phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots

Detection and partial sequence of phytochrome genes in the ferns Anemia phyllitidis (L.)Sw (Schizaeaceae) and Dryopteris filix-mas L. (Polypodiaceae) by using polymerase-chain reaction technology

Phytochrome controls several developmental steps during formation and differentiation of the fern gametophyte, including spore germination, morphogenesis of the gametophyte or differentiation of the sexual cells. To obtain information about the amino acid sequence and the regulation of phytochrome expression at the gene level, two degenerated oligonucleotides against well conserved amino acid regions were designed after an optimal alignment of the known phytochrome sequences. These primers were tested against DNA isolated from Arabidopsis thaliana, and the polymerase-chain reaction (PCR) products were cloned and sequenced. The DNA fragment produced with this method proved to be identical with a phytochrome-A-gene fragment from A. thaliana, and hence this fragment was used in further experiments to prove whether amplified DNA from fern species contains phytochrome-like DNA. With this procedure we successfully detected and cloned gene fragments both from gametophytes of Anemia phyllitidis and Dryopteris filix-mas, cultured for 7 days under vegetative conditions. In addition, poly(A)+ RNA was prepared from 7-day-old gametophytes of A. phyllitidis, induced to differentiate antheridia under generative conditions. This poly(A)+ RNA was transcribed into complementary DNA and used together with both phytochrome specific primers in a PCR experiment. We thereby obtained another DNA fragment. These data strongly suggest that A. phyllitidis has at least two phytochrome genes, and that at least one of them is expressed in light-grown gametophytes.

Phytochrome evolution: a phylogenetic tree with the first complete sequence of phytochrome from a cryptogamic plant (Selaginella martensii spring)

We have sequenced cDNA and genomic clones coding for phytochrome of the fern Selaginella. On the amino acid level, this phytochrome shares sequence homologies with phytochromes of higher plants which range between 62 (phytochrome B of Arabidopsis) and 55 (56)% [phytochrome C of Arabidopsis (Avena)]. Introns in the Selaginella gene are short and occupy positions known from phytochrome sequences of higher plants. A rooted phylogenetic tree based on mutation distances puts Selaginella phytochrome closest to the hypothetical ancestor. A similar tree arises if the tree is constructed with partial sequences (about 200 amino acids) around the chromophore attachment site. An extension of this tree by sequences of other cryptogamic plants (Mougeotia, Ceratodon, Psilotum) shows all these sequences including those of the phytochromes B and C of Arabidopsis on a branch, well separated from the branch formed by phytochromes known to accumulate in etiolated plants. The rooted phytochrome phylogenetic tree, however, is difficult to reconcile with the fossil record.

FLUORESCENCE SPECTROSCOPY OF STABLE AND LABILE PHYTOCHROME IN STEMS AND ROOTS OF ETIOLATED CRESS SEEDLINGS*

Low‐temperature (80 K) fluorescence belonging to the red light‐absorbing phytochrome form (Pr) with the emission maximum at 684 nm in stems and at 682 nm in roots was detected and described in etiolated cress seedlings. By monitoring fluorescence intensity, Pr concentration changes in stems and roots were followed during etiolated growth of seedlings. In both tissues, the changes have the same characteristics, reaching maximum concentration in stems, 37 ± 4 μ g/g fresh weight (f.w.), and in roots, 6.2 ± 1.2 μ g/g f.w., 48 h after sowing. Red (660 nm) preillumination of the sample leads to a decrease of the phytochrome content in 3 h of incubation in darkness to 29 ± 6% in stems and 59 ± 5% in roots compared with that in the red‐far‐red illuminated control samples. Assuming identical fluorescence properties, the proportion of the labile and stable pools was calculated to be 90% and 10% in stems and ˜50% in roots, respectively. It was furthermore deduced that the absolute concentration of the stable pool is about the same in both tissues, 3.1–3.7 μg/g f.w., while that of the labile pool is approximately 10 times higher in stems than in roots. Comparison of the results with data on the dependence of the photophysical and photochemical properties of phytochrome on its localization in etiolated seedlings (Sineshchekov and Sineshchekov, 1990, J. Photochem. Photobiol. 5, 197–217) suggests that the labile and stable pools correspond to the Pr states with low and high activation barriers of the photoreaction, Ea, 3–4 kJ/mol, and ca 35 kJ/mol, and with high and low photochemical activity at 80 K. The two pools also differ in the position of their fluorescence emission and excitation spectra, those of the stable pool being shifted 2 nm to the blue region.

Signal transduction by phytochrome: phytochromes have a module related to the transmitter modules of bacterial sensor proteins

A C-terminal section of phytochromes turned out to share sequence homologies with the full length of the transmitter modules (about 250 amino acids) of bacterial sensor proteins. Coinciding hydrophobic clusters within the homologous domains imply that the overall folding of the two different types of peptides is similar. Hence, phytochromes appear to possess the structural prerequisites to transmit signals in a way bacterial sensor proteins do. The bacterial sensor proteins are known to be environmental stimuli-regulated kinases belonging to two-component systems. After sensing a stimulus by the N-terminal part of the sensor protein, conformational alterations confer the signal to its (mostly) C-terminal transmitter module which in turn is transitionally autophosphorylated at a conserved histidine. From the histidine the phosphate is transferred to the receiver module of a system-specific regulator protein which eventually acts on transcription or enzyme activity. The histidine is not conserved in phytochromes. Instead, a conserved tyrosine is found spatially very close to the histidine position. This tyrosine might play the role of histidine, and kinase function might be associated with this part of phytochrome. In spite of this divergence, the structural similarities point to a common evolutionary origin of the phytochrome and bacterial modules.

Phytochrome a overexpression inhibits hypocotyl elongation in transgenic Arabidopsis

To develop a model plant system for efficient functional analysis of mutagenized phytochrome polypeptides, we have overexpressed oat phytochrome A in Arabidopsis thaliana. R1 seedlings from selfed primary transformants segregated for hypocotyl length, when grown in the light, with a ratio of 3 short to 1 of normal length. When homozygous lines were established from these two size classes, accumulation of immunologically detectable oat phytochrome cosegregated with the short-hypocotyl trait. The short-hypocotyl seedlings contained substantially more spectrally active phytochrome than their normal-sized siblings, indicating that the introduced oat protein was photoreversible. The short-hypocotyl phenotype was strictly light-dependent, since no morphological effects of phytochrome overexpression could be seen in etiolated seedlings. Overexpression of only the chromophore-bearing, N-terminal domain of phytochrome A did not induce short hypocotyls in light-grown seedlings, indicating that additional sequence is essential for photoreceptor function. Similarly, overexpression of a full-length sequence mutated at the chromophore attachment site had no effect on phenotype, indicating the absence of any detectable dominant negative effect of the chromophoreless polypeptide on the activity of endogenous Arabidopsis phytochrome. Thus, the readily scorable short-hypocotyl phenotype of Arabidopsis seedlings overexpressing phytochrome A provides a simple visual assay for rapidly monitoring the biological activity of mutagenized phytochrome A polypeptides.