Structure and expression of a maize phytochrome-encoding gene

Light-Dependent Expression and Promoter Methylation of the Genes Encoding Succinate Dehydrogenase, Fumarase, and NAD-Malate Dehydrogenase in Maize (Zea mays L.) Leaves

The expression and methylation of promoters of the genes encoding succinate dehydrogenase, fumarase, and NAD-malate dehydrogenase in maize (Zea mays L.) leaves depending on the light regime were studied. The genes encoding the catalytic subunits of succinate dehydrogenase showed suppression of expression upon irradiation by red light, which was abolished by far-red light. This was accompanied by an increase in promoter methylation of the gene Sdh1-2 encoding the flavoprotein subunit A, while methylation was low for Sdh2-3 encoding the iron-sulfur subunit B under all conditions. The expression of Sdh3-1 and Sdh4 encoding the anchoring subunits C and D was not affected by red light. The expression of Fum1 encoding the mitochondrial form of fumarase was regulated by red and far-red light via methylation of its promoter. Only one gene encoding the mitochondrial NAD-malate dehydrogenase gene (mMdh1) was regulated by red and far-red light, while the second gene (mMdh2) did not respond to irradiation, and neither gene was controlled by promoter methylation. It is concluded that the dicarboxylic branch of the tricarboxylic acid cycle is regulated by light via the phytochrome mechanism, and promoter methylation is involved with the flavoprotein subunit of succinate dehydrogenase and the mitochondrial fumarase.

Domestication-associated PHYTOCHROME C is a flowering time repressor and a key factor determining Setaria as a short-day plant

Phytochromes play vital roles in the regulation of flowering time, but little is known in Panicoideae species, especially the C₄ model Setaria. Here, genomic variations of PHYTOCHROME C (PHYC) between wild and cultivated Setaria gene pools were analysed and three SiphyC mutants were identified. The function of SiPHYC was verified by CRISPR-Cas9 approach and transcriptome sequencing. Furthermore, efficiency of indoor cultivation of SiphyC mutants were systematically evaluated. An extreme purified selection of PHYC was detected in wild to cultivated domestication process of Setaria. SiphyC mutants and knockout transgenic plants showed an early heading date and a loss of response to short-day photoperiod. Furthermore, variable expression of SiFTa, SiMADS14 and SiMADS15 might be responsible for promoting flowering of SiphyC mutants. Moreover, SiphyC mutant was four times that of the indoor plot ratio of wild-type and produced over 200 seeds within 45 d per individual. Our results suggest that domestication-associated SiPHYC repressed flowering and determined Setaria as a short-day plant, and SiphyC mutants possess the potential for creating efficient indoor cultivation system suitable for research on Setaria as a model, and either for maize or sorghum as well.

Evolutionary divergence of phytochrome protein function in Zea mays PIF3 signaling

Two maize phytochrome-interacting factor (PIF) basic helix-loop-helix (bHLH) family members, ZmPIF3.1 and ZmPIF3.2, were identified, cloned and expressed in vitro to investigate light-signaling interactions. A phylogenetic analysis of sequences of the maize bHLH transcription factor gene family revealed the extent of the PIF family, and a total of seven predicted PIF-encoding genes were identified from genes encoding bHLH family VIIa/b proteins in the maize genome. To investigate the role of maize PIFs in phytochrome signaling, full-length cDNAs for phytochromes PhyA2, PhyB1, PhyB2 and PhyC1 from maize were cloned and expressed in vitro as chromophorylated holophytochromes. We showed that ZmPIF3.1 and ZmPIF3.2 interact specifically with the Pfr form of maize holophytochrome B1 (ZmphyB1), showing no detectable affinity for the Pr form. Maize holophytochrome B2 (ZmphyB2) showed no detectable binding affinity for PIFs in either Pr or Pfr forms, but phyB Pfr from Arabidopsis interacted with ZmPIF3.1 similarly to ZmphyB1 Pfr. We conclude that subfunctionalization at the protein-protein interaction level has altered the role of phyB2 relative to that of phyB1 in maize. Since the phyB2 mutant shows photomorphogenic defects, we conclude that maize phyB2 is an active photoreceptor, without the binding of PIF3 seen in other phyB family proteins.

Tissue-specific and light-dependent regulation of phytochrome gene expression in rice

Phytochromes are red- and far red light photoreceptors in higher plants. Rice (Oryza sativa L.) has three phytochromes (phyA, phyB and phyC), which play distinct as well as cooperative roles in light perception. To gain a better understanding of individual phytochrome functions in rice, expression patterns of three phytochrome genes were characterized using promoter-GUS fusion constructs. The phytochrome genes PHYA and PHYB showed distinct patterns of tissue- and developmental stage-specific expression in rice. The PHYA promoter-GUS was expressed in all leaf tissues in etiolated seedlings, while its expression was restricted to vascular bundles in expanded leaves of light-grown seedlings. These observations suggest that light represses the expression of the PHYA gene in all cells except vascular bundle cells in rice seedlings. Red light was effective, but far red light was ineffective in gene repression, and red light-induced repression was not observed in phyB mutants. These results indicate that phyB is involved in light-dependent and tissue-specific repression of the PHYA gene in rice.

Chlorophyll deficiency in the maize elongated mesocotyl2 mutant is caused by a defective heme oxygenase and delaying grana stacking

BACKGROUND

Etiolated seedlings initiate grana stacking and chlorophyll biosynthesis in parallel with the first exposure to light, during which phytochromes play an important role. Functional phytochromes are biosynthesized separately for two components. One phytochrome is biosynthesized for apoprotein and the other is biosynthesized for the chromophore that includes heme oxygenase (HO).

METHODOLOGY/PRINCIPAL FINDING

We isolated a ho1 homolog by map-based cloning of a maize elongated mesocotyl2 (elm2) mutant. cDNA sequencing of the ho1 homolog in elm2 revealed a 31 bp deletion. De-etiolation responses to red and far-red light were disrupted in elm2 seedlings, with a pronounced elongation of the mesocotyl. The endogenous HO activity in the elm2 mutant decreased remarkably. Transgenic complementation further confirmed the dysfunction in the maize ho1 gene. Moreover, non-appressed thylakoids were specifically stacked at the seedling stage in the elm2 mutant.

CONCLUSION

The 31 bp deletion in the ho1 gene resulted in a decrease in endogenous HO activity and disrupted the de-etiolation responses to red and far-red light. The specific stacking of non-appressed thylakoids suggested that the chlorophyll biosynthesis regulated by HO1 is achieved by coordinating the heme level with the regulation of grana stacking.

Phytochrome gene expression and phylogenetic analysis in the short-day plant Pharbitis nil (Convolvulaceae): Differential regulation by light and an endogenous clock

To investigate the role of distinct phytochrome pools in photoperiodic timekeeping, we characterized four phytochrome genes in the short-day plant Pharbitis nil. Each PHY gene had different photosensory properties and sensitivity to night break that inhibits flowering. During extended dark periods, PHYE, PHYB, and PHYC mRNA accumulation exhibited a circadian rhythmicity indicative of control by an endogenous clock. Phylogenetic analysis recovered four clades of angiosperm phytochrome genes, phyA, phyB, phyC, and phyE. All except the phyE clade included sequences from both monocots and eudicots. In addition, phyA is sister to phyC and phyE sister to phyB, with gymnosperm sequences sister to either the phyA-phyC clade or to the phyB-phyE clade. These results suggest that a single duplication occurred in an ancestral seed plant before the divergence of extant gymnosperms from angiosperms and that two subsequent duplications occurred in an ancestral angiosperm before the divergence of monocots from eudicots. Thus in P. nil, a multigene family with different patterns of mRNA abundance in light and darkness contributes to the total phytochrome pool: one pool is light labile (phyA), whereas the other is light stable (phyB and phyE). In addition, PHYC mRNA represents a third phytochrome pool with intermediate photosensory properties.

Identification, characterization of functional candidate genes for host-parasite interactions in entomopathogenetic nematode Steinernema carpocapsae by suppressive subtractive hybridization

Identifying parasitism genes encoding proteins secreted from nematodes is the key to understanding the molecular basis of nematode parasitism to insects. In this paper, a cDNA with two introns and three exons encoding a cysteine protease inhibitor was identified by screening a cDNA subtractive library constructed from the nematode, Steinernema carpocapsae, induced by Galleria mellonella hemolymph. The full-length cDNA contains an open reading frame encoding a 139-amino acid protein, designated Sc-cys, with a 19-residue signal peptide. The mature protein was predicted to have a molecular weight of 12,531.59 Da, a pI of 9.44, one disulfide bond, and three conserved domains believed to be important for the inhibition of cysteine proteases. In Basic Local Alignment and Search Tool analyses, the putative protein precursor displayed 26-42% identities to a multitude of cystatins or cystatin-like proteins. Phylogenetic analysis suggested the novel cystatin is likely a new member of the family 2 cystatins. Reverse northern blot, semi-quantitative reverse transcriptase polymerase chain reaction (RT-PCR), and real-time RT-PCR analyses showed that the expression level of Sc-cys was upregulated substantially after induction by insect hemolymph. The specific analysis of genes encoding secretory proteins is providing a profile of putative parasitism genes expressed in S. carpocapsae throughout the parasitic cycle.

Subfunctionalization of PhyB1 and PhyB2 in the control of seedling and mature plant traits in maize

Phytochromes are the primary red/far-red photoreceptors of higher plants, mediating numerous developmental processes throughout the life cycle, from germination to flowering. In seed plants, phytochromes are encoded by a small gene family with each member performing both distinct and redundant roles in mediating physiological responses to light cues. Studies in both eudicot and monocot species have defined a central role for phytochrome B in mediating responses to light in the control of several agronomically important traits, including plant height, transitions to flowering and axillary branch meristem development. Here we characterize Mutator-induced alleles of PhyB1 and a naturally occurring deletion allele of PhyB2 in Zea mays (maize). Using single and double mutants, we show that the highly similar PhyB1 and PhyB2 genes encode proteins with both overlapping and non-redundant functions that control seedling and mature plant traits. PHYB1 and PHYB2 regulate elongation of sheath and stem tissues of mature plants and contribute to the light-mediated regulation of PhyA and Cab gene transcripts. However, PHYB1 and not PHYB2 contributes significantly to the inhibition of mesocotyl elongation under red light, whereas PHYB2 and to a lesser extent PHYB1 mediate the photoperiod-dependent floral transition. This sub functionalization of PHYB activities in maize has probably occurred since the tetraploidization of maize, and may contribute to flowering time variation in modern-day varieties.

Structure and expression of maize phytochrome family homeologs

To begin the study of phytochrome signaling in maize, we have cloned and characterized the phytochrome gene family from the inbred B73. Through DNA gel blot analysis of maize genomic DNA and BAC library screens, we show that the PhyA, PhyB, and PhyC genes are each duplicated once in the genome of maize. Each gene pair was positioned to homeologous regions of the genome using recombinant inbred mapping populations. These results strongly suggest that the duplication of the phytochrome gene family in maize arose as a consequence of an ancient tetraploidization in the maize ancestral lineage. Furthermore, sequencing of Phy genes directly from BAC clones indicates that there are six functional phytochrome genes in maize. Through Northern gel blot analysis and a semiquantitative reverse transcriptase polymerase chain reaction assay, we determined that all six phytochrome genes are transcribed in several seedling tissues. However, expression from PhyA1, PhyB1, and PhyC1 predominate in all seedling tissues examined. Dark-grown seedlings express higher levels of PhyA and PhyB than do light-grown plants but PhyC genes are expressed at similar levels under light and dark growth conditions. These results are discussed in relation to phytochrome gene regulation in model eudicots and monocots and in light of current genome sequencing efforts in maize.

Genetic architecture of flowering time in maize as inferred from quantitative trait loci meta-analysis and synteny conservation with the rice genome

Genetic architecture of flowering time in maize was addressed by synthesizing a total of 313 quantitative trait loci (QTL) available for this trait. These were analyzed first with an overview statistic that highlighted regions of key importance and then with a meta-analysis method that yielded a synthetic genetic model with 62 consensus QTL. Six of these displayed a major effect. Meta-analysis led in this case to a twofold increase in the precision in QTL position estimation, when compared to the most precise initial QTL position within the corresponding region. The 62 consensus QTL were compared first to the positions of the few flowering-time candidate genes that have been mapped in maize. We then projected rice candidate genes onto the maize genome using a synteny conservation approach based on comparative mapping between the maize genetic map and japonica rice physical map. This yielded 19 associations between maize QTL and genes involved in flowering time in rice and in Arabidopsis. Results suggest that the combination of meta-analysis within a species of interest and synteny-based projections from a related model plant can be an efficient strategy for identifying new candidate genes for trait variation.

Targeted analysis of orthologous phytochrome A regions of the sorghum, maize, and rice genomes using comparative gene-island sequencing

A "gene-island" sequencing strategy has been developed that expedites the targeted acquisition of orthologous gene sequences from related species for comparative genome analysis. A 152-kb bacterial artificial chromosome (BAC) clone from sorghum (Sorghum bicolor) encoding phytochrome A (PHYA) was fully sequenced, revealing 16 open reading frames with a gene density similar to many regions of the rice (Oryza sativa) genome. The sequences of genes in the orthologous region of the maize (Zea mays) and rice genomes were obtained using the gene-island sequencing method. BAC clones containing the orthologous maize and rice PHYA genes were identified, sheared, subcloned, and probed with the sorghum PHYA-containing BAC DNA. Sequence analysis revealed that approximately 75% of the cross-hybridizing subclones contained sequences orthologous to those within the sorghum PHYA BAC and less than 25% contained repetitive and/or BAC vector DNA sequences. The complete sequence of four genes, including up to 1 kb of their promoter regions, was identified in the maize PHYA BAC. Nine orthologous gene sequences were identified in the rice PHYA BAC. Sequence comparison of the orthologous sorghum and maize genes aided in the identification of exons and conserved regulatory sequences flanking each open reading frame. Within genomic regions where micro-colinearity of genes is absolutely conserved, gene-island sequencing is a particularly useful tool for comparative analysis of genomes between related species.

Maize leaves turn away from neighbors

In commercial crops, maize (Zea mays) plants are typically grown at a larger distance between rows (70 cm) than within the same row (16-23 cm). This rectangular arrangement creates a heterogeneous environment in which the plants receive higher red light (R) to far-red light (FR) ratios from the interrow spaces. In field crops, the hybrid Dekalb 696 (DK696) showed an increased proportion of leaves toward interrow spaces, whereas the experimental hybrid 980 (Exp980) retained random leaf orientation. Mirrors reflecting FR were placed close to isolated plants to simulate the presence of neighbors in the field. In addition, localized FR was applied to target leaves in a growth chamber. During their expansion, the leaves of DK696 turned away from the low R to FR ratio signals, whereas Exp980 leaves remained unaffected. On the contrary, tillering was reduced and plant height was increased by low R to FR ratios in Exp980 but not in DK696. Isolated plants preconditioned with low R/FR-simulating neighbors in a North-South row showed reduced mutual shading among leaves when the plants were actually grouped in North-South rows. These observations contradict the current view that phytochrome-mediated responses to low R/FR are a relic from wild conditions, detrimental for crop yield.

Elongated mesocotyl1, a phytochrome-deficient mutant of maize

To begin the functional dissection of light signal transduction pathways of maize (Zea mays), we have identified and characterized the light-sensing mutant elm1 (elongated mesocotyl1). Seedlings homozygous for elm1 are pale green, show pronounced elongation of the mesocotyl, and fail to de-etiolate under red or far-red light. Etiolated elm1 mutants contain no spectrally active phytochrome and do not deplete levels of phytochrome A after red-light treatment. High-performance liquid chromatography analyses show that elm1 mutants are unable to convert biliverdin IX alpha to 3Z-phytochromobilin, preventing synthesis of the phytochrome chromophore. Despite the impairment of the phytochrome photoreceptors, elm1 mutants can be grown to maturity in the field. Mature plants retain aspects of the seedling phenotype and flower earlier than wild-type plants under long days. Thus, the elm1 mutant of maize provides the first direct evidence for phytochrome-mediated modulation of flowering time in this agronomically important species.

Regulation by light and metabolites of ferredoxin-dependent glutamate synthase in maize

The regulation of Fd-glutamate synthase (Fd-GOGAT, EC 1.4.1.7) and NADH-glutamate synthase (NADH-GOGAT, EC 1.4.1.14) was investigated in maize (Zea mays L. cv. DEA) (1) during development starting from 7- to 11-day-old seedlings, (2) by treatment of 7-day-old etiolated leaves with intermittent light pulses to activate (red) and inactivate (far-red) phytochromes and (3) in 7-day-old green leaves grown under 16-h light/8-h dark cycles. Fd-GOGAT mRNA accumulated 4-fold, and the enzyme polypeptide (3-fold) and activity (3-fold) also increased in leaf cells, while NADH-GOGAT activity remained constantly low. Leaf-specific induction of Fd-GOGAT mRNA (3-fold) occurred in etiolated leaves by low fluence red light, and far-red light reversibly repressed the mRNA accumulation. Red/far-red reversible induction also occurred for Fd-GOGAT polypeptide (2-fold) and activity (2-fold), implicating the phytochrome-dependent induction of Fd-GOGAT. In contrast, NADH-GOGAT activity remained constant, irrespective of red/far-red light treatments. Fd-GOGAT showed diurnal changes under light/dark cycles with the maximum early in the morning and the minimum in the afternoon at the levels of mRNA, enzyme polypeptide and activity. Gln diurnally changed in parallel with Fd-GOGAT mRNA. The induction of Fd-GOGAT provides evidence that light and metabolites are the major signal for the Gln and Glu formation in maize leaf cells.

The phytochrome gene family in tomato and the rapid differential evolution of this family in angiosperms

A reexamination of the genome of the tomato (renamed Solanum lycopersicum L.) indicates that it contains five, or at most perhaps six, phytochrome genes (PHY), each encoding a different apoprotein (PHY). Five previously identified tomato PHY genes have been designated PHYA, PHYB1, PHYB2, PHYE, and PHYF. A molecular phylogenetic analysis is consistent with the hypothesis that the angiosperm PHY family is composed of four subfamilies (A, B, C/F, and E). Southern analyses indicate that the tomato genome does not contain both a PHYC and a PHYF. Molecular phylogenetic analyses presented here, which utilize for the first time full-length PHY sequences from two completely characterized angiosperm gene families, indicate that tomato PHYF is probably an ortholog of Arabidopsis PHYC. They also confirm that the angiosperm PHY family is undergoing relatively rapid differential evolution. Assuming PHYF is an ortholog of PHYC, PHY genes in eudicots are evolving (Ka/site) at 1.52-2.79 times the rate calculated as average for other plant nuclear genes. Again assuming PHYF is an ortholog of PHYC, the rate of evolution of the C and E subfamilies is at least 1.33 times the rate of the A and B subfamilies. PHYA and PHYB in eudicots are evolving at least 1.45 times as fast as their counterparts in the Poaceae. PHY functional domains also exhibit different evolutionary rates. The C-terminal region of angiosperm PHY (codons 800-1105) is evolving at least 2.11 times as fast as the photosensory domain (codons 200-500). The central region of a domain essential for phytochrome signal transduction (codons 652-712) is also evolving rapidly. Nonsynonymous substitutions occur in this region at 2.03-3.75 times the average rate for plant nuclear genes. It is not known if this rapid evolution results from selective pressure or from the absence of evolutionary constraint.

Both phyA and phyB mediate light-imposed repression of PHYA gene expression in Arabidopsis

The negatively photoregulated PHYA gene has a complex promoter structure in Arabidopsis, with three active transcription start sites. To identify the photoreceptors responsible for regulation of this gene, and to assess the relative roles of the three transcription start sites, we analyzed the changes in PHYA transcript levels in wild-type and photoreceptor mutant seedlings under various irradiation conditions. Continuous far-red or red light exposures each induced a significant decline in transcript levels in wild-type etiolated seedlings. Analysis of mutants specifically lacking either phyA or phyB protein demonstrated that these phytochromes are required for the negative regulation induced by far-red and red light, respectively. Ribonuclease protection experiments showed further that this negative regulation is confined almost exclusively to the shortest, most abundant PHYA transcript, and occurs predominantly in shoots. By contrast, both of the other minor transcripts in shoots, and all three transcripts in roots, exhibit near constitutive expression. This complex expression pattern indicates that the PHYA gene is subject to regulation by multiple signals, including environmental, developmental, and organ-specific signals.

Sequences within both the N- and C-terminal domains of phytochrome A are required for PFR ubiquitination and degradation

Photoconversion of the plant photoreceptor phytochrome A (phyA) from its inactive Pr form to its biologically active Pfr from initiates its rapid proteolysis. Previous kinetic and biochemical studies implicated a role for the ubiquitin/26S proteasome pathway in this breakdown and suggested that multiple domains within the chromoprotein are involved. To further resolve the essential residues, we constructed a series of mutant PHY genes in vitro and analyzed the Pfr-specific degradation of the resulting photoreceptors expressed in transgenic tobacco. One important site is within the C-terminal half of the polypeptide as its removal stabilizes oat phyA as Pfr. Within this half is a set of conserved lysines that are potentially required for ubiquitin attachment. Substitution of these lysines did not prevent ubiquitination or breakdown of Pfr, suggesting either that they are not the attachment sites or that other lysines can be used in their absence. A small domain just proximal to the C-terminus is essential for the form-dependent breakdown of the holoprotein. Removal of just six amino acids in this domain generated a chromoprotein that was not rapidly degraded as Pfr. Using chimeric photoreceptors generated from potato PHYA and PHYB, we found that the N-terminal half of phyA is also required for Pfr-specific breakdown. Only those chimeras containing the N-terminal sequences from phyA were ubiquitinated and rapidly degraded as Pfr. Taken together, our data demonstrate that, whereas an intact C-terminal domain is essential for phyA degradation, the N-terminal domain is responsible for the selective recognition and ubiquitination of Pfr.

Molecular analysis of PHYA in wild-type and phytochrome A-deficient mutants of tomato

Tomato (Lycopersicon esculentum Mill., recently redesignated Solanum lycopersicum L.), an agronomically important crop plant, has been adopted as a model species complementary to Arabidopsis in which to characterize the phytochrome family. Here we describe the cloning and molecular characterization of the gene encoding the apoprotein of phytochrome A in wild-type tomato and in the far-red-light-insensitive (fri1 and fri2) tomato mutants. The physical organization of this gene is similar to that of other angiosperm phytochromes with the four exons of the coding region interrupted by three introns. The pool of transcripts is heterogeneous due to multiple transcription start sites and to three modes of alternative splicing of the 5' leader. The leader in each alternative transcript carries multiple upstream open reading frames of considerable length. At the genomic level, both fri mutants share an identical base substitution which changes a consensus AG/ to TG/ at the 3' end of the intron between exons 1 and 2. This mutation leads to aberrant processing of the resultant pre-mRNA. While most mature transcripts retain the mutated intron, both cryptic splicing and exon skipping were also detected. Cryptic splicing occurred both upstream and downstream from the wild-type splice site. These observations are consistent with the hypothesis that exon definition in splicing of plant pre-mRNAs plays a secondary role to that of intron definition. Analysis of the frequency with which potentially functional phytochrome A apoproteins might be produced indicates that both fri1 and fri2 have less than 1% of the wild-type phytochrome A level.

Evidence for some common signal transduction events for opposite regulation of nitrate reductase and phytochrome-I gene expression by light

We have explored the possible involvement of the phosphoinositide (PI) cycle and protein kinase C (PKC) in the phytochrome (Pfr)-mediated light signal transduction pathway using nitrate reductase (NR) and phytochrome-I (PhyI) genes as model systems. We have shown earlier that phorbol myristate acetate (PMA) completely replaces the red light effect in stimulating nitrate reductase activity and transcript levels in maize. In this paper, we present detailed evidence to show that PMA mimics the red light effect and follows similar kinetics to enhance NR steady-state transcript accumulation in a nitrate-dependent manner. We also show that PMA inhibits phyI steady-state transcript accumulation in a manner similar to red light, indicating that a PKC-type enzyme(s) may be involved in mediating the light effect in both cases. Serotonin or 5-hydroxytryptamine (5-HT), a stimulator of PI turnover, was also found to mimic the red light effect in enhancing NR transcript levels and inhibiting phyI transcript accumulation, indicating the role of the PI cycle in generating second messengers for regulating the two genes. These results indicate that phytochrome-mediated light regulation of NR and phyI gene expression may involve certain common steps in the signal transduction pathway such as the PI cycle and protein phosphorylation by a PKC-type enzyme.

Abundance and half-life of the distinct oat phytochrome A3 and A4 mRNAs

Gene-preferential oligonucleotide probes were used to determined the relative abundance and half-lives of distinct oat phytochrome A (PHYA) mRNAs. Oat PHYA mRNAs are highly conserved in the 5'-untranslated region and the coding region, but the 3'-untranslated region has an overall lower sequence conservation and was the source of gene-preferential probes. PHYA3 mRNA was estimated to be ca. 61% of the oat PHYA mRNA pool present in poly(A)+ RNA from dark-grown seedlings. The half-lives for PHYA3 and PHYA4 mRNAs were both estimated to be ca. 30 min, and a similar short half-life was estimated for the average PHYA mRNA. Sequence comparisons of PHYA mRNAs from four grass species identified conserved sequences within the 5'- and 3'-untranslated regions that might be important for PHYA mRNA degradation.

Chromosome assignment of four photosynthesis-related genes and their variability in wheat species

Copy numbers of four photosynthesis-related genes, PhyA, Ppc, RbcS and Lhcb1 (*)1, in wheat genomes were estimated by slot-blot analysis, and these genes were assigned to the chromosome arms of common wheat by Southern hybridization of DNA from an aneuploid series of the cultivar Chinese Spring. The copy number of PhyA was estimated to be one locus per haploid genome, and this gene was assigned to chromosomes 4AL, 4BS and 4DS. The Ppc gene showed a low copy number of small multigenes, and was located on the short arm of homoeologous group 3 chromosomes and the long arm of chromosomes of homoeologous group 7. RbcS consisted of a multigene family, with approximately 100 copies in the common wheat genome, and was located on the short arm of group 2 chromosomes and the long arm of group 5 chromosomes. Lhcb1 (*)1 also consisted of a multigene family with about 50 copies in common wheat. Only a limited number of restriction fragments (approximately 15%) were used to determine the locations of members of this family on the long arm of group 1 chromosomes owing to the multiplicity of DNA bands. The variability of hybridized bands with the four genes was less in polyploids, but was more in the case of multigene families. RFLP analysis of polyploid wheats and their presumed ancestors was carried out with probes of the oat PhyA gene, the maize Ppc gene, the wheat RbcS gene and the wheat Lhcb1 (*)1 gene. The RFLP patterns of common wheat most closely resembled those of T. Dicoccum (Emmer wheat), T. urartu (A genome), Ae. speltoides (S genome) and Ae. squarrosa (D genome). Diversification of genes in the wheat complex appear to have occurred mainly at the diploid level. Based on RFLP patterns, B and S genomes were clustered into two major groups. The fragment numbers per genome were reduced in proportion to the increase of ploidy level for all four genes, suggesting that some mechanism(s) might operate to restrict, and so keep to a minimum, the gene numbers in the polyploid genomes. However, the RbcS genes, located on 2BS, were more conserved (double dosage), indicating that the above mechanism(s) does not operate equally on individual genes.

The phytochrome apoprotein family in Arabidopsis is encoded by five genes: the sequences and expression of PHYD and PHYE

Two novel Arabidopsis phytochrome genes, PHYD and PHYE, are described and evidence is presented that, together with the previously described PHYA, PHYB and PHYC genes, the primary structures of the complete phytochrome family of this plant are now known. The PHYD- and PHYE-encoded proteins are of similar size to the other phytochrome apoproteins and show sequence similarity along their entire lengths. Hence, red/far-red light sensing in higher plants is mediated by a diverse but structurally conserved group of soluble photoreceptors. The proteins encoded by the PHYD and PHYE genes are more closely related to phytochrome B than to phytochromes A or C, indicating that the evolution of the PHY gene family in Arabidopsis includes an expansion of a PHYB-related subgroup. The PHYB and PHYD phytochromes show greater than 80% amino acid sequence identity but the phenotypes of phyB null mutants demonstrate that these receptor forms are not functionally redundant. The five PHY mRNAs are, in general, expressed constitutively under varying light conditions, in different plant organs, and over the life cycle of the plant. These observations provide the first description of the structure and expression of a complete phytochrome family in a higher plant.

The Arabidopsis phytochrome A gene has multiple transcription start sites and a promoter sequence motif homologous to the repressor element of monocot phytochrome A genes

We have determined the sequence of the phytochrome A gene (PHYA) and its flanking DNA from Arabidopsis thaliana and have identified transcription start sites for three nested transcripts of increasing length. The overall structure of the gene is similar as regards exon/intron organization to other angiosperm PHY genes characterized. The triple transcription start site arrangement is similar to that of pea PHYA but different from the single start site of oat, rice and maize PHYA genes, indicating a possible monocot-dicot difference. Comparison of the Arabidopsis PHYA promoter sequence with others available indicates that both pea and Arabidopsis promoters contain a DNA element with a core sequence motif identical to one conserved in all existing monocot PHYA sequences and defined by functional assay in the oat PHYA gene as repressor element, RE1, responsible for negative light regulation.

Homology at the amino acid level between plant phytochromes and a regulator of asexual sporulation in Emericella (= Aspergillus) nidulans

Protein sequence comparison between the N-terminal regions of the BRLA (bristle A) protein of the ascomycete fungus Aspergillus nidulans and a number of plant phytochromes has demonstrated a moderate level of sequence similarity. The region of similarity corresponds to the phytochrome domains believed to be responsible for photoreception and which undergo light-induced conformational changes, although a putative chromophore-binding site is not evident. Over 22% of residues are conserved and 24% conservatively substituted between residues 1 and 272 of BRLA and the N-terminal domains of Type 1 phytochromes from dicotyledonous species. A lower level of similarity, but over the same region, is observed in comparison with a wider range of phytochromes. Given the known role of BRLA as a transcriptional activator involved in conidiation, and the red/far-red reversible photoregulation of this developmental process, the similarity with phytochromes may be significant.

Structural studies on the photoreceptor phytochrome: reevaluation of the epitope for monoclonal antibody Z-3B1

The photoreceptor phytochrome is widely distributed in the plant kingdom from angiosperms to ferns, mosses and algae. The epitope for the monoclonal antibody Z-3B1 which exhibits wide-ranging cross-reactivity with phytochromes from higher and lower plants was mapped by the combination of several methods: by Western blot with proteolytic fragments of known localization, by sequence comparison of phytochromes from various plants, and by production of overlapping fusion proteins. The only sequence which is common to all positively-reacting fusion proteins is the sequence A-830 to R-859. This sequence must contain the Z-3B1 epitope. The best candidate is suggested to be the T-cell antigenic sequence K-Y-V/I-E-A/C-L-L-T (= K-848 to T-855). The significance of the highly conserved epitope in all phytochromes is discussed.

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.

Events in the phytochrome molecule after irradiation

The photoconversion of Pr to Pfr has been investigated by a large number of investigators. We have previously demonstrated that Z, E isomerization of the tetrapyrrole chromophore is involved in the photoconversion. It is the best candidate for the primary photoreaction. Conformation and configuration of the Pr chromophore will be compared with that of chromophores in phycocyanin. The crystal structure of phycocyanin had been elucidated by x-ray analysis. Proton transfer and/or Z, E isomerization of the tetrapyrrole are probably involved in different steps of the photoconversion in phytochrome and in photoreversible phycobiliproteins. Fluorescence decay kinetics of irradiated Pr and intermediate formation show heterogeneity. Possible reasons for this heterogeneity will be discussed.

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.

Structural domains of phytochrome deduced from homologies in amino acid sequences

A method of semiempirical identification of structural domains is proposed. The procedure is based on the comparison of amino acid sequences in groups of homologous proteins. This approach was tested using 32 known protein sequences from different cytochrome b5, cytochrome c, lysozyme, hemoglobin, and myoglobin proteins. The method presented was able to identify all structural domains of these reference proteins. A consensus secondary structure provided information on structural content of these domains predicting correctly 21 of 23 (91%) of alpha-helices. We applied this method to six homologous phytochrome sequences from Avena, Arabadopsis, Cucurbita, Maize, Oryza, and Pisum. Some of the identified domains can be assigned to the known tertiary structure categories. For example, an alpha/beta domain is localized in the region known to stabilize the phytochrome chromophore in the red light absorbing form (Pr). One alpha-helical and one alpha/beta domains are localized in regions important for the chromophore stabilization in the far-red absorbing form (Pfr). From an analysis of noncovalent interaction patterns in another domain it is proposed that a phytochrome dimer contact involves two segments localized between residues 730 and 821 (using numbering of aligned sequences). Also, a possible antiparallel beta-sheet structure of this region has been suggested. According to this model, the long axis of the interacting structures is perpendicular to a twofold symmetry axis of the phytochrome dimer.

Molecular modeling of phytochrome

Molecular models of phytochrome were generated to gain insight into structure-function relationships of this important, tetrapyrrole-containing plant protein. Molecular dynamics simulation of a 51-amino acid segment surrounding the chromophore attachment site in oat phytochrome (Cys-321) generated a folded structure. Cys-321 was located within this structure in a beta-turn at the entrance of a distinct pocket. When attached to this amino acid, a semicircular conformation of the Pr chromophore easily fit within the pocket, with the sidechain carboxyl groups in association with Arg and Lys residues in the peptide backbone. Models of Z and E isomers at the C-4 or C-15 double bonds were generated to produce potential conformations of the Pfr chromophore. Comparison of predicted reactivity of the tetrapyrrole, deduced from the models, with that described in the extensive literature on phytochrome clearly indicated that isomerization at C-4 is consistent with experimental data. Isomerization at C-4 caused the chromphore to move partially out of the pocket and brought the sidechain carboxyl groups and ring D to the surface of the polypeptide. This change in orientation is compatible with the observed interaction of Pfr with metal ions, which possibly is a component in the physiological activity of this protein.

Phytochromes and bacterial sensor proteins are related by structural and functional homologies. Hypothesis on phytochrome-mediated signal-transduction

Phytochrome and bacterial sensor proteins are related by functional and structural homologies. They are both sensors of environmental stimuli and share structural homologies which comprise a domain of about 250 amino acids (about 28 kg.mol-1). This domain is C-terminal in phytochromes and in several bacterial sensor proteins. In both groups of sensors this domain undergoes conformational changes which are caused by the N-terminal part sensing the stimulus. In the case of bacterial sensors, the conformational alteration is, regulated by additional proteins, conferred to a corresponding regulator protein which then acts on transcription. The coincidences between the two groups of sensors are striking enough to assume phytochrome to transduce signals in a way comparable to the bacterial two-component systems.

phyB is evolutionarily conserved and constitutively expressed in rice seedling shoots

Southern blot analysis indicates that the rice genome contains single copies of genes encoding type A (phyA) and type B (phyB) phytochromes. We have isolated overlapping cDNA and genomic clones encoding the entire phyB polypeptide. This monocot sequence is more closely related to phyB from the dicot, Arabidopsis (73% amino acid sequence identity), than it is to the phyA gene in the rice genome (50% identity). These data support the proposal that phyA and phyB subfamilies diverged early in plant evolution and that subsequent divergence accompanied the evolution of monocots and dicots. Moreover, since rice and Arabidopsis phyB polypeptides are more closely related to one another (73% identity) than are monocot and dicot phyA sequences (63-65% identity), it appears that phyB has evolved more slowly than phyA. Sequence conservation between phyA and phyB is greatest in a central core region surrounding the chromophore attachment site, and least toward the amino-terminal and carboxy-terminal ends of the polypeptides, although hydropathy analysis suggests that the overall structure of the two phytochromes has been conserved. Gene-specific Northern blot analysis indicates that, whereas phyA is negatively regulated by phytochrome in rice seedling shoots in the manner typical of monocots, phyB is constitutively expressed irrespective of light treatment. In consequence, phyA and phyB transcripts are equally abundant in fully green tissue. Since Arabidopsis phyB mRNA levels are also unaffected by light, the present results suggest that this mode of regulation is evolutionarily conserved among phyB genes, perhaps reflecting differences in the functional roles of the different phytochrome subfamilies.

A trans-acting factor that binds to a GT-motif in a phytochrome gene promoter

The regulatory photoreceptor, phytochrome, controls the expression of numerous genes, including its own phyA genes, which are transcriptionally repressed in response to light. Functional analysis of a rice phyA gene promoter, by means of microprojectile-mediated gene transfer, indicates that a GT motif, GCGGTAATT, closely related to elements in the promoters of a number of other light-regulated genes, is critical for expression. Partial complementary DNA clones have been obtained for a rice nuclear protein, designated GT-2, that binds in a highly sequence-specific fashion to this motif. Mutational analysis shows that the paired G's are most crucial to binding. GT-2 has domains related to certain other transcription factors. Northern blot analysis shows that GT-2 messenger RNA levels decline in white light although red and far red light pulses are ineffective.

Phytochrome in lower plants. Detection and partial sequence of a phytochrome gene in the moss Ceratodon purpureus using the polymerase chain reaction

The polymerase chain reaction was carried out with primers hybridizing to conserved regions of the phytochrome genes. With DNA from the moss Ceratodon purpureus 5 overlapping fragments were obtained resulting in a continuous nucleotide sequence of 1474 bp. The deduced amino acid sequence showed homology of around 60% with all known phytochrome sequences. The sequences contained a conserved chromophore attachment site. In light-grown Ceratodon protonemata the phytochrome mRNA with the size of about 4.5 kb was detected.

Down-regulation of phytochrome mRNA abundance by red light and benzyladenine in etiolated cucumber cotyledons

Northern blot analysis revealed that a single 4.2 kb phytochrome mRNA species was detectable in cotyledons excised from five-day-old etiolated cucumber seedlings. Intact etiolated five-day-old cucumber seedlings were given a red light or benzyladenine treatment, and cotyledons were harvested at various times following treatment. The abundance of phytochrome mRNA in the cotyledons was quantitated using 32P-labeled RNA probes and slot blot analysis. By 2 h after irradiation the phytochrome mRNA level was reduced to 40% of the initial abundance and reaccumulation began by 3 h after irradiation. Reaccumulation of phytochrome mRNA to the time-zero dark control level was achieved by 10 h after treatment. A decrease in phytochrome mRNA abundance was evident by 2 h after benzyladenine treatment, and a maximal reduction to 45% of the time-zero dark control was attained by 4 h after treatment. No recovery of the phytochrome mRNA level was evident by 8 h after benzyladenine treatment. The abundance of actin mRNA was unaffected by benzyladenine treatment.

Novel phytochrome sequences in Arabidopsis thaliana: structure, evolution, and differential expression of a plant regulatory photoreceptor family

Phytochrome is a plant regulatory photoreceptor that mediates red light effects on a wide variety of physiological and molecular responses. DNA blot analysis indicates that the Arabidopsis thaliana genome contains four to five phytochrome-related gene sequences. We have isolated and sequenced cDNA clones corresponding to three of these genes and have deduced the amino acid sequence of the full-length polypeptide encoded in each case. One of these proteins (phyA) shows 65-80% amino acid sequence identity with the major, etiolated-tissue phytochrome apoproteins described previously in other plant species. The other two polypeptides (phyB and phyC) are unique in that they have low sequence identity (approximately 50%) with each other, with phyA, and with all previously described phytochromes. The phyA, phyB, and phyC proteins are of similar molecular mass, have related hydropathic profiles, and contain a conserved chromophore attachment region. However, the sequence comparison data indicate that the three phy genes diverged early in plant evolution, well before the divergence of the two major groups of angiosperms, the monocots and dicots. The steady-state level of the phyA transcript is high in dark-grown A. thaliana seedlings and is down-regulated by light. In contrast, the phyB and phyC transcripts are present at lower levels and are not strongly light-regulated. These findings indicate that the red/far light-responsive phytochrome photoreceptor system in A. thaliana, and perhaps in all higher plants, consists of a family of chromoproteins that are heterogeneous in structure and regulation.