The phytochrome red/far-red photoreceptor superfamily

The phytochrome protein superfamily reveals a diversity of mechanisms of action

The phytochrome gene family in grasses (Poaceae): A phylogeny and evidence that grasses have a subset of the loci found in dicot angiosperms

The phytochrome nuclear gene family encodes photoreceptor proteins that mediate developmental responses to red and far red light throughout the life of the plant. From studies of the dicot flowering plant Arabidopsis, the family has been modeled as comprising five loci, PHYA-PHYE. However, it has been shown recently that the Arabidopsis model may not completely represent some flowering plant groups because additional PHY loci related to PHYA and PHYB of Arabidopsis apparently have evolved independently several times in dicots, and monocot flowering plants may lack orthologs of PHYD and PHYE of Arabidopsis. Nonetheless, the phytochrome nucleotide data were informative in a study of organismal evolution because the loci occur as single copy sequences and appear to be evolving independently. We have continued our investigation of the phytochrome gene family in flowering plants by sampling extensively in the grass family. The phytochrome nuclear DNA data were cladistically analyzed to address the following questions: (1) Are the data consistent with a pattern of differential distribution of phytochrome genes among monocots and higher dicots, with homologs of PHYA, B, C, D, and E present in higher dicots, but of just PHYA, B, and C in monocots, and (2) what phylogenetic pattern within Poaceae do they reveal? Results of these analyses, and of Southern blot experiments, are consistent with the observation that the phytochrome gene family in grasses comprises the same subset of loci detected in other monocots. Furthermore, for studies of organismal phylogeny in the grass family, the data are shown to provide significant support for relationships that are just weakly resolved by other data sets

Phytochrome genes in higher plants: Structure,expression, and evolution

© 2006 Springer. All Rights Reserved. Phytochromes play critical roles in monitoring light quantity, quality, and periodicity in plants and they relay this photosensory information to a large number of signaling pathways that regulate plant growth and development. Given these complex functions, it is not surprising that the phytochrome apoproteins are encoded by small multigene families and that different forms of phytochrome regulate different aspects of photomorphogenesis. Over the course of the last decade, progress has been made in defining the number, molecular properties, and biological activities of the photoreceptors that constitute a plant R/FR sensing system. This chapter summarizes our current understanding of the structure of the genes that encode the phytochrome apoproteins (the PHY genes), the expression patterns of those genes, the nature of the phytochrome apoprotein family, and PHY gene evolution in seed plants. Phytochrome was discovered and its basic photochemical properties were first described through physiological studies of light-sensitive seed germination and photoperiodic effects on flowering (Borthwick, et al., 1948, Borthwick, et al., 1952). The pigment itself was initially isolated from extracts of dark-grown (etiolated) plant tissue in 1959 (Butler, et al., 1959), but it was not until much later that phytochrome was purified to homogeneity in an undegraded form (Vierstra and Quail, 1983). DNA sequences of gene and cDNA clones for oat etiolated-tissue spectroscopically in planta and purified in its native form, this dark-tissue phytochrome (now called phyA) remains the most completely biochemically and spectroscopically characterized form of the receptor. At various times throughout the first 40 years of the study of the abundant etiolated-tissue phytochrome, evidence for the presence and activity of additional forms of phytochrome, often referred to as green-tissue or light-stable phytochromes, was obtained. Initially, in physiological experiments, it was sometimes not possible to correlate specific in vivo phytochrome activities with the phytochrome provided the first complete descriptions of the apoprotein (Hershey et al., 1985). Because it accumulates to levels that permit it to be assayed known spectroscopic properties of the molecule. Later, direct evidence for multiple species of phytochrome in plants and in plant extracts was obtained using both spectroscopic and immunochemical methods (reviewed in Pratt, 1995). The molecular identities of these additional phytochrome forms were ultimately deduced from cDNA clones that were isolated by nucleic acid similarity to etiolated-tissue phytochrome sequences (Sharrock and Quail, 1989). More recently, analysis of a large number of complete and partial PHY gene or cDNA sequences from a broad sampling of plant phylogenetic groups and sequencing of several plant genomes have resulted in a much clearer and more general picture of what constitutes a higher plant R/FR photoreceptor family. It is likely that the major types of long-wavelength photosensing pigments have now been identified and the challenge that lies ahead is to understand how the signalling mechanisms, expression patterns, and interactions of these molecules contribute to plant responses to the R/FR environment. Extending the investigation of phytochrome gene families and their functions to additional angiosperm and gymnosperm genera will be an integral component of this effort and of our ability to utilize this growing understanding of phytochrome function to modify the agricultural properties of plants and to better understand the history of land plants

Monophyletic subgroups of the tribe Millettieae (Leguminosae) as revealed by phytochrome nucleotide sequence data

Phylogenetic analysis of phytochrome (PHY) genes reveals the identity and relationships of four PHY loci among papilionoid Leguminosae. A phylogenetic analysis of loci combined according to species suggests that most of the tribe Millettieae belongs to one of two monophyletic clades: the Derris-Lonchocarpus or the Tephrosia clade. Together these two form a monophyletic group that is sister to a lineage represented by Millettia grandis of Millettia sect. Compresso-gemmatae. Collectively, this large monophyletic group is referred to as the Millettieae-core group, which based on our sampling, includes species of Millettieae that do not accumulate the nonprotein amino acid canavanine and that mostly have pseudoracemose or pseudopaniculate inflorescences. This new phylogenetic framework assists in targeting additional taxa for future sampling. For example, the \u27American Derris\u27 (Deguelia), which accumulate canavanine, might not be members of the Millettieae core group. Afgekia is also predicted not to be a member because it accumulates canavanine and has an inflorescence of terminal racemes. PHY gene analysis specifically reveals that certain genera traditionally classified in Millettieae are actually distantly related to the Millettieae core group, such as Austrosteensia, Callerya, Craibia, Cyclolobium, Fordia, Platycyamus, Poecilanthe, and Wisteria

Biological activity and dimerization state of modified phytochrome A proteins

<div><p>To assess potential physical interactions of type I phyA with the type II phyB-phyE phytochromes <i>in vivo</i>, transgenes expressing fusion gene forms of phyA were introduced into the Arabidopsis <i>phyA</i> mutant background. When a single c-Myc (myc) epitope is added to either the N- or C-terminus of phyA, the constructs completely complement <i>phyA</i> mutant phenotypes. However, addition of larger tags, such as six consecutive myc epitopes or the yellow fluorescent protein sequence, result in fusion proteins that show reduced activity. All the tagged phyA proteins migrate as dimers on native gels and co-immunoprecipitation reveals no binding interaction of phyA to any of the type II phys in the dark or under continuous far-red light. Dimers of the phyA 1–615 amino acid N-terminal photosensory domain (NphyA), generated <i>in vivo</i> with a yeast GAL4 dimerization domain and attached to a constitutive nuclear localization sequence, are expressed at a low level and, although they cause a <i>cop</i> phenotype in darkness and mediate a very low fluence response to pulses of FR, have no activity under continuous FR. It is concluded that type I phyA in its Pr form is present in plants predominantly or exclusively as a homodimer and does not stably interact with type II phys in a dimer-to-dimer manner. In addition, its activity in mediating response to continuous FR is sensitive to modification of its N- or C-terminus.</p></div

Evolution of the Phytochrome Gene Family and Its Utility for Phylogenetic Analyses of Angiosperms

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Activities of the epitope-tagged phyA proteins under continuous FR light.

<p>(A) Morphologies of seedlings of the indicated genotypes grown for one day in the dark and 4 days at 22°C under three different fluences of continuous FR. (B) Continuous FR fluence response curves of hypocotyl length in transgenic lines expressing modified phyA proteins (means ±SE; n = 20–30).</p

Activities of epitope-tagged phyA proteins in regulating VLFR and extended-day flowering time.

<p>(A) Hypocotyl lengths of seedlings grown for 1 day in darkness followed by 3 days at 22°C under FR pulses (3 min 31 μmol m^-2 s^-1 FR + 57 min dark) (means ±SE; n = 20–30). Asterisks indicate significant differences (*<i>p</i> value < 0.05) relative to the wild type plants. (B) Days to flowering under short days with low fluence FR-enriched day extension (22°C; 8 h fluorescent light at 200 μmol m^-2 s^-1, 8 h incandescent light at 2 μmol m^-2 s^-1, 8 h dark) (means ±SE; n = 13–19). Asterisks indicate significant differences (*<i>p</i> value < 0.05, **<i>p</i> < 0.01, ***<i>p</i> < 0.001) relative to the wild type plants.</p