Evolutionary Studies Illuminate the Structural-Functional Model of Plant Phytochromes

Abstract

A synthesis of insights from functional and evolutionary studies reveals how the phytochrome photoreceptor system has evolved to impart both stability and flexibility. Phytochromes in seed plants diverged into three major forms, phyA, phyB, and phyC, very early in the history of seed plants. Two additional forms, phyE and phyD, are restricted to flowering plants and Brassicaceae, respectively. While phyC, D, and E are absent from at least some taxa, phyA and phyB are present in all sampled seed plants and are the principal mediators of red/far-red-induced responses. Conversely, phyC-E apparently function in concert with phyB and, where present, expand the repertoire of phyB activities. Despite major advances, aspects of the structural-functional models for these photoreceptors remain elusive. Comparative sequence analyses expand the array of locus-specific mutant alleles for analysis by revealing historic mutations that occurred during gene lineage splitting and divergence. With insights from crystallographic data, a subset of these mutants can be chosen for functional studies to test their importance and determine the molecular mechanism by which they might impact light perception and signaling. In

PHYTOCHROME C plays a major role in the acceleration of wheat flowering under long-day photoperiod

“…Phytochromes are encoded by three genes (PHYA, PHYB, and PHYC) in most monocot species whereas eudicot plant species possess additional genes (PHYD-F) derived from PHYB duplications (7,8). Studies in model plant species have shown that PHYA is required for growth in deep shade and for seedling deetiolation (9) whereas members of the PHYB clade play major roles in shade-avoidance responses (10,11).…”

Crystal structure of the photosensing module from a red/far-red light-absorbing plant phytochrome

“…Examples include a long N-terminal extension (NTE) in plant Phys and pervasive sequence variations within the PAS, GAF, and PHY domains and the downstream OPM (3,4). For a more authoritative view, we present the crystal structure of a Phy PSM from a seed plant, that of PhyB from Arabidopsis thaliana, and extensively characterize its solution and photochemical properties.…”

“…This information then regulates nearly all aspects of plant growth and development from seed germination to senescence. Notably, seed plants typically express three Phy isoforms (PhyA, PhyB, and PhyC) that control distinct and overlapping photoresponses, with PhyB having a dominant role in green tissues (2,3).…”

PHYTOCHROME C Is an Essential Light Receptor for Photoperiodic Flowering in the Temperate Grass, Brachypodium distachyon

“…Certain groups of plants, such as diploid grasses, have only one copy of PHYA, PHYB, and PHYC, although lineage-specific duplications and losses of phytochrome genes have occurred in many groups of flowering plants (Mathews 2010). Phytochrome mutants in the model plant systems Arabidopsis (Arabidopsis thaliana, Brassicaceae) and rice (Oryza sativa, Poaceae) have contributed to the elucidation of the functional roles of the various phytochromes.…”

“…Flowering plants typically contain three types of phytochromes referred to as PHYTOCHROME A (PHYA), PHY-TOCHROME B (PHYB), and PHYTOCHROME C (PHYC) (Mathews 2010). Certain groups of plants, such as diploid grasses, have only one copy of PHYA, PHYB, and PHYC, although lineage-specific duplications and losses of phytochrome genes have occurred in many groups of flowering plants (Mathews 2010).…”