenarios, I., 2012. Phytochrome interacting factors 4 and 5 control seedling growth in changing light conditions by directly controlling auxin signaling. The Plant Journal, 71(5), pp.699-711.

PIFs regulate auxin to promote stem growth