Characterization of Phytochrome Interacting Factors from the Moss Physcomitrella patens Illustrates Conservation of Phytochrome Signaling Modules in Land Plants

Abstract

Across the plant kingdom, phytochrome (PHY) photoreceptors play an important role during adaptive and developmental responses to light. In , light-activated PHYs accumulate in the nucleus, where they regulate downstream signaling components, such as phytochrome interacting factors (PIFs). PIFs are transcription factors that act as repressors of photomorphogenesis; their inhibition by PHYs leads to substantial changes in gene expression. The nuclear function of PHYs, however, has so far been investigated in only a few non-seed plants. Here, we identified putative target genes of PHY signaling in the moss and found light-regulated genes that are putative orthologs of PIF-controlled genes in Arabidopsis. Phylogenetic analyses revealed that an ancestral PIF-like gene was already present in streptophyte algae, i.e., before the water-to-land transition of plants. The PIF homologs in the genome of resemble Arabidopsis PIFs in their protein domain structure, molecular properties, and physiological effects, albeit with notable differences in the motif-dependent PHY interaction. Our results suggest that PIFs are involved in PHY signaling. The PHY-PIF signaling node that relays light signals to target genes has been largely conserved during land plant evolution, with evidence of lineage-specific diversification.

PEATmoss (Physcomitrella Expression Atlas Tool): a unified gene expression atlas for the model plant Physcomitrella patens

“…Raw data for the RNA‐seq experiments included in PEATmoss and not available in other tools are stored at the SRA (Leinonen et al , ) with the library names BBTWT, BBTWU, BBTWS, BBTWW, BBTWY, BBTWX, BAOBH, BAOBP, BAOBS, BBTXA, BBTXB, BBTWZ, BAOBT, BAOBN, BBTXG, BAOAW, BAOAX, BAOBA, BAOAZ, BAOBC, BAOAU, BAOBG, BAOBU, BAOBO, BAOBB, BAOAY, BAOBW, BAOAT, BBTXC, and BBTWO. ArrayExpress accession numbers for the CombiMatrix data are E‐MTAB‐2165 (Beike et al , ), E‐MTAB‐913, E‐MTAB‐914, E‐MTAB‐915, E‐MTAB‐916, E‐MTAB‐917, E‐MTAB‐919, E‐MTAB‐976, E‐MEXP‐2508 (Hiss et al , ), and E‐MTAB‐2227 (Possart et al , ). ArrayExpress accession numbers for the NimbleGen data are E‐MTAB‐3069 (Ortiz‐Ramirez et al , ) and E‐MTAB‐4630 (Hiss et al , ).…”

Plant Strategies for Enhancing Access to Sunlight

“…PIFs are central integrators of internal and external cues regulating plant growth and development [43][44][45]. They are conserved in land plants, pointing to an early evolutionary origin of this signaling module [46,47]. Arabidopsis has eight PIF/PIF-like proteins which can interact with phyB but only play partially overlapping roles at different stages of development: PIF1, PIF3-8 and PIL1/PIF2 [44].…”

Phytochromes and Phytochrome Interacting Factors

“…Sequence analysis of the P. patens genome identifies four putative PIF orthologs (PpPIF1-PpPIF4; Possart et al, 2017). PpPIFs contain an APA motif and a potential APB-like motif similar to those found in Arabidopsis and other angiosperm PIFs.…”