Phytochrome regulation of nuclear gene expression

Light regulated modulation of Z-box containing promoters by photoreceptors and downstream regulatory components, COP1 and HY5, in Arabidopsis

The Z-box is one of the light-responsive elements (LREs) found in the promoters of light inducible genes. We have studied the light responsive characteristics of Z-box containing synthetic as well as native promoters. We show that promoters with Z-box as a single LRE or paired with another LRE can respond to a broad spectrum of light. The response is primarily mediated by phyA, phyB and CRY1 photoreceptors at their respective wavelengths of light. We have demonstrated that CAB1 and Z-GATA containing promoters are down-regulated in hy5 mutants in the light. On the other hand, a promoter with Z-box alone is down-regulated in hy5 mutants both in dark and in light conditions, suggesting involvement of a similar regulatory system in the regulation of the promoter in two distinct developmental pathways: skotomorphogenesis and photomorphogenesis. Furthermore, similar to the CAB1 promoter, a Z-GATA containing promoter is derepressed in cop1 mutants in the dark. DNA-protein interaction studies reveal the presence of a DNA-binding activity that is specific to Z-box. These results provide insights into the regulation of the Z-box LRE mediated by various light signaling components.

Identification by large-scale screening of phytochrome-regulated genes in etiolated seedlings of Arabidopsis using a fluorescent differential display technique

Phytochrome A (PhyA)-regulated genes in 6-d-old etiolated seedlings of Arabidopsis Landsberg erecta were identified by fluorescent differential display. To screen for PhyA-regulated genes, mRNA fingerprints of the wild type and the phyA-201 mutant were compared from samples prepared 4 h after far-red light irradiation. Approximately 30,000 bands of cDNA were displayed by fluorescent differential display, and 24 differentially expressed bands were observed. Sequence analysis revealed that they represent 20 distinct genes. Among them, 15 genes were confirmed as PhyA regulated by northern-blot (or reverse transcription-polymerase chain reaction) analysis. Thirteen up-regulated genes included 12 known genes that encode nine photosynthetic proteins, two enzymes involved in the biosynthesis of chlorophyll, one DNA damage repair/toleration-related protein, and one unknown gene. Two down-regulated genes were identified as encoding a xyloglucan endotransglycosylase-related protein and a novel member of the ASK protein kinase family. In the phyA-201 mutant and the phyA-201phyB-1 double mutant, expression of all of these genes was photoreversibly up- or down-regulated by type II phytochromes. The results indicate that modes of photoperception differ between PhyA and PhyB, but that both types of phytochromes have overlapping effects on the photoregulation of gene expression.

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.

Combinatorial interaction of light-responsive elements plays a critical role in determining the response characteristics of light-regulated promoters in Arabidopsis

We have studied the roles of PhyA, PhyB and CRY1 photoreceptors and the downstream light-signaling components, COP1 and DET1, in mediating high-irradiance light-controlled activity of promoters containing synthetic light-responsive elements (LRE). Promoters with paired LREs were able to respond to a wide spectrum of light through multiple photoreceptors, while the light-inducible single LRE promoters primarily responded to a specific wavelength of light. In addition, our results indicate that Cry1 is involved in PhyB-mediated red-light induction of the G-GATA/NOS101 promoter, and that both Cry1 and PhyB are required for effective repression of the GT1/NOS101 promoter by red or blue light. An interaction between PhyA and PhyB in mediating GT1-GATA/NOS101 promoter light activation was also observed. Furthermore, our data indicate that COP1 and DET1 exert negative control in the dark only on paired LRE promoters but not single LRE promoters. From these results, we conclude that the combinatorial interaction of LREs is essential in determining the ability of light-responsive promoters to be modulated by crucial cellular regulators and to respond to diverse light environments.

Phosphorylation/dephosphorylation steps are key events in the phytochrome-mediated enhancement of nitrate reductase mRNA levels and enzyme activity in maize

We provide evidence to show that the increase in nitrate reductase (NR) transcript level stimulated by red light is mediated via a phosphorylation-dependent step. The light-stimulated enhancement of NR transcript level was significantly inhibited by H-7, a protein kinase inhibitor, whereas okadaic acid (OKA), a phosphatase inhibitor, had no effect. Phorbol myristate acetate (PMA), an activator of protein kinase C (PKC) enhanced the NR transcript level in dark-grown leaves. No correlation between changes in NR transcript level and NR activity (NRA) was observed. Inhibition of NRA by OKA and stimulation by H-7 indicated that NRA is increased by dephosphorylating the enzyme. We have identified a protein kinase (C type) that can phosphorylate the purified NR in vitro without the involvement of other accessory proteins. By in vivo labelling with 32P and immunoprecipitation of NR with NR antibodies it was found that in the presence of OKA most NR protein (NRP) was present in phosphorylated state, while with H-7 the reverse was seen. The red (R) and far-red (FR) light reversible experiments suggested that phytochrome (Pfr, an active form) stimulation of NRA is mediated by dephosphorylation of the enzyme, suggesting that Pfr regulates both NR transcription and NRA via phosphorylation/dephosphorylation steps controlled by separate signal transduction pathways.

Regulation of nitrate and nitrite reductase expression in Nicotiana plumbaginifolia leaves by nitrogen and carbon metabolites

Nitrate (NR) and nitrite reductase (NiR) catalyse the reduction of nitrate to ammonium. The regulation of NR and NiR gene expression by carbohydrates (C) and nitrogen (N) metabolites was studied using detached leaves. In the dark, glucose fructose and sucrose supplied to detached green leaves of dark-adapted Nicotiana plumbaginifolia plants resulted in NR mRNA and protein accumulation and the loss of circadian rhythmicity in the size of the transcript pool. The characterization of transgenic plants expressing either a NR cDNA controlled by the 35S CaMV promoter or a transcriptional fusion between the tobacco nia1 (NR structural gene) promoter and the beta-glucuronidase reporter gene, led us to conclude that C metabolite control is taking place at the transcriptional level. Under low light conditions (limiting photosynthetic conditions), the supply of glutamine or glutamate resulted in a drop in the level of NR mRNA. Exogenously supplied carbohydrates partially antagonized this inhibitory effect suggesting that the availability of N and C metabolites affects the expression of the NR gene. The effects of carbohydrates and glutamine on NiR expression were also studied. NiR mRNA levels in the dark were relatively insensitive to feeding with glucose. Glutamate and glutamine were less efficient at decreasing NiR mRNA than NR mRNA levels. In contrast to NR, NiR mRNA levels were significantly increased by light treatments, indicating that NiR display regulatory characteristics reminiscent of photosynthetic genes such as the small subunit of ribulose bisphosphate carboxylase than to NR.

In vivo analysis of plant RNA structure: soybean 18S ribosomal and ribulose-1,5-bisphosphate carboxylase small subunit RNAs

A method to investigate the structure of RNA molecules within intact plant tissues has been developed. The RNA structures are analyzed using dimethyl sulfate (DMS), which modifies substituents of adenine and cytosine residues within single-stranded regions of RNA molecules. Reactive sites are identified by primer extension analysis. Using this procedure, an analysis of the secondary structure of the cytoplasmic 18S ribosomal RNA in soybean seedling leaves has been completed. DMS modification data are in good agreement with the phylogenetic structure predicted for soybean 18S rRNA. However, there are a few notable exceptions where residues thought to be involved in double-stranded regions in all 18S rRNAs are strongly modified in soybean leaf samples. These data taken together with the phylogenetic structure suggest that alternate structures may exist in vivo. The further applicability of this technique is demonstrated by comparing the modification pattern obtained in vivo to that obtained in vitro for a particular mRNA molecule encoding the small subunit of ribulose-1,5-bisphosphate carboxylase. The results obtained are compared to a predicted minimum energy secondary structure. The data indicate that the conformation of RNA molecules within the cell may not be reflected in a structural analysis of purified mRNA molecules.

Control of cab gene expression in synchronized Chlamydomonas reinhardtii cells

In light-dark synchronized Chlamydomonas reinhardtii cultures transcripts of at least two members of the cab gene family coding for chlorophyll a/b binding proteins are highly abundant in the light, but almost undetectable in the dark. "Run-on" transcription assays in isolated nuclei were used to show that the rapid increase in cab mRNA levels during the light phase is primarily due to regulation at the transcriptional level. Functionally unrelated inhibitors such as dipyridyl and cycloheximide as well as anaerobic conditions block chlorophyll synthesis, presumably by interfering with the conversion of magnesium protoporphyrin monomethyl ester to protochlorophyllide. Under these conditions, cab mRNA does not accumulate and nuclei isolated from inhibitor-treated cells do not support cab gene transcription. Inhibitors such as dioxoheptanoic acid and diphenyl ether herbicides block earlier steps within the chlorophyll synthesis pathway without substantial effects on cab mRNA accumulation and transcription. A possible control of transcription by intermediates of the chlorophyll biosynthesis pathway is discussed.

Light is required for conidiation in Aspergillus nidulans

Light is necessary for asexual sporulation in Aspergillus nidulans but will elicit conidiation only if irradiation occurs during a critical period of development. We show that conidiation is induced by red light and suppressed by an immediate shift to far red light. Conidiation-specific gene functions switch from light-independent to light-dependent activities coincident with the expression of brlA, a regulator of conidiophore development. We also show that light dependence is abolished by a mutation in the velvet gene, which allows conidiation to occur in the absence of light. We propose that the initiation of late gene expression is regulated by velvet and controlled by a red light photoreceptor, whose properties are reminiscent of phytochrome-mediated responses observed in higher plants.

Phytochrome-regulated expression of genes encoding light-harvesting chlorophyll a/b-protein in two long hypocotyl mutants and wild type plants of Arabidopsis thaliana

The cab genes which encode the light-harvesting chlorophyll a/b-protein (LHCP) are expressed normally with respect to phytochrome regulation in the hy-3 and hy-5 long hypocotyl mutants of Arabidopsis thaliana. In etiolated seedlings of these mutants as well as of the wild type, 1 min of red light elevates cab mRNA levels substantially within 2 h; this increase is reversed if far-red light is given immediately after the red light treatment. We conclude that the genetic defects in these mutants do not affect steps in the signal transduction pathway leading to the regulated expression of cab genes. Additionally, the mRNA from one of the three known A. thaliana cab genes, AB140, is similar in quantity to the mRNAs from the other two, AB165 and AB180, in dark-grown seedlings of hy-3 and hy-5 as well as the parent A. thaliana (Landsberg) after a brief red light treatment. This aspect of cab gene expression differs from the strain Columbia of A. thaliana in which AB140 mRNA is the predominant message. In mature white light-grown plants of the strain Columbia, AB140 as well as a combination of AB165 and AB180 mRNAs are expressed at high levels, suggesting that AB165 and/or AB180 may be developmentally regulated.

Photoreceptors controlling transcription of rbcS genes in green leaf tissue of Pisum sativum

We have investigated the photoreceptors controlling transcription of genes encoding the small subunit (rbcS) of ribulose 1,5-bisphosphate carboxylase-oxygenase in green leaf tissue of pea (Pisum sativum). RbcS transcription was measured by hybridising labelled transcripts of isolated nuclei to rbcS cDNA clones. Transfer of green Pisum leaf tissue to darkness for 5 h causes a substantial decrease in the rate of rbcS transcription and the rate is restored rapidly when the plants are returned to white light. Low fluence rates of red light are ineffective in restoring the rate of rbcS transcription, suggesting that phytochrome alone does not fully mediate the response. Blue light is similarly effective to white light of an equal fluence rate (120 mumol m-2 s-1) in restoring the rate of rbcS transcription in the dark-treated plants, indicating that a blue light photoreceptor is involved. However, red light at the same fluence rate produces about 65% of the effect of blue or white light, showing that the blue light photoreceptor is not the only photoreceptor controlling rbcS transcription in the green leaf tissue. The identity of the photoreceptor responsible for the red light effect is discussed. Similar effects of blue and red light are observed at the level of transcript abundance in dark-grown pea leaf tissue given a brief illumination with red light, which potentiates the tissue for rapid transcript accumulation in white light.

Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light

The signal transduction pathways that lead to chloroplast biogenesis in plants are largely unknown. We describe here the identification and initial characterization of a novel genetic locus which fits the criteria of a regulatory gene located in a central pathway controlling light-mediated development. In the absence of light, these Arabidopsis thaliana mutants, designated det1 (de-etiolated 1), constitutively display many characteristics that are light-dependent in wild-type plants, including leaf and chloroplast development, anthocyanin accumulation, and accumulation of mRNAs for several light-regulated nuclear and chloroplast genes. The switch between dark and light growth modes thus appears to be a programmed step in a developmental pathway that is defined by det1. We suggest a model where the primary role of light on gene expression is mediated by the activation of leaf development. Further, the recessive nature of the det1 mutation implies that there is negative growth control on leaf development in dicotyledonous plants in the absence of light.

Regulation and expression of the multigene family coding light-harvesting chlorophyll a/b-binding proteins of photosystem II

The current state of knowledge concerning the expression of the nuclear genes that code the light-harvesting chlorophyll a/b-binding polypeptides of photosystem II is presented. This review covers the structure of these genes, the complex multistep pathway involved in their expression, and the environmental and other factors which regulate their expression. Some of the effects of these factors are mediated, at least in part, at the level of transcription, but other effects can be explained only by the existence of multiple posttranscriptional regulatory steps.