The rice phytochrome gene: structure, autoregulated expression, and binding of GT-1 to a conserved site in the 5' upstream region

Genome-wide expression analysis of LBD genes in tomato (Solanum lycopersicum L.) under different light conditions

Lateral organ boundaries (LOB) domain (LBD) genes, a gene family that encodes the transcription factors (TFs) of plants, plays crucial functions in the development and growth of plants. Currently, genome-wide studies of the LBD family are still limited to tomato (Solanum lycopersicum L.), which is considered an important economic crop. In this study, we performed a genome-wide analysis of LBD in tomato. In total, 56 LBDs were found in the tomato genome. Protein alignment and phylogenetic classification showed that LBDs were conserved with other species. Since light emitting diodes (LEDs) light have promising applications for tomato growth. To better understand the potential function of LBDs in response to LED light in tomato, we conducted a genome-wide expression analysis of LBD genes under different light conditions. As expected, different LED lights affected the tomato growth (e.g. hypocotyl length). RNA-seq data showed that eight LBDs in tomato seedlings were differentially expressed under different light treatments, including white, blue, red, and far-red light, compared to the dark-grown condition. It indicates that these LBDs might regulate plant development in different LED light conditions. Interestingly, two LBD genes (SlLBD1 and SlLBD2) were found to be differentially expressed in four distinct lights, which might be involved in regulating the plant architecture via a complicated TF network, which can be taken into consideration in further investigation.

Trihelix Transcription Factor ZmThx20 Is Required for Kernel Development in Maize

Maize kernels are the harvested portion of the plant and are related to the yield and quality of maize. The endosperm of maize is a large storage organ that constitutes 80–90% of the dry weight of mature kernels. Maize kernels have long been the study of cereal grain development to increase yield. In this study, a natural mutation that causes abnormal kernel development, and displays a shrunken kernel phenotype, was identified and named “shrunken 2008 (sh2008)”. The starch grains in sh2008 are loose and have a less proteinaceous matrix surrounding them. The total storage protein and the major storage protein zeins are ~70% of that in the wild-type control (WT); in particular, the 19 kDa and 22 kDa α-zeins. Map-based cloning revealed that sh2008 encodes a GT-2 trihelix transcription factor, ZmThx20. Using CRISPR/Cas9, two other alleles with mutated ZmThx20 were found to have the same abnormal kernel. Shrunken kernels can be rescued by overexpressing normal ZmThx20. Comparative transcriptome analysis of the kernels from sh2008 and WT showed that the GO terms of translation, ribosome, and nutrient reservoir activity were enriched in the down-regulated genes (sh2008/WT). In short, these changes can lead to defects in endosperm development and storage reserve filling in seeds.

Effects of Light Quality and Phytochrome Form on Melatonin Biosynthesis in Rice

Light is an important factor influencing melatonin synthesis in response to cadmium treatment in rice. However, the effects of light quality on, and the involvement of phytochrome light receptors in, melatonin production have not been explored. In this study, we used light-emitting diodes (LEDs) to investigate the effect of light wavelength on melatonin synthesis, and the role of phytochromes in light-dependent melatonin induction in rice. Upon cadmium treatment, peak melatonin production was observed under combined red and blue (R + B) light, followed by red (R) and blue light (B). However, both far-red (FR) LED light and dark treatment (D) failed to induce melatonin production. Similarly, rice seedlings grown under the R + B treatment showed the highest melatonin synthesis, followed by those grown under B and R. These findings were consistent with the results of our cadmium treatment experiment. To further confirm the effects of light quality on melatonin synthesis, we employed rice photoreceptor mutants lacking functional phytochrome genes. Melatonin induction was most inhibited in the phytochrome A mutant (phyA) followed by the phyB mutant under R + B treatment, whereas phyB produced the least amount of melatonin under R treatment. These results indicate that PhyB is an R light receptor. Expression analyses of genes involved in melatonin biosynthesis clearly demonstrated that tryptophan decarboxylase (TDC) played a key role in phytochrome-mediated melatonin induction when rice seedlings were challenged with cadmium.

A high-density genetic map constructed using specific length amplified fragment (SLAF) sequencing and QTL mapping of seed-related traits in sesame (Sesamum indicum L.)

BACKGROUND

Sesame (Sesamum indicum L., 2n = 2x = 26) is an important oilseed crop with high oil content but small seed size. To reveal the genetic loci of the quantitative seed-related traits, we constructed a high-density single nucleotide polymorphism (SNP) linkage map of an F₂ population by using specific length amplified fragment (SLAF) technique and determined the quantitative trait loci (QTLs) of seed-related traits for sesame based on the phenotypes of F₃ progeny.

RESULTS

The genetic map comprised 2159 SNP markers distributed on 13 linkage groups (LGs) and was 2128.51 cM in length, with an average distance of 0.99 cM between adjacent markers. QTL mapping revealed 19 major-effect QTLs with the phenotypic effect (R²) more than 10%, i.e., eight QTLs for seed coat color, nine QTLs for seed size, and two QTLs for 1000-seed weight (TSW), using composite interval mapping method. Particularly, LG04 and LG11 contained collocated QTL regions for the seed coat color and seed size traits, respectively, based on their close or identical locations. In total, 155 candidate genes for seed coat color, 22 for seed size traits, and 54 for TSW were screened and analyzed.

CONCLUSIONS

This report presents the first QTL mapping of seed-related traits in sesame using an F₂ population. The results reveal the location of specific markers associated with seed-related traits in sesame and provide the basis for further seed quality traits research.

Identification and in Silico Characterization of GT Factors Involved in Phytohormone and Abiotic Stresses Responses in Brachypodium distachyon

GT factors play critical roles in plant growth and development and in response to various environmental stimuli. Considering the new functions of GT factors on the regulation of plant stress tolerance and seeing as few studies on Brachypodium distachyon were available, we identified GT genes in B. distachyon, and the gene characterizations and phylogenies were systematically analyzed. Thirty-one members of BdGT genes were distributed on all five chromosomes with different densities. All the BdGTs could be divided into five subfamilies, including GT-1, GT-2, GTγ, SH4, and SIP1, based upon their sequence homology. BdGTs exhibited considerably divergent structures among each subfamily according to gene structure and conserved functional domain analysis, but the members within the same subfamily were relatively structure-conserved. Synteny results indicated that a large number of syntenic relationship events existed between rice and B. distachyon. Expression profiles indicated that the expression levels of most of BdGT genes were changed under abiotic stresses and hormone treatments. Moreover, the co-expression network exhibited a complex regulatory network between BdGTs and BdWRKYs as well as that between BdGTs and BdMAPK cascade gene. Results showed that GT factors might play multiple functions in responding to multiple environmental stresses in B. distachyon and participate in both the positive and negative regulation of WRKY- or MAPK-mediated stress response processes. The genome-wide analysis of BdGTs and the co-regulation network under multiple stresses provide valuable information for the further investigation of the functions of BdGTs in response to environment stresses.

Comparison of Trihelix transcription factors between wheat and Brachypodium distachyon at genome-wide

BACKGROUND

Plant Trihelix transcription factors, specifically bind to GT elements and play important roles in plant physiology and development. Wheat is a main cereal crop. Brachypodium distachyon is a close relative of wheat and has been described as a new model species for studying of grass functional genomics. Presently, little is known about wheat and B. distachyon Trihelix genes.

RESULTS

In 51 species, 2387 Trihelix genes were identified, including 80 wheat Trihelix genes and 27 B. distachyon Trihelix genes. Consistent with the results of previous studies, these genes were classified into five subfamilies: GT-1, GT-2, SIP1, GTγ, and SH4. Members of the same subfamily shared similar gene structures and common motifs. Most TaGT and BdGT genes contained many kinds of cis-elements, such as development-, stress-, and phytohormone-related cis-acting elements. Additionally, 21 randomly selected TaGT genes were mainly expressed in the roots and flowers, while the expression of 19 selected BdGT genes was constitutive. These results indicate that the roles of Trihelix genes in wheat and B. distachyon might have diversified during the evolutionary process. The expression of the most selected TaGT and BdGT genes was down-regulated when exposed to low temperatures, NaCl, ABA, and PEG, implying that TaGT and BdGT genes negatively respond to abiotic stress. On the contrary, the expression of some genes was up-regulated under heat stress.

CONCLUSIONS

Trihelix genes exist extensively in plants and have many functions. During the evolutionary process, this gene family expanded and their functions diversified. As a result, the expression pattern and functions of members of the same family might be different. This study lays a foundation for further functional analyses of TaGT and BdGT genes.

Genomic, expressional, protein-protein interactional analysis of Trihelix transcription factor genes in Setaria italia and inference of their evolutionary trajectory

Background

Trihelix transcription factors (TTF) play important roles in plant growth and response to adversity stress. Until now, genome-wide identification and analysis of this gene family in foxtail millet has not been available. Here, we identified TTF genes in the foxtail millet and its grass relatives, and characterized their functional domains.

Results

As to sequence divergence, TTF genes were previously divided into five subfamilies, I-V. We found that Trihelix family members in foxtail millet and other grasses mostly preserved their ancestral chromosomal locations during millions of years’ evolution. Six amino acid sites of the SIP1 subfamily possibly were likely subjected to significant positive selection. Highest expression level was observed in the spica, with the SIP1 subfamily having highest expression level. As to the origination and expansion of the gene family, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Overtime, starting from the subfamily O, certain genes evolved to form subfamilies III and I, and later from subfamily I to develop subfamilies II and V. The oldest gene, Si1g016284, has the most structural changes, and a high expression in different tissues. What’s more interesting is that it may have bridge the interaction with different proteins.

Conclusions

By performing phylogenetic analysis using non-plant species, notably we showed that a subgroup of subfamily IV was the oldest, and therefore was separated to define a new subfamily O. Starting from the subfamily O, certain genes evolved to form other subfamilies. Our work will contribute to understanding the structural and functional innovation of Trihelix transcription factor, and the evolutionary trajectory.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-5051-9) contains supplementary material, which is available to authorized users.

Reducing shade avoidance responses in a cereal crop

Several researchers have hypothesized that shade avoidance behaviour is favoured by natural selection because it increases the fitness of individuals. Shade avoidance can be disadvantageous for crops, however, because it reduces allocation of resources to reproductive yield, increases the risk of lodging and reduces weed suppression. One approach to develop varieties with reduced shade avoidance and enhanced agronomic performance is by inducing mutations followed by phenotypic screening. We treated spring wheat seeds with ethyl methanesulfonate and screened the seedlings repeatedly under green filters for plants showing reduced elongation of the first leaf sheath and second leaf lamina. The shade avoidance responses of five promising mutant lines were further compared to non-mutated plants in a climate chamber experiment with added far-red light. Two of the selected lines displayed significantly reduced elongation under all light treatments while two lines showed reduced elongation only in added far-red light. The most promising mutant line did not differ in height from the non-mutated cultivar in neutral light, but elongated 20.6% less in strong far-red light. This traditional forward approach of screening mutagenized spring wheat produced plants with reduced shade avoidance responses. These mutants may generate new molecular handles to modify the reaction of plants to changes in light spectral distribution in traditional and novel cultivation systems.

Light and Temperature Signalling at the Level of CBF14 Gene Expression in Wheat and Barley

The wheat and barley CBF14 genes have been newly defined as key components of the light quality-dependent regulation of the freezing tolerance by the integration of phytochrome-mediated light and temperature signals. To further investigate the wavelength dependence of light-induced CBF14 expression in cereals, we carried out a detailed study using monochromatic light treatments at an inductive and a non-inductive temperature. Transcript levels of CBF14 gene in winter wheat Cheyenne, winter einkorn G3116 and winter barley Nure genotypes were monitored. We demonstrated that (1) CBF14 is most effectively induced by blue light and (2) provide evidence that this induction does not arise from light-controlled CRY gene expression. (3) We demonstrate that temperature shifts induce CBF14 transcription independent of the light conditions and that (4) the effect of temperature and light treatments are additive. Based on these data, it can be assumed that temperature and light signals are relayed to the level of CBF14 expression via separate signalling routes.

Light-hormone interaction in the red-light-induced suppression of photomorphogenesis in rice seedlings

Red light perceived by the shoot bottom suppresses photomorphogenesis in rice seedlings mediated by phytochrome A. Shoots of these seedlings grown in red light having their shoot bottom exposed were deficient in chlorophyll and accumulated high concentration of trans-zeatin riboside. However, reduced presence of isopentynyl adenosine, dihydrozeatin riboside was observed in shoots of red-light-grown non-green seedlings in comparison to green seedling. The message abundance of cytokinin receptor (OsHK5), transporters (OsENT1, OsENT2), and response regulators (OsRR4, OsRR10) was downregulated in these red-light-grown non-green seedlings. Attenuation of greening process was reversed by application of exogenous cytokinin analogue, benzyladenine, or supplementing red light with blue light. In the same vein, the suppression of gene expression of cytokinin receptor, transporters, and type-A response regulators was reversed in red-light-grown seedlings treated with benzyladenine suggesting that the disarrayed cytokinin (CK) signaling cascade is responsible for non-greening of seedlings grown in red light. The reversal of red-light-induced suppression of photomorphogenesis by blue light and benzyladenine demonstrates the interaction of light and cytokinin signaling cascades in the regulation of photomorphogenesis. Partial reversal of greening process by exogenous application of benzyladenine suggests, apart from CKs perception, transportation and responsiveness, other factors are also involved in modulation of suppression of photomorphogenesis by red light.

Phytochrome B Mediates the Regulation of Chlorophyll Biosynthesis through Transcriptional Regulation of ChlH and GUN4 in Rice Seedlings

Accurate regulation of chlorophyll synthesis is crucial for chloroplast formation during the greening process in angiosperms. In this study, we examined the role of phytochrome B (phyB) in the regulation of chlorophyll synthesis in rice seedlings (Oryza sativa L.) through the characterization of a pale-green phenotype observed in the phyB mutant grown under continuous red light (Rc) irradiation. Our results show that the Rc-induced chlorophyll accumulation can be divided into two components—a phyB-dependent and a phyB-independent component, and that the pale-green phenotype is caused by the absence of the phyB-dependent component. To elucidate the role of the missing component we established an Rc-induced greening experiment, the results of which revealed that several genes encoding proteins on the chlorophyll branch were repressed in the phyB mutant. Notable among them were ChlH and GUN4 genes, which encode subunit H and an activating factor of magnesium chelatase (Mg-chelatase), respectively, that were largely repressed in the mutant. Moreover, the kinetic profiles of chlorophyll precursors suggested that Mg-chelatase activity simultaneously decreased with the reduction in the transcript levels of ChlH and GUN4. These results suggest that phyB mediates the regulation of chlorophyll synthesis through transcriptional regulation of these two genes, whose products exert their action at the branching point of the chlorophyll biosynthesis pathway. Reduction of 5-aminolevulinic acid (5-ALA) synthesis could be detected in the mutant, but the kinetic profiles of chlorophyll precursors indicated that it was an event posterior to the reduction of the Mg-chelatase activity. It means that the repression of 5-ALA synthesis should not be a triggering event for the appearance of the pale-green phenotype. Instead, the repression of 5-ALA synthesis might be important for the subsequent stabilization of the pale-green phenotype for preventing excessive accumulation of hazardous chlorophyll precursors, which is an inevitable consequence of the reduction of Mg-chelatase activity.

The phytochrome gene family in soybean and a dominant negative effect of a soybean PHYA transgene on endogenous Arabidopsis PHYA

KEY MESSAGE

The evolutionary origin of the phytochrome genes in soybean was analyzed. The expression profiles of PHYA paralogs were characterized. The heterologous expression of GmPHYA1 in Arabidopsis resulted in longer hypocotyls. The phytochromes (PHY) are a small family of red/far-red light photoreceptors which regulate a number of important developmental responses in plants. So far, the members of the PHY gene family in soybean (Glycine max) remain unclear and an understanding of each member's physiological functions is limited. Our present in silico analysis revealed that the soybean genome harbors four PHYA, two PHYB and two PHYE, totally four pairs of eight PHY loci. The phylogenetic analysis suggested that the four PHY paralogous pairs originated from the latest round of genome duplication (~13 million years ago) and the four copies of PHYA were remnants of the two rounds of genome duplication (~58 and ~13 million years ago). A possible evolutionary history of PHYA homologs in the three legume species (soybean, Medicago truncatula, and Lotus japonicus) was proposed and the fate of duplicate soybean PHYA genes following polyploidization was discussed. The expression profiles of a soybean PHYA paralogous pair (GmPHYA1 and GmPHYA2) showed that the transcript abundance was highest in the aerial organs of young plants. The physiological role of GmPHYA1 was explored by observing the de-etiolation phenotype of transgenic Arabidopsis plants constitutively expressing GmPHYA1. The GmPHYA1 protein interfered with the function of endogenous PHYA with respect to de-etiolation in a dominant negative manner when exogenously expressed in Arabidopsis. The elucidation of the PHY gene family members in soybean provide us with a general description and understanding of the photoreceptor gene family in this important crop plant.

Overexpression of a phytochrome-regulated tandem zinc finger protein gene, OsTZF1, confers hypersensitivity to ABA and hyposensitivity to red light and far-red light in rice seedlings

Tandem zinc finger proteins (TZFs) in plants are involved in gene regulation, developmental responses, and hormone-mediated environmental responses in Arabidopsis. However, little information about the functions of the TZF family in monocots has been reported. Here, we investigated a cytoplasmic TZF protein, OsTZF1, which is involved in photomorphogenesis and ABA responses in rice seedlings. The OsTZF1 gene was expressed at relatively high levels in leaves and shoots, although its transcripts were detected in various organs. Red light (R)- and far-red light (FR)-mediated repression of OsTZF1 gene expression was attributed to phytochrome B (phyB) and phytochrome C (phyC), respectively. In addition, OsTZF1 expression was regulated by salt, PEG, and ABA. Overexpression of OsTZF1 caused a long leaf sheath relative to wild type (WT) under R and FR, suggesting that OsTZF1 probably acts as a negative regulator of photomorphogenesis in rice seedlings. Moreover, ABA-induced growth inhibition of rice seedlings was marked in the OsTZF1-overexpression lines compared with WT, suggesting the positive regulation of OsTZF1 to ABA responses. Genome-wide expression analysis further revealed that OsTZF1 also functions in other hormone or stress responses. Our findings supply new evidence on the functions of monocot TZF proteins in phytochrome-mediated light and hormone responses.

KEY MESSAGE

OsTZF1 encodes a cytoplasm-localized tandem zinc finger protein and is regulated by both ABA and phytochrome-mediated light signaling. OsTZF1 functions in phytochrome-mediated light and ABA responses in rice.

The gene encoding Arabidopsis acyl-CoA-binding protein 3 is pathogen inducible and subject to circadian regulation

In Arabidopsis thaliana, acyl-CoA-binding protein 3 ( ACBP3), one of six ACBPs, is unique in terms of the C-terminal location of its acyl-CoA-binding domain. It promotes autophagy-mediated leaf senescence and confers resistance to Pseudomonas syringae pv. tomato DC3000. To understand the regulation of ACBP3, a 1.7 kb 5'-flanking region of ACBP3 and its deletion derivatives were characterized using β-glucuronidase (GUS) fusions. A 374 bp minimal fragment (-151/+223) could drive GUS expression while a 1698 bp fragment (-1475/+223) conferred maximal activity. Further, histochemical analysis on transgenic Arabidopsis harbouring the largest (1698 bp) ACBP3pro::GUS fusion displayed ubiquitous expression in floral organs and vegetative tissues (vascular bundles of leaves and stems), consistent with previous results showing that extracellularly localized ACBP3 functions in plant defence. A 160 bp region (-434/-274) induced expression in extended darkness and caused down-regulation in extended light. Electrophoretic mobility shift assay (EMSA) and DNase I footprinting assay showed that the DNA-binding with one finger box (Dof-box, -341/-338) interacted specifically with leaf nuclear proteins from dark-treated Arabidopsis, while GT-1 (-406/-401) binds both dark- and light-treated Arabidopsis, suggesting that Dof and GT-1 motifs are required to mediate circadian regulation of ACBP3. Moreover, GUS staining and fluorometric measurements revealed that a 109 bp region (-543/-434) was responsive to phytohormones and pathogens. An S-box of AT-rich sequence (-516/-512) was identified to bind nuclear proteins from pathogen-infected Arabidopsis leaves, providing the basis for pathogen-inducible regulation of ACBP3 expression. Thus, three cis-responsive elements (Dof, GT-1, and the S-box) in the 5'-flanking region of ACBP3 are proven functional in the regulation of ACBP3.

The trihelix family of transcription factors--light, stress and development

GT factors are the founding members of the trihelix transcription factor family. They bind GT elements in light regulated genes, and their nature was uncovered in a burst of activity in the 1990s. Study of the trihelix family then slowed. However, interest is now re-awakening. Genomic studies have revealed 30 members of this family in Arabidopsis and 31 in rice, falling into five clades. Newly discovered functions involve responses to salt and pathogen stresses, the development of perianth organs, trichomes, stomata and the seed abscission layer, and the regulation of late embryogenesis. Thus the time is ripe for a review of the genomic and functional information now emerging for this neglected family.

Genomic basis for light control of plant development

Light is one of the key environmental signals regulating plant growth and development. Therefore, understanding the mechanisms by which light controls plant development has long been of great interest to plant biologists. Traditional genetic and molecular approaches have successfully identified key regulatory factors in light signaling, but recent genomic studies have revealed massive reprogramming of plant transcriptomes by light, identified binding sites across the entire genome of several pivotal transcription factors in light signaling, and discovered the involvement of epigenetic regulation in light-regulated gene expression. This review summarizes the key genomic work conducted in the last decade which provides new insights into light control of plant development.

Ectopic expression reveals a conserved PHYB homolog in soybean

Phytochromes sense red/far-red light and trigger a cascade of physiological responses in plant. Here, a phytochrome B homolog, GmPHYB1, was amplified from the soybean genome, and its expression profiles were obtained for various parts of the plant and at various developmental stages. The gene was ectopically expressed in Arabidopsis thaliana, driven by CaMV 35S promoter, to study the physiological functions of the gene product. The overexpressors of GmPHYB1 behaved similarly to those of AtPHYB, but with some subtle differences with respect to the acceleration of flowering under short day conditions and the growth of the hypocotyl under certain light fluence rate. The results suggested that this soybean PHYB homolog was well conserved both at the level of sequence and physiological function.

Comprehensive metabolite profiling of phyA phyB phyC triple mutants to reveal their associated metabolic phenotype in rice leaves

The phytochrome photoreceptors regulate plant growth and development throughout their life cycle. Rice (Oryza sativa) possesses three phytochromes, phyA, phyB, and phyC. Physiological, genetic, and biochemical analyses of null mutants of each phytochrome have revealed the function of each in rice. However, few studies have investigated the relationship between phytochrome signaling and metabolism. In the present study, non-targeted metabolite analysis by gas chromatography time-of-flight mass spectrometry (GC/TOF-MS) and targeted metabolite analysis by capillary electrophoresis electrospray ionization mass spectrometry (CE/ESI-MS) were employed to investigate metabolic changes in rice phyA phyB phyC triple mutants. Distinct metabolic profiles between phyA phyB phyC triple mutants and the wild type (WT), as well as those between young and mature leaf blades, could be clearly observed by principal component analysis (PCA). The metabolite profiles indicated high accumulation of amino acids, organic acids, sugars, sugar phosphates, and nucleotides in the leaf blades of phyA phyB phyC triple mutants, especially in the young leaves, compared with those in the WT. Remarkable overaccumulation of monosaccharide, such as glucose (53.4-fold), fructose (42.5-fold), and galactose (24.5-fold), was observed in young leaves of phyA phyB phyC triple mutants. These metabolic phenotypes suggest that sugar metabolism, carbon partitioning, sugar transport, or some combination of these is impaired in the phyA phyB phyC triple mutants, and conversely, that phytochromes have crucial roles in sugar metabolism.

Tissue-specific expression of the PNZIP promoter is mediated by combinatorial interaction of different cis-elements and a novel transcriptional factor

Recent studies demonstrated that PNZIP and its homologs encode a special cyclase and play an important role in chlorophyll biosynthesis in higher plants. To investigate the molecular mechanism governing the PNZIP gene, the PNZIP promoter was isolated and analyzed. Deletion analysis indicated that G-box is an important element in the regulation of the reporter gene expression. Further mutation assay demonstrated that G-box and GATACT elements are necessary and sufficient for the high and tissue-specific expression of the GUS gene. Using yeast one-hybrid screening, we have isolated a novel tobacco bZIP protein, NtbZIP, which can specifically recognize the G-box of the PNZIP promoter. The NtbZIP protein shares a limited amino acid homology to Arabidopsis ABI5 and AtAREB1 and very low homology to other bZIP proteins. Northern blot analysis showed that the NtbZIP gene is not induced by exogenous ABA and is expressed in different tobacco organs. Cotransformation assays showed that the NtbZIP protein could activate the transcription of the GUS gene driven by the PNZIP promoter. Transgenic tobaccos analysis demonstrated that constitutively expressing antisense NtbZIP gene resulted in a lower NTZIP synthesis and reduced chlorophyll levels. We suggest that NTZIP is a target gene of NtbZIP, which is involved in the regulation of chlorophyll biosynthesis.

Conservation and divergence of light-regulated genome expression patterns during seedling development in rice and Arabidopsis

Genome-wide 70-mer oligonucleotide microarrays of rice (Oryza sativa) and Arabidopsis thaliana were used to profile genome expression changes during light-regulated seedling development. We estimate that the expression of approximately 20% of the genome in both rice and Arabidopsis seedlings is regulated by white light. Qualitatively similar expression profiles from seedlings grown under different light qualities were observed in both species; however, a quantitatively weaker effect on genome expression was observed in rice. Most metabolic pathways exhibited qualitatively similar light regulation in both species with a few species-specific differences. Global comparison of expression profiles between rice and Arabidopsis reciprocal best-matched gene pairs revealed a higher correlation of genome expression patterns in constant light than in darkness, suggesting that the genome expression profile of photomorphogenesis is more conserved. Transcription factor gene expression under constant light exposure was poorly conserved between the two species, implying a faster-evolving rate of transcription factor gene expression in light-grown plants. Organ-specific expression profiles during seedling photomorphogenesis provide genome-level evidence for divergent light effects in different higher plant organs. Finally, overrepresentation of specific promoter motifs in root- and leaf-specific light-regulated genes in both species suggests that these cis-elements are important for gene expression responses to light.

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.

The novel MYB protein EARLY-PHYTOCHROME-RESPONSIVE1 is a component of a slave circadian oscillator in Arabidopsis

Using fluorescent differential display, we identified, from approximately 8000 displayed bands, a DNA fragment showing rapid induction in response to red light irradiation. This EARLY-PHYTOCHROME-RESPONSIVE1 gene (EPR1) encodes a novel nucleus-localized MYB protein harboring a single MYB domain that is highly similar to the circadian oscillator proteins CCA1 and LHY. EPR1 is regulated by both phytochrome A and phytochrome B, and the red-light induction of EPR1 is not inhibited by cycloheximide, demonstrating that EPR1 represents a primary phytochrome-responsive gene. Our results show that EPR1 overexpression results in enhanced far-red light-induced cotyledon opening and delayed flowering. In wild-type Arabidopsis plants grown in continuous light, the EPR1 transcript exhibits circadian rhythmicity similar to that of CCA1 and LHY. Moreover, EPR1 suppresses its own expression, suggesting that this protein is part of a regulatory feedback loop. Constitutive expression of CCA1 and LHY results in the loss of EPR1 rhythmicity, whereas increased levels of EPR1 have no effect on the central oscillator. We propose that EPR1 is a component of a slave oscillator that contributes to the refinement of output pathways, ultimately mediating the correct oscillatory behavior of target genes.

Rice PHYC gene: structure, expression, map position and evolution

Although sequences representing members of the phytochrome (phy) family of photoreceptors have been reported in numerous species across the phylogenetic spectrum, relatively few phytochrome genes (PHY) have been fully characterized. Using rice, we have cloned and characterized the first PHYC gene from a monocot. Comparison of genomic and cDNA PHYC sequences shows that the rice PHYC gene contains three introns in the protein-coding region typical of most angiosperm PHY genes, in contrast to Arabidopsis PHYC, which lacks the third intron. Mapping of the transcription start site and 5'-untranslated region of the rice PHYC transcript indicates that it contains an unusually long, intronless, 5'-untranslated leader sequence of 715 bp. PHYC mRNA levels are relatively low compared to PHYA and PHYB mRNAs in rice seedlings, and are similar in dark- and light-treated seedlings, suggesting relatively low constitutive expression. Genomic mapping shows that the PHYA, PHYB, and PHYC genes are all located on chromosome 3 of rice, in synteny with these genes in linkage group C (sometimes referred to as linkage group A) of sorghum. Phylogenetic analysis indicates that rice phyC is closely related to sorghum phyC, but relatively strongly divergent from Arabidopsis phyC, the only full-length dicot phyC sequence available.

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.

EVOLUTION OF LIGHT-REGULATED PLANT PROMOTERS

In this review, we address the phylogenetic and structural relationships between light-responsive promoter regions from a range of plant genes, that could explain both their common dependence on specific photoreceptor-associated transduction pathways and their functional versatility. The well-known multipartite light-responsive elements (LREs) of flowering plants share sequences very similar to motifs in the promoters of orthologous genes from conifers, ferns, and mosses, whose genes are expressed in absence of light. Therefore, composite LREs have apparently evolved from cis-regulatory units involved in other promoter functions, a notion with significant implications to our understanding of the structural and functional organization of angiosperm LREs.

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.

Effects of synergistic signaling by phytochrome A and cryptochrome1 on circadian clock-regulated catalase expression

Persistent oscillation in constant conditions is a defining characteristic of circadian rhythms. However, in plants transferred into extended dark conditions, circadian rhythms in mRNA abundance commonly damp in amplitude over two or three cycles to a steady state level of relatively constant, low mRNA abundance. In Arabidopsis, catalase CAT3 mRNA oscillations damp rapidly in extended dark conditions, but unlike catalase CAT2 and the chlorophyll a/b binding protein gene CAB, in which the circadian oscillations damp to low steady state mRNA abundance, CAT3 mRNA oscillations damp to high steady state levels of mRNA abundance. Mutational disruption of either phytochrome- or cryptochrome-mediated light perception prevents damping of the oscillations in CAT3 mRNA abundance and reveals strong circadian oscillations that persist for multiple cycles in extended dark conditions. Damping of CAT3 mRNA oscillations specifically requires phytochrome A but not phytochrome B and also requires the cryptochrome1 blue light receptor. Therefore, we conclude that synergistic signaling mediated through both phytochrome A and cryptochrome1 is required for damping of circadian CAT3 mRNA oscillations in extended dark conditions.

Light regulated transcription in higher plants

Studies on the function of plant promoters have demonstrated the presence of regulatorycis-acting elements that mediate developmental or environmental signals. Analysis of many light-responsive genes showed thatcis-acting elements responsible for light regulated transcription are located within the 5' upstream region. Numerous light responsivecis-acting elements andtrans-acting factors have been identified and characterized. The present article reviews the recent advances in studies of light regulated transcriptional regulation and signal transduction.

Combinatorial interplay of promoter elements constitutes the minimal determinants for light and developmental control of gene expression in Arabidopsis

Higher plants are able to integrate environmental and endogenous signals to regulate gene expression for optimal development. To define the minimal sequence requirement sufficient to integrate light and developmental signals in controlling promoter activity, we carried out a systematic analysis of the roles of four well-conserved 'light-responsive elements (LREs)' common to many nuclear-encoded photosynthetic genes. A gain-of-function assay using basal promoter-reporter fusions in stable transgenic Arabidopsis was employed to demonstrate that pairwise combinations of the LREs, but not the individual elements alone, can confer light-inducible expression to the reporter gene independently of the basal promoter context and the light-triggered morphological changes. The activity of the synthetic promoters with the paired LREs can be modulated at least by the phytochrome system. Further, those synthetic light-regulated promoters confer a photosynthetic cell-specific expression pattern and respond to the chloroplast development state. Our data suggest that distinct combinatorial interactions of LREs can serve as minimal autonomous promoter determinants which integrate light and developmental signals and modulate promoter activity.

The PR-1a promoter contains a number of elements that bind GT-1-like nuclear factors with different affinity

The 900 bp promoter region of the tobacco PR-1a gene was divided into eight fragments using PCR. The fragments were tested for their ability to bind to nuclear factors isolated from tobacco leaf. Band shift assays demonstrated that all but one of the fragments specifically interacted with nuclear proteins. From competition experiments it was determined that the same nuclear factors bind various promoter fragments with different affinity. Moreover, efficient competition with a synthetic tetramer of box II of the rbcS promoter indicated that GT-1-like nuclear factors are involved in these interactions. Furthermore, in comparison to extracts from untreated plants, nuclear protein preparations from tobacco mosaic virus-infected tobacco showed a reduced GT-1 binding activity. These results will be discussed in relation to induced PR-1a gene expression.

Light suppresses 3-Hydroxy-3-methylglutaryl coenzyme A reductase gene expression in Arabidopsis thaliana

3-Hydroxy-3-methylglutaryl (HMG) coenzyme A reductase mRNA accumulates preferentially in dark-grown Arabidopsis plants. As one step toward understanding the role that light plays in the regulation of the mevalonate pathway in plants, we characterized the suppression of HMG1 gene expression in response to illumination wavelength, duration, and fluence rate. The accumulation of HMG1 mRNA by dark treatment is suppressed by continuous exposure to white light and is dependent on the amount of light perceived during the period of illumination. By using promoter/reporter gene fusions we also demonstrate that this reaction is mediated by cis-acting elements that reside in the Arabidopsis HMG1 promoter and, therefore, is likely to be controlled at the transcriptional level. HMG1 expression is differentially responsive to continuous blue and red light but not to far-red light. In contrast, changes in HMG1 mRNA levels were not observed in response to brief light pulses of any spectrum, suggesting that continuous illumination is required for sustained and maximal suppression of HMG coenzyme A reductase expression. Taken together, these data indicate that light-mediated control of the HMG1 gene is mediated by a regulatory circuit that monitors aspects of both spectral quality and fluence and involves either multiple photoreceptors or a single photoreceptor that is differentially sensitive to both blue and red light.

Expression of functional oat phytochrome A in transgenic rice

To investigate the biological functions of phytochromes in monocots, we generated, by electric discharge particle bombardment, transgenic rice (Oryza sativa cv Gulfmont) that constitutively expresses the oat phytochrome A apoprotein. The introduced 124-kD polypeptide bound chromophore and assembled into a red- and far-red-light-photoreversible chromoprotein with absorbance spectra indistinguishable from those of phytochrome purified from etiolated oats. Transgenic lines expressed up to 3 and 4 times more spectrophotometrically detectable phytochrome than wild-type plants in etiolated and green seedlings, respectively. Upon photo-conversion to the far-red-absorbing form of phytochrome, oat phytochrome A was degraded in etiolated seedlings with kinetics similar to those of endogenous rice phytochromes (half-life approximately 20 min). Although plants overexpressing phytochrome A were phenotypically indistinguishable from wild-type plants when grown under high-fluence white light, they were more sensitive as etiolated seedlings to light pulses that established very low phytochrome equilibria. This indicates that the introduced oat phytochrome A was biologically active. Thus, rice ectopically expressing PHY genes may offer a useful model to help understand the physiological functions of the various phytochrome isoforms in monocotyledonous plants.

Tissue-specific and light-responsive regulation of the promoter region of the Arabidopsis thaliana chloroplast omega-3 fatty acid desaturase gene (FAD7)

The Arabidopsis FAD7 gene encodes a chloroplast omega-3 fatty acid desaturase that catalyzes the desaturation of lipid-linked dienoic fatty acids (18:2 and 16:2). An 825 bp FAD7 promoter fragment upstream from the transcriptional start point contained several short sequences which were homologous to the cis-elements (box II, G-box, etc.) conserved in many light-responsive genes. We introduced the FAD7 promoter fused to the beta-glucuronidase (GUS) or the luciferase (LUC) reporter gene into tobacco plants. The -825 promoter sequence conferred tissue-specific and light-responsive expression to both these reporter genes in transgenic tobacco, indicating that these expressions of the FAD7 gene were regulated mainly at the transcriptional level. Histochemical GUS staining showed that the activity of the FAD7 promoter is restricted to the tissues with chloroplast-containing cells although the staining was noticeably absent in the chloroplast-containing cells associated with vascular systems. The 5' deletion experiments of the promoter revealed that the -362/-166 region, containing two putative box II sequences, was responsible for the tissue-specific and light-responsive expression of the FAD7 gene.

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.

Identification of NADPH:protochlorophyllide oxidoreductases A and B: a branched pathway for light-dependent chlorophyll biosynthesis in Arabidopsis thaliana

Illumination releases the arrest in chlorophyll (Chl) biosynthesis in etiolated angiosperm seedlings through the enzymatic photoreduction of protochlorophyllide (Pchlide) to chlorophyllide (Chlide), the first light-dependent step in chloroplast biogenesis. NADPH: Pchlide oxidoreductase (POR, EC 1.3.1.33), a nuclear-encoded plastid-localized enzyme, mediates this unique photoreduction. Paradoxically, light also triggers a drastic decrease in the amounts of POR activity and protein before the Chl accumulation rate reaches its maximum during greening. While investigating this seeming contradiction, we identified two distinct Arabidopsis thaliana genes encoding POR, in contrast to previous reports of only one gene in angiosperms. The genes, designated PorA and PorB, by analogy to the principal members of the phytochrome photoreceptor gene family, display dramatically different patterns of light and developmental regulation. PorA mRNA disappears within the first 4 h of greening, whereas PorB mRNA persists even after 16 h of illumination, mirroring the behavior of two distinct POR protein species. Experiments designed to help define the functions of POR A and POR B demonstrate exclusive expression of PorA in young seedlings and of PorB both in seedlings and in adult plants. Accordingly, we propose the existence of a branched light-dependent Chl biosynthesis pathway in which POR A performs a specialized function restricted to the initial stages of greening and POR B maintains Chl levels throughout angiosperm development.

Transgenic analysis of the 5'- and 3'-flanking regions of the NADH-dependent hydroxypyruvate reductase gene from Cucumis sativus L

The 5'- and 3'-flanking regions of HPRA, a cucumber gene that encodes hydroxypyruvate reductase, were evaluated for regulatory activity with respect to light responsiveness and organ specificity. To define the functional regions of the 5'-flanking region of HPRA, a series of deletions was generated and the remaining portions fused to the beta-glucuronidase (GUS) reporter gene (uidA) containing a minimal 35S promoter truncated at -90. The region from -66 to +39 was found to be necessary for light-regulated expression of the uidA reporter gene, while the region from -382 to -67 was found to be necessary for its leaf-specific expression. Further deletion of the HPRA 5' flanking region to -590 resulted in high levels of root expression, suggesting the presence of a negative regulatory element responsible for silencing root expression of the HPRA gene between -590 and -383. The 3'-flanking region of the HPRA gene downstream of the polyadenylation site contains several sequence motifs resembling regulatory elements present in the promoters of several light-responsive genes. An 823 bp portion of the HPRA 3'-flanking region containing these putative regulatory elements enhanced GUS expression in leaves when placed downstream of the uidA reporter gene in the forward orientation, but not in the reverse orientation. When placed 5' of the -90 35S promoter, the 823 bp fragment enhanced slightly, independently of orientation, the root tip-specific expression pattern intrinsic to the -90 35S promoter, indicating that in some cases this region can act as a transcriptional enhancer.

Domain analysis of the plant DNA-binding protein GT1a: requirement of four putative alpha-helices for DNA binding and identification of a novel oligomerization region

Light is an important environmental signal that can influence diverse developmental processes in plants. Many plant nuclear genes respond to light at the level of transcription initiation. GT-1 and GT2 are nuclear factors which interact with DNA sequences in many light-responsive gene promoters. cDNA clones which encode proteins with sequence binding specificities similar to those of these two factors have been isolated. They show significant amino acid sequence similarities within three closely spaced, putative alpha-helices that were predicted by secondary structure analysis but do not show significant homologies with any other reported DNA-binding protein. In this work, N- and C-terminal deletions of tobacco GT1a were generated by in vitro transcription and translation, and their DNA-binding activities and subunit structures were studied. The results suggest that the C-terminal domain of GT1a is critical for protein oligomerization, while a region predicted to contain four closely spaced alpha-helices is required for DNA binding. Direct chemical cross-linking and gel filtration analyses of full-length and truncated derivatives of GT1a suggest that this factor can exist in solution as a homotetramer and that oligomerization is independent of DNA binding. This study thus establishes two independent functional domains in this class of eukaryotic trans-acting factors. Possible implications of the multimeric nature of GT1a in relation to the known characteristics of light-responsive promoter architecture are discussed.

Phytochrome-Mediated Light Regulation of PHYA- and PHYB-GUS Transgenes in Arabidopsis thaliana Seedlings

Phytochrome wild-type gene-[beta]-glucuronidase (PHY-GUS) gene fusions were used in transgenic Arabidopsis to compare the activity levels and light regulation of the PHYA and PHYB promoters and to identify the photoreceptors mediating this regulation. In dark-grown seedlings, both promoters are 4-fold more active in shoots than in roots,but the PHYA promoter is nearly 20-fold more active than that of PHYB in both organs. In shoots, white light represses the activities of the PHYA and PHYB promoters 10- and 2-fold, respectively, whereas in roots light has no effect on the PHYA promoter but increases PHYB promoter activity 2-fold. Consequently, PHYA promoter activity remains higher than that of PHYB in light in both shoots (5-fold) and roots (11-fold). Experiments with narrow-waveband light and photomorphogenic mutants suggest that no single photoreceptor is necessary for full white-light-directed PHYA repression in shoots, but that multiple, independent photoreceptor pathways are sufficient alone or in combination. In contrast, phytochrome B appears both necessary and sufficient for a light-mediated decrease in PHYB activity in shoots, and phytochrome A mediates a far-red-light-stimulated increase in PHYB promoter activity. Together, the data indicate that the PHYA and PHYB genes are regulated in divergent fashion at the transcriptional level, both developmentally and by the spectral distribution of the prevailing light, and that this regulation may be important to the photosensory function of the two photoreceptors.

Metabolic regulation of the gene encoding glutamine-dependent asparagine synthetase in Arabidopsis thaliana

Here, we characterize a cDNA encoding a glutamine-dependent asparagine synthetase (ASN1) from Arabidopsis thaliana and assess the effects of metabolic regulation on ASN1 mRNA levels. Sequence analysis shows that the predicted ASN1 peptide contains a purF-type glutamine-binding domain. Southern blot experiments and cDNA clone analysis suggest that ASN1 is the only gene encoding glutamine-dependent asparagine synthetase in A. thaliana. The ASN1 gene is expressed predominantly in shoot tissues, where light has a negative effect on its mRNA accumulation. This negative effect of light on ASN1 mRNA levels was shown to be mediated, at least in part, via the photoreceptor phytochrome. We also investigated whether light-induced changes in nitrogen to carbon ratios might exert a metabolic regulation of the ASN1 mRNA accumulation. These experiments demonstrated that the accumulation of ASN1 mRNA in dark-grown plants is strongly repressed by the presence of exogenous sucrose. Moreover, this sucrose repression of ASN1 expression can be partially rescued by supplementation with exogenous amino acids such as asparagine, glutamine, and glutamate. These findings suggest that the expression of the ASN1 gene is under the metabolic control of the nitrogen to carbon ratio in cells. This is consistent with the fact that asparagine, synthesized by the ASN1 gene product, is a favored compound for nitrogen storage and nitrogen transport in dark-grown plants. We have put forth a working model suggesting that when nitrogen to carbon ratios are high, the gene product of ASN1 functions to re-direct the flow of nitrogen into asparagine, which acts as a shunt for storage and/or long-distance transport of nitrogen.

Saturated molecular map of the rice genome based on an interspecific backcross population

A molecular map has been constructed for the rice genome comprised of 726 markers (mainly restriction fragment length polymorphisms; RFLPs). The mapping population was derived from a backcross between cultivated rice, Oryza sativa, and its wild African relative, Oryza longistaminata. The very high level of polymorphism between these species, combined with the use of polymerase chain reaction-amplified cDNA libraries, contributed to mapping efficiency. A subset of the probes used in this study was previously used to construct an RFLP map derived from an inter subspecific cross, providing a basis for comparison of the two maps and of the relative mapping efficiencies in the two crosses. In addition to the previously described PstI genomic rice library, three cDNA libraries from rice (Oryza), oat (Avena) and barley (Hordeum) were used in this mapping project. Levels of polymorphism detected by each and the frequency of identifying heterologous sequences for use in rice mapping are discussed. Though strong reproductive barriers isolate O. sativa from O. longistaminata, the percentage of markers showing distorted segregation in this backcross population was not significantly different than that observed in an intraspecific F2 population previously used for mapping. The map contains 1491 cM with an average interval size of 4.0 cM on the framework map, and 2.0 cM overall. A total of 238 markers from the previously described PstI genomic rice library, 250 markers from a cDNA library of rice (Oryza), 112 cDNA markers from oat (Avena), and 20 cDNA markers from a barley (Hordeum) library, two genomic clones from maize (Zea), 11 microsatellite markers, three telomere markers, eleven isozymes, 26 cloned genes, six RAPD, and 47 mutant phenotypes were used in this mapping project. Applications of a molecular map for plant improvement are discussed.

Molecular dissection of GT-1 from Arabidopsis

We isolated and characterized an Arabidopsis cDNA encoding the DNA binding protein GT-1. This protein factor, which contains 406 amino acids, is highly homologous to the previously described tobacco DNA binding protein GT-1a/B2F but is 26 amino acids longer. Recombinant Arabidopsis GT-1, which was obtained from in vitro translation, bound to probes consisting of four copies of pea small subunit of ribulose bisphosphate carboxylase rbcS-3A box II and required the same GGTTAA core binding site as the binding activity of an Arabidopsis nuclear protein preparation. However, unlike the truncated tobacco GT-1a prepared from Escherichia coli extracts, the full-length Arabidopsis GT-1 bound to pea rbcS-3A box III and Arabidopsis chlorophyll a/b binding protein CAB2 light-responsive elements, both of which contain GATA motifs. Deletion and mutational analyses suggested that the predicted trihelix region of GT-1 is essential for DNA binding. Moreover, GT-1 binds to target DNA as a dimer, and its C-terminal region contains a putative dimerization domain that enhances the binding activity. Transient expression of the GT-1::beta-glucuronidase fusion protein in onion cells revealed the presence of a nuclear localization signal(s) within the first 215 amino acids of GT-1.

Identification of potential regulatory elements in the far-upstream region of the Arabidopsis thaliana plastocyanin promoter

The far-upstream region of the Arabidopsis thaliana plastocyanin (Pc) promoter acts positively on transcription. This -1580 to -710 region (relative to the translation start site) has enhancer-like properties since it is also functional when situated downstream of the gene. Using tobacco nuclear extracts, this region was tested for protein-binding sites. Two short binding sequences were identified. The AT-rich sequence separating these binding sites shows extensive homology to the sequences separating the paired GT-1-binding sites of the pea rbcS-3A promoter. The requirements for complex formation strongly suggest that a GT-1-like protein binds to the two identified boxes in the Pc promoter. Sequence comparisons revealed that both boxes fit within the moderate consensus sequence needed for GT-1-binding. This GT-1-like DNA-binding activity is present in light-grown as well as in dark-adapted plants. Therefore, the possible role for GT-1 in light regulation of transcription does not depend upon its de novo synthesis. In some of the gel mobility shift assays, an additional DNA-protein complex was formed. The formation of this complex was only observed if the heteropolymer poly(dAdT).poly(dAdT) was used as a non-specific competitor and was dependent on the CpG density of the probe used.

Comparative analysis of microsatellite DNA polymorphism in landraces and cultivars of rice

Genetic polymorphisms of ten microsatellite DNA loci were examined among 238 accessions of landraces and cultivars that represent a significant portion of the distribution range for both indica and japonica groups of cultivated rice. In all, 93 alleles were identified with these ten markers. The number of alleles varied from a low of 3 or 4 at each of four loci, to an intermediate value of 9-14 at five loci, and to an extraordinarily high 25 at one locus. The numbers of alleles per locus are much larger than those detected using other types of markers. The number of alleles detected at a locus is significantly correlated with the number of simple sequence repeats in the targeted microsatellite DNA. Indica rice has about 14% more alleles than japonica rice, and such allele number differences are more pronounced in landraces than in cultivars. The indica-japonica differentiation component accounted for about 10% of the diversity in the total sample, and twice as much differentiation was detected in cultivars as in landraces. About two-thirds as many alleles were observed in cultivars as in landraces; another two-thirds of the alleles in the cultivar group were found in modern elite cultivars or parents of hybrid rice. The majority of the simple sequence repeat (SSR) alleles that were present in high or intermediate frequencies in landraces ultimately survived into modern elite cultivars and hybrids. The greater resolving power and the efficient production of massive amounts of SSR data may be particularly useful for germplasm assessment and evolutionary studies of crop plants.

Transcribed repetitive DNA sequences in telomeric regions of rice (Oryza sativa)

We have isolated and characterized from rice three repetitive DNA sequences, Os48, Osc-567, and OsG3-430. Our results indicate that these repetitive sequences are highly transcribed, and transcripts complementary to both strands of the Os48 family of sequences account for up to 3% of the total cellular RNA. Pulsed-field gel electrophoresis, restriction mapping, and DNA sequence analyses have revealed a complex pattern of structural organization of the three families of repetitive sequences. Os48 and Osc-567 are organized in long tandem arrays, whereas copies of the OsG3-340 sequence are interspersed with other sequences including arrays of the Os48 and Osc567 families. Interestingly, the three families of repetitive sequences are closely linked not only to each other, but also to telomeric sequences of rice, suggesting that transcription of these repetitive sequences may occur in regions very close to telomeres in rice.

Transcriptional photoregulation of cell-type-preferred expression of maize rbcS-m3: 3' and 5' sequences are involved

In the C4 plant maize, members of the rbcS gene family, encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase, are not expressed in mesophyll cells (MC) but are expressed strongly in the adjacent bundle sheath cells (BSC). Expression of genes in an in situ transient expression assay indicates that the photostimulated expression seen in BSC during the first 24 h that leaves of dark-grown seedlings are illuminated requires rbcS-m3 sequences lying between -211 bp and +434 bp of the transcription start site. Photoregulated partial suppression of rbcS-m3 expression in MC, on the other hand, requires gene sequences that lie between -907 bp and -445 bp together with sequences that lie between +720 and +957 bp within the 3' transcribed region of the gene. Suppression in MC occurs during the second 24-h period that dark-grown seedlings have been illuminated, but not during the first 24 h. The 3' +720- to +957-bp region is also effective in lowering MC expression when it is relocated to a position > 2 kbp upstream of the transcription start site. Thus, suppression of rbcS-m3 expression in MC has, at the least, a substantial transcriptional component. As reported earlier, a converse pattern of suppression in BSC and stimulation of expression in MC is seen in the control of cab-m1 in maize leaves.

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.

Promoters from genes for plastid proteins possess regions with different sensitivities toward red and blue light

The light-regulated expression of eight nuclear-encoded genes for plastid proteins from spinach (Spinacia oleracea) (RBCS-1 and CAB-1; ATPC and ATPD, encoding the subunits gamma and delta of the ATP synthase; PC and FNR; PSAD and PSAF, encoding the subunits II and III of photosystem I reaction center) was analyzed with promoter/beta-glucuronidase (GUS) gene fusions in transgenic tobacco (Nicotiana tabacum and Nicotiana plumbaginifolia) seedlings and mature plants under standardized light and growth conditions. Unique response patterns were found for each of these promoters. GUS activities differed more than 30-fold. Strong promoters were found for the PC and PSAD genes. On the other hand, the ATPC promoter was relatively weak. Expression of the CAB/GUS gene fusion in etiolated material was at the detection limit; all other chimeric genes were expressed in the dark as well. Light stimulation of GUS activities ranged from 3- (FNR promoter) to more than 100-fold (CAB-1 promoter). The FNR promoter responded only to red light (RL) and not significantly to blue light (BL), whereas the PC promoter contained regions with different sensitivities toward RL and BL. Furthermore, different RNA accumulation kinetics were observed for the PSAF, CAB, FNR, and PC promoter/GUS gene fusions during de-etiolation, which, at least in the case of the PSAF gene, differed from the regulation of the corresponding endogenous genes in spinach and tobacco. The results suggest either that not all cis elements determining light-regulated and quantitative expression are present on the spinach promoter fragments used or that the spinach cis-regulatory elements respond differently to the host (tobacco) regulatory pathway(s). Furthermore, as in tobacco, but not in spinach, the trans-gene hardly responds to single light pulses that operate through phytochrome. Taken together, the results suggest that the genes have been independently translocated from the organelle to the nucleus during phylogeny. Furthermore, each gene seems to have acquired a unique set of regulatory elements.

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.