Mosses do express conventional, distantly B-type-related phytochromes. Phytochrome of Physcomitrella patens (Hedw.)

Phytochrome cytoplasmic signaling

Extensive studies in both lower and higher plants indicate that plant phytochrome photoreceptors signal not only by regulating transcription in the nucleus but also by acting within the cytoplasm, the latter signaling routes acting within minutes or even seconds and also providing directional information. Directional signals seem to arise from phytochromes attached anisotropically to the plasma membrane. Neochromes-phytochrome-phototropin hybrid photoreceptors probably attached to the plasma membrane-provide this signal in various ferns and perhaps certain algae but are absent from other groups. In mosses and probably higher plants too, a subpopulation of canonical phytochromes interact with phototropins at the plasma membrane and thereby steer directional responses. Phytochromes also seem able to regulate translation in the cytoplasm. This review discusses putative phytochrome functions in these contexts.

Functional characterization of HY5 homolog genes involved in early light-signaling in Physcomitrella patens

The developmental programs of Physcomitrella patens, a basal lineage of land plants, are regulated by phytohormones and light-signaling responses. In this study, our attention was focused on the HY5-family of transcription factors, which are known to play important roles immediately downstream of photoreceptors during the early photomorphogenesis of Arabidopsis thaliana. We retrieved two HY5-homologs, named PpHY5a and PpHY5b, from the whole genome sequence database of P. patens. Arabidopsis transgenic plants overproducing the basic leucine zipper (bZIP) domain of PpHY5a exhibited a phenotype of short hypocotyls, suggesting a functional relationship between PpHY5 and Arabidopsis HY5. A loss-of-function Δhy5a Δhy5b double mutant was defective in the vigorous protrusion of caulonema cells from the protonema networks of P. patens under light and dark conditions. These results suggest that the function of HY5-homologs in P. patens is evolutionarily conserved, and is implicated in a process of caulonema development.

Phototropins mediate blue and red light-induced chloroplast movements in Physcomitrella patens

Phototropin is the blue-light receptor that mediates phototropism, chloroplast movement, and stomatal opening in Arabidopsis. Blue and red light induce chloroplast movement in the moss Physcomitrella patens. To study the photoreceptors for chloroplast movement in P. patens, four phototropin genes (PHOTA1, PHOTA2, PHOTB1, and PHOTB2) were isolated by screening cDNA libraries. These genes were classified into two groups (PHOTA and PHOTB) on the basis of their deduced amino acid sequences. Then phototropin disruptants were generated by homologous recombination and used for analysis of chloroplast movement. Data revealed that blue light-induced chloroplast movement was mediated by phototropins in P. patens. Both photA and photB groups were able to mediate chloroplast avoidance, as has been reported for Arabidopsis phot2, although the photA group contributed more to the response. Red light-induced chloroplast movement was also significantly reduced in photA2photB1photB2 triple disruptants. Because the primary photoreceptor for red light-induced chloroplast movement in P. patens is phytochrome, phototropins may be downstream components of phytochromes in the signaling pathway. To our knowledge, this work is the first to show a function for the phototropin blue-light receptor in a response to wavelengths that it does not absorb.

Comparative genomics of Physcomitrella patens gametophytic transcriptome and Arabidopsis thaliana: implication for land plant evolution

The mosses and flowering plants diverged >400 million years ago. The mosses have haploid-dominant life cycles, whereas the flowering plants are diploid-dominant. The common ancestors of land plants have been inferred to be haploid-dominant, suggesting that genes used in the diploid body of flowering plants were recruited from the genes used in the haploid body of the ancestors during the evolution of land plants. To assess this evolutionary hypothesis, we constructed an EST library of the moss Physcomitrella patens, and compared the moss transcriptome to the genome of Arabidopsis thaliana. We constructed full-length enriched cDNA libraries from auxin-treated, cytokinin-treated, and untreated gametophytes of P. patens, and sequenced both ends of >40,000 clones. These data, together with the mRNA sequences in the public databases, were assembled into 15,883 putative transcripts. Sequence comparisons of A. thaliana and P. patens showed that at least 66% of the A. thaliana genes had homologues in P. patens. Comparison of the P. patens putative transcripts with all known proteins, revealed 9,907 putative transcripts with high levels of similarity to vascular plant genes, and 850 putative transcripts with high levels of similarity to other organisms. The haploid transcriptome of P. patens appears to be quite similar to the A. thaliana genome, supporting the evolutionary hypothesis. Our study also revealed that a number of genes are moss specific and were lost in the flowering plant lineage.

Characterization of cDNA of the liverwort phytochrome gene, and phytochrome involvement in the light-dependent and light-independent protochlorophyllide oxidoreductase gene expression in Marchantia paleacea var. diptera

The cDNA of the phytochrome gene in the liverwort Marchantia paleacea var. diptera (MpdPHY1) was isolated. MpdPHY1 encoded a conventional phytochrome apoprotein. The MpdPHY1 transcript was accumulated in the dark and suppressed in the light. The degradation of the MpdPHY1 transcript by red light irradiation had red/far-red reversibility, suggesting that the liverwort phytochrome gene expression was regulated by a phytochrome. Northern blot analysis of the transcripts in cells irradiated by red/far-red light revealed that the liverwort phytochrome was involved in the expressions of chlB, chlL, chlN, or por, which encode subunits of light-independent and light-dependent protochlorophyllide oxidoreductase, respectively.

Isolation of homeodomain-leucine zipper genes from the moss Physcomitrella patens and the evolution of homeodomain-leucine zipper genes in land plants

Homeobox genes encode transcription factors involved in many aspects of developmental processes. The homeodomain-leucine zipper (HD-Zip) genes, which are characterized by the presence of both a homeodomain and a leucine zipper motif, form a clade within the homeobox superfamily and were previously reported only from vascular plants. Here we report the isolation of 10 HD-Zip genes (named PPHB:1-PPHB:10) from the moss Physcomitrella patens. Based on a phylogenetic analysis of the 10 PPHB: genes and previously reported vascular plant HD-Zip genes, all of the PPHB: genes except Pphb3 belong to three of the four HD-Zip subfamilies (HD-Zip I, II, and III), indicating that these subfamilies originated before the divergence of the vascular plant and moss lineages. Pphb3 is sister to the HD-Zip II subfamily and has some distinctive characteristics, including the difference of the a(1) and d(1) sites of its leucine zipper motif, which are well conserved in each HD-Zip subfamily. Comparison of the genetic divergence of representative HD-Zip I and II genes showed that the evolutionary rate of HD-Zip I genes was faster than that of HD-Zip II genes.

Light irradiation induces fragmentation of the plasmodium, a novel photomorphogenesis in the true slime mold Physarum polycephalum: action spectra and evidence for involvement of the phytochrome

A new photomorphogenesis was found in the plasmodium of the true slime mold Physarum polycephalum: the plasmodium broke temporarily into equal-sized spherical pieces, each containing about eight nuclei, about 5 h after irradiation with light. Action spectroscopic study showed that UVA, blue and far-red lights were effective, while red light inhibited the far-red-induced fragmentation. Difference absorption spectra of both the living plasmodium and the plasmodial homogenate after alternate irradiation with far-red and red light gave two extremes at 750 and 680 nm, which agreed with those for the induction and inhibition of the fragmentation, respectively. A kinetic model similar to that of phytochrome action explained quantitatively the fluence rate-response curves of the fragmentation. Our results indicate that one of the photoreceptors for the plasmodial fragmentation is a phytochrome.

Characterization and expression of the phytochrome gene family in the moss Ceratodon purpureus

In the moss Ceratodon purpureus, phytochrome is encoded by two different genes, CpPHY1 and CpPHY2. CpPHY2 represents a conventional type phytochrome characterized by a C-terminus homologous to the catalytic domain of bacterial sensor histidine kinases, whereas CpPHY1 represents an unique phytochrome, which carries a C-terminus homologous to the catalytic domain of eukaryotic serine/threonine/tyrosine kinases. Southern blot analysis revealed that CpPHY1 is present in different Ceratodon cultivars which were collected in Germany and in Finland, implying that CpPHY1 represents a functional and active gene in Ceratodon, but CpPHY1 homologous genes could not be detected in another moss, Physcomitrella patens, or in Arabidopsis thaliana. cDNA analysis of CpPHY1 revealed the presence of a hitherto unnoticed intron within the 3' region. This results in a change of the sequence of the 11 C-terminal amino acids from KLSSHSYLTSK to FSSYQDSYPSTEELS. CpPHY1 and CpPHY2 mRNAs appear to accumulate in a light-independent manner, with CpPHY2 being much more strongly expressed than CpPHY1. Accordingly, in crude protein extracts, CpPHY2 is clearly detectable by Western blot analysis, whereas CpPHY1 is not. Light-dependent expression of CpPHY2 can be detected at the post-transcriptional level; during a 7-day period of dark adaptation, pronounced CpPHY2 accumulation occurs. Upon transfer to white light, dark-accumulated CpPHY2 is depleted within 24 h. That depletion can be completely inhibited by the photosynthesis inhibitor 3-(3,4-dichlorophenyl)-1,1-dimethyl urea (DCMU), implying that photosynthesis is strongly involved in the adjustment of phytochrome steady-state concentrations in Ceratodon. The presence of an ORF within the 5' UTR region of CpPHY2 (uORF) encoding peptide MKEFSSTSRSLMIVGIY suggests regulation at the translational level. The uORF resides on a short intron which is excised from the 5' leader in a light-dependent manner, resulting in the formation of an alternative uORF encoding peptide MEEEEDCVP.

The phytochromes: a biochemical mechanism of signaling in sight?

The biochemical mechanism by which the phytochrome family of plant sensory photoreceptors transmit perceived informational light signals downstream to transduction pathway components is undertermined. The recent sequencing of the entire genome of the cyanobacterium Synechocystis, however, has revealed a protein that has an NH2-terminal domain with striking sequence similarity to the photosensory NH2-terminal domain of the phytochromes, and a COOH-terminal domain strongly related to the transmitter histidine kinase module of bacterial two-component sensors. The Synechocystis protein is capable of autocatalytic chromophore ligation and exhibits photoreversible light-absorption changes analogous to the phytochromes, indicating its capacity to function as an informational photoreceptor. Together with earlier observations that the COOH-terminal domains of the plant phytochromes also have sequence similarity to the histidine kinases, these data suggest that the cyanobacteria utilize photoregulated histidine kinases as a sensory system and that the plant phytochromes may be evolutionary descendants of these photoreceptors.

Tetracycline-regulated reporter gene expression in the moss Physcomitrella patens

As ancestors of higher plants, mosses offer advantages as simple model organisms in studying complex processes such as development and signal transduction. Overexpression of transgenes after genetic transformation is a powerful technique in such studies. To establish a controllable expression system for this experimental approach we expressed a chimeric protein consisting of the Tn1O-encoded Tet repressor and the activation domain of Herpes simplex virion protein 16 in the moss Physcomitrella patens. We showed that this protein activates transcription from a suitable target promoter (Top 1O) containing seven operators upstream of a TATA box. In media containing very low levels of tetracycline (1 mg/l), expression levels of a beta-glucuronidase (GUS) reporter gene dropped to <1% of that in the absence of tetracycline. This regulation is due to interference of tetracycline with the DNA binding activity of the Tet repressor portion of the chimeric transcriptional activator. Stable transformants grown for three weeks on tetracycline-containing media showed negligible GUS activity, whereas GUS was expressed strongly within 24 h of transfer to tetracycline-free media. Potent and stringently regulated expression of other, physiologically active genes is thus readily available in the moss system using the convenient ToplO expression system.

Photosensory perception and signal transduction in plants

Genetic and molecular studies are beginning to unravel the complexities of the signaling circuitry that plants use to sense and transduce information concerning the prevailing light environment. The past year has witnessed definition of discrete photosensory roles for phytochromes A and B, the cloning of a gene encoding the first apparent blue-light photoreceptor from any organism, the cloning of genes encoding additional members of the COP/DET/FUS class of light-responsive master regulators, and evidence that G proteins, Ca2+/calmodulin, and cGMP may be signaling intermediates in phototransduction.