Abstract
BackgroundPhytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Prototypical phytochromes exhibit an N-terminal tridomain (PGP) consisting of PAS, GAF and PHY domains and a C-terminal histidine kinase (HK).ResultsThe mode of evolution of streptophyte, fungal and diatom phytochromes from bacteria is analyzed using two programs for sequence alignment and six programs for tree construction. Our results suggest that Bacteroidetes present the most ancient types of phytochromes. We found many examples of lateral gene transfer and rearrangements of PGP and HK sequences. The PGP and HK of streptophyte phytochromes seem to have different origins. In the most likely scenario, PGP was inherited from cyanobacteria, whereas the C-terminal portion originated from a proteobacterial protein with multiple PAS domains and a C-terminal HK. The plant PhyA and PhyB lineages go back to an early gene duplication event before the diversification of streptophytes. Fungal and diatom PGPs could have a common prokaryotic origin within proteobacteria. Early gene duplication is also obvious in fungal phytochromes.ConclusionsThe dominant question of the origin of plant phytochromes is difficult to tackle because the patterns differ among phylogenetic trees. We could partially overcome this problem by combining several alignment and tree construction algorithms and comparing many trees. A rearrangement of PGP and HK can directly explain the insertion of the two PAS domains by which streptophyte phytochromes are distinguished from all other phytochromes.Electronic supplementary materialThe online version of this article (doi:10.1186/s13104-015-1082-3) contains supplementary material, which is available to authorized users.
Highlights
Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi
Phytochromes are photoreceptors with a bilin chromophore that are found in plants, bacteria and fungi but missing in animals and Archaea
Phytochromes are often lacking in algae, but they have been found in the Zygnematales Mougeotia scalaris and Mesotaenium caldariorum [2], diatoms [3], brown algae, Prasinophytes and glaucophytes [4]
Summary
Phytochromes are red light-sensitive photoreceptors that control a variety of developmental processes in plants, algae, bacteria and fungi. Phytochromes are photoreceptors with a bilin chromophore that are found in plants, bacteria and fungi but missing in animals and Archaea. In plants, they act as the dominant photoreceptors affecting most developmental processes, from stimulation of seed germination over de-etiolation and shade avoidance to flowering [1]. Phytochromes present two spectrally distinct long-lived forms, termed Pr and Pfr, that serve as red-absorbing and far-red absorbing forms, respectively [16]. Some bacterial phytochromes termed “bathy-phytochromes” convert from Pr to Pfr in darkness [7,22,23], these phytochromes have a Pfr dark state
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