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 the case of gene families, where redundancy hinders isolation of some proportion of the relevant mutants, the approach may be particularly useful.

Figure 1.

Relationships, Physiological Response Modes, and Dimerization Properties of Arabidopsis Phytochromes A to E. SA, shade avoidance. Bold font indicates predominant form of dimer detected, if one exists; gray font indicates a dimer that is not detected unless phyB is absent (Clack et al., 2009).

Figure 2.

Viridophyte Phytochrome Tree. Black branches trace the relationships of Arabidopsis PHYA-E; gymnosperm PHYN, O, and P (green branches) are shown to be orthologs of PHYA, C, and B, respectively. The optimal maximum likelihood tree and bootstrap percentages (numbers above branches, except for the PHYO/C node, where it is below the branch) were inferred from analyses of full-length or nearly-full-length amino acid sequences using RAxML 7.0.4 (Stamatakis, 2006), a phytochrome-specific amino acid transition matrix (Mathews et al., 2010); the thorough (designated with the f -i switch) bootstrap option was used. Outgroups for rooting the tree are the PHY sequences from M. caldariorum and M. scalaris. Seed plant species relationships are discussed by Mathews et al. (2010). Amino acid alignment is provided as Supplemental Data Set 1 online.

Figure 3.

Location by Branch and Domain of Positively Selected Amino Acid Sites in Seed Plant Phytochromes. (A) Summary seed plant phytochrome tree. Hatch marks on a branch represent amino acid sites inferred to have been subject to positive selection along that branch using the branch-site test (Zhang et al., 2005). Numbers by branch labels indicate how many radical amino acid changes map to a particular branch in the tree using a parsimony-based approach (Maddison and Maddison, 2003). Sequence alignments for the branch-site tests are provided in Supplemental Data Sets 2 to 4 online. (B) Domain structure of Arabidopsis PHYA. The N-terminal PAS, GAF, and PHY domains of plant PHY and Synechocystis Cph1 are homologous. The N-terminal extension (NTE) and the HKRD are unique to plant PHY. It is unclear whether plant PHYs have a helix comparable to α 1 in Cph1. (C) Topology of the photosensory module of Synechocystis Cph1. Sites inferred to be under positive selection in seed plant phytochromes (open circles) are clustered in the region of the knot that forms the interface between the PAS and GAF domains. A, NA, PBE, and E refer to the branch of the phytochrome phylogeny on which a site was inferred to be under selection; X indicates an amino acid site at which the residue is variable.