Figure 1.

Architecture of Representative Members of the Phy Superfamily within Seed and Seedless Plants (Neochromes), Algae (Glaucophyte), Proteobacteria, and Cyanobacteria (PAS-Less and CBCRs).

Shown are Arabidopsis (At) PhyB, Cyanophora paradoxa CCMP329 (glaucophyte, Cpar) GPS1, Synechocystis PCC6803 (Syn) Cph1 and Cph2, D. radiodurans (Dr) BphP, R. palustris (Rp) BphP1, R. centenum (Rc) Ppr, Neurospora crassa (Nc) Phy1, Synechococcus OSB’ (SyB) Cph1, T. elongatus (Te) PixJ, N. punctiforme (Np) F2854, F. diplosiphon (Fd) RcaE and IflA, and A. capillus-veneris (Ac) neochrome NEO1. The known or likely bilin type for each Phy is indicated in parenthesis. Domains include conserved residues in diguanylate phosphodiesterase (EAL), cGMP phosphodiesterase/adenylyl cyclase/FhlA (GAF), conserved residues in diguanylate cyclase (GGDEF), histidine kinase/adenylyl cyclase/methyl binding protein/phosphatase (HAMP), histidine kinase (HK), histidine-kinase-related (HKR), 2-helix output sensor (HOS), light/oxygen/voltage (LOV), methyl-accepting chemotaxis protein (MCP), Phy N-terminal extension (NTE), Period/Arnt/Single-Minded (PAS), PAS domain followed by C-terminal motif similar to PAS domain (PAS/PAC), Phy-specific (PHY), photoactive yellow protein (PYP), response regulator (RR), serine/threonine-kinase (S/T-K), and predicted transmembrane (TM). The knot lasso and hairpin motifs are indicated by the green and orange loops, respectively. Confirmed and predicted lassos/hairpins are in solid and dashed lines, respectively. Cys, cysteine residue that covalently binds the chromophores: bilin, flavin, or p-hydroxycinnamic acid. H, phosphoacceptor histidine in HK domains; D, phosphoacceptor aspartate in RR domains; C, C terminus; N, N terminus.