Light regulation of specific mRNA species in Lemna gibba L. G-3

Demonstration of transcriptional regulation of specific genes by phytochrome action

We have developed an in vitro transcription system that uses nuclei isolated from Lemna gibba G-3. The in vitro transcripts include sequences homologous to hybridization probes for the small subunit of ribulose-1,5-bisphosphate carboxylase [3-phospho-D-glycerate carboxy-lyase (dimerizing), EC 4.1.1.39], the light-harvesting chlorophyll a/b-protein, and rRNA. Light-harvesting chlorophyll a/b-protein sequences are transcribed to a greater extent in nuclei isolated from plants grown in darkness with 2 min of red light every 8 hr than in nuclei isolated from dark-treated plants. Furthermore, the amount of these transcripts measured in plants given a single minute of red light after dark treatment is increased over the amount measured in dark-treated plants. The effect of red light is at least partially reversible by 10 min of far-red light given immediately after the red light pulse. Transcription of both rRNA and small subunit sequences is also stimulated by a single minute of red light as compared to dark-treated tissue. However, the relative magnitudes of the increases compared to the dark levels are smaller than the increase seen for the chlorophyll a/b-protein, possibly because of the higher level of transcription of these sequences in the dark. The effect of red light on the transcription of small subunit and rRNA sequences is also reversible by immediate treatment with 10 min of far-red light. Pulse chase studies of dark-treated nuclei for up to 110 min do not show substantial turnover of in vitro labeled small subunit and chlorophyll a/b-protein transcripts. We therefore conclude that phytochrome action has induced specific changes in transcription of these genes.

Regulation of protein metabolism: Coupling of photosynthetic electron transport to in vivo degradation of the rapidly metabolized 32-kilodalton protein of the chloroplast membranes

In Spirodela oligorrhiza, mature chloroplasts copiously synthesize and degrade a 32-kilodalton membrane protein. The rates of synthesis and degradation are controlled by light intensity, the protein being unstable in the light and stable in the dark. Light-driven synthesis, but not degradation, is dependent on ATP. Degradation is blocked by herbicides inhibiting photosystem II electron transport, such as diuron and atrazine. Thus, both anabolism and catabolism of the 32-kilodalton protein are photoregulated, with degradation coupled to electron transport rather than phosphorylation.

Nonsense mutations in the Chlamydomonas chloroplast gene that codes for the large subunit of ribulosebisphosphate carboxylase/oxygenase

The Chlamydomonas reinhardtii chloroplast mutants 18-5B and 18-7G lack both the chloroplast-encoded large subunit and nuclear-encoded small subunit of the chloroplast enzyme ribulose-1,5-bisphosphate carboxylase/oxygenase (EC 4.1.1.39). A chloroplast intergenic-suppression model has been postulated to account for the genetic instability of 18-5B revertants. Here, we have determined the molecular basis of the 18-5B and 18-7G mutants. They contain nonsense mutations close to the 3' and 5' ends of their large-subunit genes, respectively. Pulse-chase experiments revealed that the 18-5B mutant produces a truncated large subunit that is unstable. In connection with previous experiments, this work identifies nonsense suppression in the chloroplast. Small subunits are also synthesized but then degraded in the mutants. Thus, the coordinated absence of subunits is achieved through degradation of the small subunit in the specific absence of the large subunit.

Herbicide resistance in transgenic plants expressing a bacterial detoxification gene

The herbicide bromoxynil (3,5-dibromo-4-hydroxybenzonitrile) is a photosynthetic (photosystem II) inhibitor in plants. A gene, bxn, encoding a specific nitrilase that converts bromoxynil to its primary metabolite 3,5-dibromo-4-hydroxybenzoic acid, was cloned from the natural soil bacterium Klebsiella ozaenae. For expression in plants, the bxn gene was placed under control of a light-regulated tissue-specific promoter, the ribulose bisphosphate carboxylase small subunit. Transfer of this chimeric gene and expression of a bromoxynil-specific nitrilase in leaves of transgenic tobacco plants conferred resistance to high levels of a commercial formulation of bromoxynil. The results presented indicate a successful approach to obtain herbicide resistance by introducing a novel catabolic detoxification gene in plants.

Structural diversity and differential light control of mRNAs coding for angiosperm glyceraldehyde-3-phosphate dehydrogenases

Subunits A and B of chloroplast glyceraldehyde-3-phosphate dehydrogenase are synthesized as higher molecular weight precursors when polyadenylylated mRNA from angiosperm seedlings is translated in vitro by wheat germ ribosomes. The in vivo levels of mRNA coding for these precursors are strongly light dependent, and the increase in translational activity stimulated by continuous white light, relative to dark-grown seedlings, is at least 5- to 10-fold for the seven plant species investigated. As opposed to this, light does not seem to change mRNA levels coding for cytosolic glyceraldehyde-3-phosphate dehydrogenase, and the polypeptides synthesized in vitro have the same size as the authentic subunits. In addition, precursors of the chloroplast enzyme were identified for 12 different angiosperm species and compared with their respective subunits synthesized in vivo. The patterns of the in vitro and in vivo products correlate in several major characteristics. They both display a remarkable interspecific heterogeneity with respect to size and number of polypeptides. The peptide extensions of the enzyme precursors calculated from these data vary between 4,000 and 12,000 daltons and seem to fall into three major size classes. The present data demonstrate that chloroplast glyceraldehyde-3-phosphate dehydrogenase, like its cytosolic counterpart, is encoded in the nucleus. Yet, the two dehydrogenases are controlled differently at both the ontogenetic and phylogenetic levels. They follow separate biosynthetic pathways with respect to light regulation, post-translational processing, and transport and also exhibit different evolutionary rates. The fast evolutionary change observed for the chloroplast enzyme contrasts sharply with the conservative structure and sequence of the cytosolic enzyme.

Discoveries in Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase): a historical perspective

Historic discoveries and key observations related to Rubisco (Ribulose 1,5-bisphosphate carboxylase/oxygenase), from 1947 to 2006, are presented. Currently, around 200 papers describing Rubisco research are published each year and the literature contains more than 5000 manuscripts on the subject. While trying to ensure that all the major events over this period are recorded, this analysis will inevitably be incomplete and will reflect the areas of particular interest to the authors.

Phytochrome regulation of nuclear gene expression in plants

The photoregulation of gene expression in higher plants was extensively studied during the 1980s, in particular the light-responsive cis -acting elements and trans -acting factors of the Lhcb and rbcS genes. However, little has been discovered about: (1) which plant genes are regulated by light, and (2) which photoreceptors control the expression of these genes. In the 1990s, the functional analysis of the various photoreceptors has progressed rapidly using photoreceptor-deficient mutants, including those of the phytochrome gene family. More recently however, advanced techniques for gene expression analysis, such as fluorescent differential display and DNA microarray technology, have become available enabling the global identification of genes that are regulated by particular photoreceptors. In this paper we describe distinct and overlapping effects of individual phytochromes on gene expression in Arabidopsis thaliana.

Light-independent synthesis of LHC IIb polypeptides and assembly of the major pigmented complexes during the initial stages of Pinus palustris seedling development

Pinus palustris has a greatly reduced need for light to initiate chloroplast development in comparison to angiosperms. Light is not required for chlorophyll synthesis in dark-grown Pinus palustris seedlings. However, embryos do not contain chlorophyll, and synthesis is limited to seedlings having cotyledon lengths between about 0.5 cm and 2.0 cm. The final amount of chlorophyll accumulated by dark-grown seedlings is about one fifth of that in light-grown seedlingsat the same stage. The major light-harvesting chlorophyll a/b-polypeptides of Photosystem II (LHC IIb) are absent in the embryos but begin to accumulate in seedlings of 0.5 cm cotyledon length, irrespective of the light conditions. Although dark-grown seedlings accumulate most of the pigmented complexes seen in light-grown seedlings, there are differences in the subunit structure of some of them. These findings suggest that the majority of the components of the photosynthetic membrane do not require light for induction of synthesis or assembly into complexes, but that the final forms seen in light-grown seedlings may require light.

Light-induced biogenesis of light-harvesting complex I (LHC I) during chloroplast development in barley (hordeum vulgare). Studies using cDNA clones of the 21- and 20-kilodalton LHC I apoproteins

The light-harvesting complex (LHC) Ib pigment-proteins form the major component of the LHC I complex in higher plants. They comprise chlorophylls a and b, xanthophylls, and at least two polypeptide subunits of 21 and 20 kD in barley (Hordeum vulgare). We have identified two cDNA clones, LHC Ib-21 and LHC Ib-20, encoding the 21- and 20-kD LHC Ib apoproteins, respectively. N-terminal protein sequences of the purified LHC Ib polypeptides were used for the unequivocal correlation of these clones to their respective apoproteins. The cDNA clones encode two proteins that have strong sequence similarity to other LHC I and LHC II pigment-binding polypeptides of photosystems I and II. The 21-kD polypeptide contains 201 amino acid residues (22.14 kD), and the 20-kD polypeptide contains 200 amino acid residues (22.18 kD). The biogenesis of the LHC Ib apoproteins and the pigmented LHC I during the light-induced development of the chloroplast was studied. Accumulation of the two LHC Ib mRNAs is induced by light, and their amount is regulated by phytochrome. LHC Ib polypeptide accumulation in the thylakoid membrane temporally lags behind transcript accumulation. The rates of accumulation of LHC Ib transcripts and of their apoproteins lag behind those of the major LHC II component, LHC IIb. Complete assembly of the LHC Ib pigment-protein, as observed by low-temperature fluorescence spectroscopy, requires exposure of dark-grown seedlings to 72 h or more of light.

Biosynthesis of the chloroplast cytochrome b6f complex: studies in a photosynthetic mutant of Lemna

The biosynthesis of the cytochrome b6f complex has been studied in a mutant, no. 1073, of Lemna perpusilla that contained less than 1% of the four protein subunits when compared with a wild-type strain. RNA gel blot analyses of the mutant indicated that the chloroplast genes for cytochrome f, cytochrome b6, and subunit IV (petA, petB, and petD, respectively) are transcribed and that the petB and petD transcripts undergo their normal processing. Analysis of polysomal polyA+ RNA indicated that the level of translationally active mRNA for the nuclear-encoded Rieske Fe-S protein (petC) was reduced by greater than 100-fold in the mutant. Immunoprecipitation of in vivo labeled proteins indicated that both cytochrome f and subunit IV are synthesized and that subunit IV has a 10-fold higher rate of protein turnover in the mutant. These results are discussed in terms of the assembly of the cytochrome complex and the key role of the Rieske Fe-S protein in this process.

A potential role for RNA turnover in the light regulation of plant gene expression: ribulose-1,5-bisphosphate carboxylase small subunit in soybean

Post-transcriptional regulation of the genes encoding the small subunit (rbcS) of ribulose-1,5-bisphosphate carboxylase was examined in soybean seedlings. Substantial discrepancies were detected between relative in vitro transcription rates and steady-state RNA levels in light- and dark-grown seedling leaves, indicating that rbcS RNA may be degraded more rapidly in light than in darkness. Additional data imply that the turnover mechanism is rapidly induced by light, maintained for some time in darkness, and that it may be negatively controlled by far-red light. The proposed RNA turnover system does not affect all RNAs equally since a soybean actin gene showed equivalent in vitro transcription rates and RNA levels in light and darkness. Soybean rbcS genes may be subject to a novel mode of control in which light-induced expression is accompanied by an increased rate of RNA degradation. Models for the specific regulation of rbcS RNA stability in response to light are presented.

Differential Expression of the Arabidopsis 2S Albumin Genes and the Effect of Increasing Gene Family Size

We studied the expression of the four genes encoding 2S albumin seed storage proteins (at2S1 to at2S4) in Arabidopsis thaliana. All four genes followed similar temporal profiles throughout development, but at2S2 and at2S3 were expressed at significantly higher levels than at2S1 or at2S4. In situ hybridization showed that at2S2 to at2S4 mRNAs were present throughout the embryo, whereas at2S1 was expressed at levels similar to at2S2 and at2S3 in the embryo axis but at only insignificant levels in the cotyledons. The different members of the gene family are, thus, likely to be regulated by different combinations of cis-acting elements, but it cannot be ruled out that post-transcriptional factors play a role. We studied the effect of enlarging the gene family by introducing an extra, nearly identical gene driven by the promoter of at2S1. The data were consistent with a model in which the expression of at2S2 to at2S4 is not affected by that of at2S1, and in which, at least at low copy numbers of the introduced gene, there is no limit on the overall amount of RNA that the at2S gene family can produce.

Proteolytic activity during senescence of plants

Although information has rapidly developed concerning the intracellular localization of plant proteins, relatively few reports concern the intracellular location of endo- and exo-proteolytic activities. Relatively few proteases have been purified, characterized, and associated with a specific cellular location. With the exception of the processing proteases involved in transport of proteins across membranes, little progress has yet been made concerning determination of in vivo products of specific proteases. Information on the turnover of individual proteins and the assessment of rate-limiting steps in pathways as proteins are turned over is steadily appearing. Since chloroplasts are the major site of both protein synthesis and, during senescence, degradation, it was important to show unambiguously that chloroplasts can degrade their own constituents. Another important contribution was to obtain evidence that the chloroplasts contain proteases capable of degrading their constituents. This work has been more tenuous because of the low activities found and the possibility of contamination by vacuolar enzymes during the isolation of organelles. The possible targeting of cytoplasmic proteins for degradation by facilitating their transport into vacuoles is a field which hopefully will develop more rapidly in the future. Information on targeting of proteins for degradation via the ubiquitin (Ub) degradation pathway is developing rapidly. Future research must determine how much unity exists across the different eukaryotic systems. At present, it has important implications for protein turnover in plants, since apparently Ub is involved in the degradation of phytochrome. Little information has been developed regarding what triggers increased proteolysis with the onset of senescence, although it appears to involve protein synthesis. Thus far, the evidence indicates that the complement of proteases prior to senescence is sufficient to carry out the observed protein degradation. This field of study has great practical implications, e.g. maintaining photosynthesis during seed-fill in order to obtain greater crop yields. The current use of stay green' variants in the populations of several crop plants to produce increased yields shows the potential for future development. The near future should see exciting discoveries in these areas of research that will have far reaching effects on the construction of transgenic plants for future research accomplishments and agricultural use.

Identification of upstream regulatory elements involved in the developmental expression of the Arabidopsis thaliana cab1 gene

We studied cis regulatory elements controlling the light-dependent organ-specific expression of Arabidopsis thaliana chlorophyll a/b binding protein gene (cab1) by stably transforming tobacco plants using a tumor-inducing (Ti) plasmid vector system. The results from the 5' and internal deletion analyses indicate that there are at least three cis-acting elements that are involved in the light-dependent developmental expression of cab1 gene. Two such elements are located at the immediate upstream regulatory region and the other element is located at the further upstream region. The 1120-base-pair (bp) DNA fragment containing the immediate and far upstream region can confer light-inducible organ specificity on the truncated nos promoter. However, deletion of the 39-bp DNA fragment at the immediate upstream regulatory region from this hybrid promoter resulted in a nonfunctional promoter, revealing that the 39-bp region is important for the cab promoter specificity. Further analyses of this region suggest that a potential Z-DNA-forming sequence (ATACGTGT) is involved in light-dependent developmental expression of the cab1 gene. Two additional Z-DNA-forming sequences (ACACATAT) that are inverted repeats of this sequence are also found in the upstream region where the additional regulatory elements are expected.

The major light-harvesting complex of Photosystem II: aspects of its molecular and cell biology

The light-harvesting complex of photosystem II (LHC II) contains one major (LHC IIb) and at least three minor chlorophyll-protein components. The apoproteins of LHC IIb (LHCP) are encoded by nuclear genes and synthesized in the cytoplasm as a higher molecular weight precursor(s) (pLHCP). Several genes coding for pLHCP have been cloned from various higher plant species. The expression of these genes is dependent upon a variety of factors such as light, the developmental stage of the plastids and the plant. After its synthesis in the cytoplasm, pLHCP is imported into plastids, inserted into thylakoids, processed to its mature form, and assembled into LHC IIb. The pathway of assembly of LHC IIb in the thylakoid membranes is currently being investigated in several laboratories. We present a model that gives some details of the steps in the assembly process. Many of the steps involved in the synthesis and assembly are dependent on light and the stage of plastid development.

Isolation of tobacco SSU genes: characterization of a transcriptionally active pseudogene

Genomic clones containing three genes for the small subunit (SSU) of ribulose bisphosphate carboxylase were isolated from tobacco. Detailed analysis was performed on two of these clones to give a clearer picture of this multigene family in tobacco. This analysis demonstrated that one of the clones contained a pseudogene that was unusual in that it was transcriptionally active. This is the first transcriptionally active pseudogene that has been reported in plants. In addition, another clone was found to contain coding sequences which are 100% homologous to a previously-cloned tobacco SSU gene (Mazur, B.J. and Chiu, C-F. [1985] Nuc. Acids Res. 13, 2372-2386), indicating that gene duplication and/or gene conversion may have played a role in the evolution of the tobacco SSU family.

Purification and characterization of a light-harvesting chlorophyll-a/b-protein of photosystem I of Lemna gibba

The photosystem I (PSI) complex of Lemna gibba, isolated by deriphat/polyacrylamide gel electrophoresis of thylakoids solubilized in glycosidic surfactants, has been fractionated into its two chlorophyll-protein complexes: a core component (CCI) and a light-harvesting component (LHCI), using either non-denaturing gel electrophoresis or ion-exchange chromatography/sucrose gradient centrifugation. Both methods yielded an LHCI component that contained only one apoprotein of approximately 20 kDa. All the chlorophyll b and lutein of the PSI complex is associated with this LHCI preparation. The chlorophyll a/b ratio of this chlorophyll-protein is 2.5, and lutein is essentially the only carotenoid present. While the purified LHCI from Lemna cross-reacts with antibodies raised against spinach LHCPIb of Lam et al. [FEBS Lett. 168, 10-14 (1984)], no cross-reactivity occurred between it and the major light-harvesting chlorophyll-a/b-protein of PSII, LHCII beta. This and a comparison of the amino acid and pigment compositions of the apoproteins of the LHCI and LHCII beta chlorophyll-proteins indicate that these are two distinct but similar chlorophyll-proteins.

Translational regulation of light-induced ribulose 1,5-bisphosphate carboxylase gene expression in amaranth

The regulation of the genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase was examined in amaranth cotyledons in response to changes in illumination. When dark-grown cotyledons were transferred into light, synthesis of the large- and small-subunit polypeptides was initiated very rapidly, before any increase in the levels of their corresponding mRNAs. Similarly, when light-grown cotyledons were transferred to total darkness, synthesis of the large- and small-subunit proteins was rapidly depressed without changes in mRNA levels for either subunit. In vitro translation or in vivo pulse-chase experiments indicated that these apparent changes in protein synthesis were not due to alterations in the functionality of the mRNAs or to protein turnover, respectively. These results, in combination with our previous studies, suggest that the expression of ribulose 1,5-bisphosphate carboxylase genes can be adjusted rapidly at the translational level and over a longer period through changes in mRNA accumulation.

Transcriptional regulation of a gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean tissue is linked to the phytochrome response

The effects of white light, far-red light, and darkness on the transcription of a soybean ribulose-1,5-biphosphate carboxylase small subunit gene, SRS1, were investigated. RNA was labeled with [alpha-32P]UTP in nuclei isolated from plants grown under different conditions of light and darkness and used to probe Southern blots and dot blots. The levels of small subunit mRNA synthesis were normalized to ribosomal RNA synthesis. We demonstrate that the SRS1 gene is transcribed at a rate 16- to 32-fold higher in plants grown in the light than in those grown in darkness. Transcription of the small subunit increased dramatically when plants grown in darkness were given 30 min to 6 h of light and then leveled off after 24 to 48 h of exposure. When light-grown seedlings were exposed to greater than 2 h of darkness, a gradual decrease in transcription was detected. This decrease in transcription reached basal dark-grown levels after 48 h of exposure to darkness. The increase in transcription in etiolated seedlings treated with white light for 15 min could be reduced to basal levels if the treatment was followed by treatment with far-red light for 15 min. In addition, transcription in ligh-grown seedlings was reduced to basal levels when plants were exposed to far-red light for 15 min. The transcription of this ribulose-1,5-biphosphate carboxylase small subunit gene is strongly positively regulated by white light, is negatively regulated by far-red light, and exhibits a classic phytochrome-linked response.

Transcriptional and post-transcriptional regulation of ribulose 1,5-bisphosphate carboxylase gene expression in light- and dark-grown amaranth cotyledons

The regulation of expression of the genes encoding the large subunit (LSU) and small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase (RuBPCase) was examined in 1- through 8-day-old, dark-grown (etiolated) and light-grown amaranth cotyledons. RuBPCase specific activity in light-grown cotyledons increased during this 8-day period to a level 15-fold higher than in dark-grown cotyledons. Under both growth conditions, the accumulation of the LSU and SSU polypeptides was not coordinated. Initial detection of the SSU occurred 1 and 2 days after the appearance of the LSU in light- and dark-grown cotyledons, respectively. Furthermore, although the levels of the LSU were similar in both light- and dark-grown seedlings, the amount of the SSU followed clearly the changes in enzyme activity. Synthesis of these two polypeptides was dramatically different in etiolated versus light-grown cotyledons. In light the synthesis of both subunits was first observed on day 2 and continued throughout the growth of the cotyledons. In darkness the rate of synthesis of both subunits was much lower than in light and occurred only as a burst between days 2 and 5 after planting. However, mRNAs for both subunits were present in etiolated cotyledons at similar levels on days 4 through 7 (by Northern analysis) and were functional in vitro, despite their apparent inactivity in vivo after day 5. In addition, since both LSU and SSU mRNA levels were lower in dark- than in light-grown seedlings, our results indicate that both transcriptional and post-transcriptional controls modulate RuBPCase production in developing amaranth cotyledons.

Translational regulation of light-induced ribulose 1,5-bisphosphate carboxylase gene expression in amaranth

The regulation of the genes encoding the large and small subunits of ribulose 1,5-bisphosphate carboxylase was examined in amaranth cotyledons in response to changes in illumination. When dark-grown cotyledons were transferred into light, synthesis of the large- and small-subunit polypeptides was initiated very rapidly, before any increase in the levels of their corresponding mRNAs. Similarly, when light-grown cotyledons were transferred to total darkness, synthesis of the large- and small-subunit proteins was rapidly depressed without changes in mRNA levels for either subunit. In vitro translation or in vivo pulse-chase experiments indicated that these apparent changes in protein synthesis were not due to alterations in the functionality of the mRNAs or to protein turnover, respectively. These results, in combination with our previous studies, suggest that the expression of ribulose 1,5-bisphosphate carboxylase genes can be adjusted rapidly at the translational level and over a longer period through changes in mRNA accumulation.

Functional and mutational analysis of the light-harvesting chlorophyll a/b protein of thylakoid membranes

The precursor for a Lemna light-harvesting chlorophyll a/b protein (pLHCP) has been synthesized in vitro from a single member of the nuclear LHCP multigene family. We report the sequence of this gene. When incubated with Lemna chloroplasts, the pLHCP is imported and processed into several polypeptides, and the mature form is assembled into the light-harvesting complex of photosystem II (LHC II). The accumulation of the processed LHCP is enhanced by the addition to the chloroplasts of a precursor and a co-factor for chlorophyll biosynthesis. Using a model for the arrangement of the mature polypeptide in the thylakoid membrane as a guide, we have created mutations that lie within the mature coding region. We have studied the processing, the integration into thylakoid membranes, and the assembly into light-harvesting complexes of six of these deletions. Four different mutant LHCPs are found as processed proteins in the thylakoid membrane, but only one appears to have an orientation in the membrane that is similar to that of the wild type. No mutant LHCP appears in LHC II. The other two mutant LHCPs cannot be detected within the chloroplasts. We conclude that stable complex formation is not required for the processing and insertion of altered LHCPs into the thylakoid membrane. We discuss the results in light of our model.

The implication of a plastid-derived factor in the transcriptional control of nuclear genes encoding the light-harvesting chlorophyll a/b protein

In carotenoid-deficient albina mutants of barley and in barley plants treated with the herbicide Norflurazon the light-dependent accumulation of the mRNA for the light-harvesting chlorophyll a/b protein (LHCP) is blocked. Thus, the elimination of a functional chloroplast, either as a result of mutation or as a result of herbicide treatment, can lead to the specific suppression of the expression of a nuclear gene encoding a plastid-localized protein. These results confirm and extend earlier observations on maize [Mayfield and Taylor (1984) Eur. J. Biochem. 144, 79-84]. The inhibition of mRNA accumulation appears to be specific for the LHCP; the mRNAs encoding the small subunit of ribulose-1,5-bisphosphate carboxylase and the NADPH: protochlorophyllide oxidoreductase are relatively unaffected. The failure of the albina mutants and of Norflurazon-treated plants to accumulate the LHCP mRNA is not exclusively caused by an instability of the transcript but rather by the inability of the plants to enhance the rate of transcription of the LHCP genes during illumination. Several chlorophyll-deficient xantha mutants of barley, which are blocked after protoporphyrin IX or Mg-protoporphyrin, and the chlorophyll-b-less mutant chlorina f2 accumulate the LHCP mRNA to almost normal levels during illumination. Thus, if any of the reactions leading to chlorophyll formation is involved in the control of LHCP mRNA accumulation it should be one between the formation of protochlorophyllide and the esterification of chlorophyllide a. While the nature of the regulatory factor(s) has not been identified our results suggest that, in addition to phytochrome (Pfr), plastid-dependent factors are required for a continuous light-dependent transcription of nuclear genes encoding the LHCP.

Transcriptional and post-transcriptional regulation of ribulose 1,5-bisphosphate carboxylase gene expression in light- and dark-grown amaranth cotyledons

The regulation of expression of the genes encoding the large subunit (LSU) and small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase (RuBPCase) was examined in 1- through 8-day-old, dark-grown (etiolated) and light-grown amaranth cotyledons. RuBPCase specific activity in light-grown cotyledons increased during this 8-day period to a level 15-fold higher than in dark-grown cotyledons. Under both growth conditions, the accumulation of the LSU and SSU polypeptides was not coordinated. Initial detection of the SSU occurred 1 and 2 days after the appearance of the LSU in light- and dark-grown cotyledons, respectively. Furthermore, although the levels of the LSU were similar in both light- and dark-grown seedlings, the amount of the SSU followed clearly the changes in enzyme activity. Synthesis of these two polypeptides was dramatically different in etiolated versus light-grown cotyledons. In light the synthesis of both subunits was first observed on day 2 and continued throughout the growth of the cotyledons. In darkness the rate of synthesis of both subunits was much lower than in light and occurred only as a burst between days 2 and 5 after planting. However, mRNAs for both subunits were present in etiolated cotyledons at similar levels on days 4 through 7 (by Northern analysis) and were functional in vitro, despite their apparent inactivity in vivo after day 5. In addition, since both LSU and SSU mRNA levels were lower in dark- than in light-grown seedlings, our results indicate that both transcriptional and post-transcriptional controls modulate RuBPCase production in developing amaranth cotyledons.

Transcriptional regulation of a gene encoding the small subunit of ribulose-1,5-bisphosphate carboxylase in soybean tissue is linked to the phytochrome response

The effects of white light, far-red light, and darkness on the transcription of a soybean ribulose-1,5-biphosphate carboxylase small subunit gene, SRS1, were investigated. RNA was labeled with [alpha-32P]UTP in nuclei isolated from plants grown under different conditions of light and darkness and used to probe Southern blots and dot blots. The levels of small subunit mRNA synthesis were normalized to ribosomal RNA synthesis. We demonstrate that the SRS1 gene is transcribed at a rate 16- to 32-fold higher in plants grown in the light than in those grown in darkness. Transcription of the small subunit increased dramatically when plants grown in darkness were given 30 min to 6 h of light and then leveled off after 24 to 48 h of exposure. When light-grown seedlings were exposed to greater than 2 h of darkness, a gradual decrease in transcription was detected. This decrease in transcription reached basal dark-grown levels after 48 h of exposure to darkness. The increase in transcription in etiolated seedlings treated with white light for 15 min could be reduced to basal levels if the treatment was followed by treatment with far-red light for 15 min. In addition, transcription in ligh-grown seedlings was reduced to basal levels when plants were exposed to far-red light for 15 min. The transcription of this ribulose-1,5-biphosphate carboxylase small subunit gene is strongly positively regulated by white light, is negatively regulated by far-red light, and exhibits a classic phytochrome-linked response.

Phytochrome control of in vitro transcription of specific genes in isolated nuclei from barley (Hordeum vulgare)

The transcriptional rates of four different genes in shoots of barley grown under different light regimes were quantified by monitoring nuclear RNA transcripts using gene-specific hybridization probes. Isolated nuclei were pulse-labelled with [alpha-32P]UTP and the relative rates of light-harvesting chlorophyll a/b protein (LHCP) mRNA, NADPH:protochlorophyllide oxidoreductase mRNA, B1 hordein mRNA, and 26-S rRNA synthesis were measured. Irradiation of dark-grown plants with a red light pulse increased the rate of LHCP mRNA synthesis tenfold within 3 h, and the rate of rRNA synthesis more than twofold within 9 h. The relative rate of synthesis of the oxidoreductase mRNA decreased following a red light pulse reaching a minimum after 3-6 h. As a direct proof of phytochrome involvement in the light-induced stimulation of LHCP and the repression of the oxidoreductase transcripts for both responses, red/far-red reversibility could be demonstrated. We conclude that phytochrome is able both to increase the transcription of certain nuclear genes and decrease the transcription of others.

Maize plastid photogenes: mapping and photoregulation of transcript levels during light-induced development

Positively photoregulated regions that show increased transcript levels upon illumination of dark-grown seedlings are scattered over approximately 19% of the maize plastid chromosome. Some photogenes, i.e., genes within these regions, are transcribed individually, whereas others that are transcribed as polycistronic mRNAs appear to be functionally organized into operons. Multiple light-induced transcripts are complementary to most photogenes; these mRNAs are not present in equimolar amounts during plastid photomorphogenesis, but particular transcripts predominate at specific stages of development. Most, but not all, photogene RNA pools reach a maximum size (after either 10, 20, or 44 h of illumination) and then fall to approximately preillumination levels. These data and other considerations argue that photogene expression control is fundamentally transcriptional and that there is more than one expression class. Transcripts of the maize plastid gene for the large subunit of ribulose bisphosphate carboxylase reach a maximum by 20 h of illumination; transcripts of the nuclear gene for the small subunit of this enzyme continue to accumulate and fall considerably later. These data suggest that the level of transcription of the latter gene in the nucleus may be regulated by events in the chloroplast.

Carotenoid-deficient maize seedlings fail to accumulate light-harvesting chlorophyll a/b binding protein (LHCP) mRNA

Yellow leaves of chlorophyll-deficient seedlings and white leaves of carotenoid-deficient seedlings contain no detectable light-harvesting chlorophyll a/b binding proteins (LHCP). Chlorophyll-deficient leaves contain plastids which are arrested in development prior to chloroplast formation [Mascia, P.N. and Robertson, D.S. (1978) Planta (Berl.) 143, 207-211] while carotenoid-deficient leaves contain plastids which are arrested in development at a rudimentary stage [Bachmann, M. D., Robertson, D.S., Bowen, C.C., and Anderson, I.C. (1967) J. Ultrastruc. Res. 21, 41-60]. Chlorophyll-deficient leaves have normal levels of nuclear-encoded LHCP mRNA while carotenoid-deficient leaves contain only trace amounts of LHCP mRNA. Similar results were obtained with carotenoid deficiencies caused by nuclear gene mutations and by treatment with the herbicide norflurazon which blocks carotenoid biosynthesis. We conclude that events at early stages of plastid development influence the accumulation of a nuclear-encoded mRNA.

In vitro expression and characterization of the translation start site of the psbA gene product (QB protein) from higher plants

The psbA gene from higher plants, which codes for the atrazine herbicide binding protein of photosystem II (QB protein), has been recently sequenced by various laboratories. From these data there are two potential translation sites, one yielding a protein of 38,500 kd and another a protein of 34,500 kd. In the present study, cloned psbA gene sequences from maize, tobacco, and pea have been expressed in a highly defined E. coli in vitro transcription/translation system. In order to determine the start site of translation, we also have employed a simplified E. coli system designed to synthesize the first di- or tripeptide of the gene product. From these results, it is clear that the first ATG of the longest open reading frame of the psbA gene, that begins fMet-Thr, is not recognized in vitro. Instead, the next downstream Met at position 37 is the initiation site, since the expected dipeptide fMet-Ile is synthesized from all psbA clones. These data are in accord with the in vivo results that the gene product is a precursor protein of 34,500 kd.

Nucleotide sequence encoding the precursor of the small subunit of ribulose 1,5-bisphosphate carboxylase from Lemna gibba L.G-3

We have sequenced a cDNA clone, pLgSSU, which encodes the small subunit of ribulose 1,5-bisphosphate carboxylase of Lemna gibba L.G-3 a monocot plant. This clone contains a 832 basepair insert which encodes the entire 120 amino acids of the mature small subunit polypeptide (Mr = 14,127). In addition this clone encodes 53 amino acids of the amino terminal transit peptide of the precursor polypeptide and 242 nucleotides of the 3' non-coding region. Comparison of the nucleotide sequence of pLgSSU with Lemna gibba genomic sequences homologous to the 5' end of the cDNA clone suggests that nucleotides encoding four amino-terminal amino acids of the transit peptide are not included in the cDNA clone. The deduced amino acid sequence of the Lemna gibba mature small subunit polypeptide shows 70-75% homology to the reported sequences of other species. The transit peptide amino acid sequence shows less homology to other species. There is 50% homology to the reported soybean sequence and only 25% homology to the transit sequence of another monocot, wheat.

Phytochrome control of RNA levels in developing pea and mung-bean leaves

We have examined phytochrome effects on the abundance of transcripts from several nuclear and chloroplast genes in buds of dark-grown pea seedlings and primary leaves of dark-grown mung-bean seedlings. Probes for nuclear-coded RNAs were selected from a library of cDNA clones and included those corresponding to the small subunit (SS) of ribulosebisphosphate carboxylase and a chlorophyll a/b binding protein (AB). Transcripts from chloroplast genes for RuBP carboxylase large subunit (LS) and a 32,000-dalton photosystem II polypeptide (PII) were assayed with cloned fragments of the chloroplast genome. In addition, we present data on transcripts from a number of other nuclear genes of unknown function, several of which change in abundance during light-induced development. Transcript levels were measured as a proportion of total RNA by a dot blot assay in which RNA from different tissues or stages is fixed to nitrocellulose and hybridized with (32)P-labeled probes prepared from cloned DNAs. Several patterns of induction can be seen. For example, although both SS and AB RNAs show positive, red/far-red reversible responses in both pea and mung bean, in pea buds the induction ratio for SS RNA is much higher than that for AB RNA, while just the reverse is true for mung-bean leaves. In addition, treatment with lowfluence red light produces full induction of the pea AB RNA, while SS RNA in the same tissue does not reach a maximum steady-state level until after about 24 h of supplementary high-intensity white light. In pea buds, chloroplast genes (LS, PII) also show clear responses to phytochrome, as measured by the steady-state levels of their RNA products. Chloroplast DNA levels (as a fraction of the total cellular DNA) show the same response pattern, which may indicate that in peas many of the light effects we see are related to a general stimulation of chloroplast development. In mung beans, the levels of plastid DNA and RNA are already quite high in the leaves of 7-d dark-grown seedlings, and light effects are much less pronounced. The results are consistent with the notion that chloroplast development is arrested at a later stage in dark-grown mung-bean leaves than in etiolated pea buds.

Phytochrome Control of the Expression of Two Nuclear Genes Encoding Chloroplast Proteins in Lemna gibba L. G-3

Hybridization probes for two nuclear-coded chloroplast proteins of Lemna gibba L. G-3 have been constructed in order to investigate phytochrome regulation of specific sequences. The first probe is a cDNA clone encoding the small subunit of ribulose 1,5-bisphosphate carboxylase. This probe was isolated from a set of Lemna cDNA clones in the bacterial plasmid pBR322. The second probe is a subclone of a genomic clone encoding the light-harvesting chlorophyll a/b-protein. This clone was isolated from a set of genomic clones constructed in the lambda vector Charon 4 with L. gibba DNA fragments generated by partial EcoR1 digestion. The identity of these clones was confirmed by in vitro translation of RNA which hybridized to the cloned DNA. Plants grown under continuous white light contain high concentrations of both RNA sequences; however, when these plants are put into darkness the concentration of these RNAs decreases rapidly relative to the total amount of RNA. Plants grown in the dark with intermittent red light (2 minutes/8 hours) and put into complete darkness for 8 days also contain lower concentrations of the sequences in the total RNA. One minute of red light after this dark period results in a rapid increase in the levels of RNA hybridizing to the probes. The effect of red light can be reversed by far-red light. These experiments demonstrate that phytochrome action can rapidly influence either the rates of transcription or the rates of degradation of these mRNAs.

Nascent polypeptide chains exit the ribosome in the same relative position in both eucaryotes and procaryotes

We located the polypeptide nascent chain as it leaves cytoplasmic ribosomes from the plant Lemna gibba by immune electron microscopy using antibodies against the small subunit of the enzyme ribulose-1,5-bisphosphate carboxylase. Similar studies with Escherichia coli ribosomes, using antibodies directed against the enzyme beta-galactosidase, show that the polypeptide nascent chain emerges in the same relative position in plants and bacteria. The eucaryotic ribosomal exit site is on the large subunit, approximately 75 A from the interface between subunits and nearly 160 A from the central protuberance, the presumed site for peptidyl transfer. This is the first functional site on both the eucaryotic and procaryotic ribosomes to be determined.

Diversity of abundant mRNA sequences and patterns of protein synthesis in etiolated and greened pea seedlings

The diversity of abundant mRNA sequences in various parts of 4-d etiolated pea seedlings (Pisum sativum L. var. Rondo CB) was compared by a cell-free translation of the mRNAs in the presence of [(35)S]methionine and by an analysis of the products by two-dimensional electrofocussing/ electrophoresis (2D separation). The various parts of the seedlings were also examined for the pattern of protein synthesis in vivo. Proteins were labeled by injection of [(35)S]methionine into the cotyledons, followed by 2D separation of the products. Over 95% of the abundant mRNA sequences and newly synthesized abundant polypeptides were shared by all parts of etiolated seedlings, including the cotyledons. However, a few distinct differences were observed when comparing mRNAs of roots and shoots; the most prominent among these were a group of six abundant mRNA sequences found exclusively in shoots. Only about 30% of the polypeptides synthesized on isolated RNA could be traced in equivalent positions on the gels as the polypeptides synthesized in vivo. Analysis of total RNA from light-grown pea seedlings showed the appearance of some twenty-five translation products not found with total RNA from etiolated seedlings, while about nine other translation products disappeared. At least ten of the light-induced RNA sequences were also present after growth in low-intensity red light (λ>600 nm) and are therefore thought to be controlled by the phytochrome system. Comparison of 11-d light-grown pea plants with 4-d light-grown seedlings did not reveal additional translatable RNA sequences, indicating that the major morphogenetic changes that occur after 4 d are not accompanied by significant changes in the pattern of abundant RNA sequences.

Synthesis and turnover of the light-harvesting chlorophylla/b-protein inLemna gibba grown with intermittent red light: possible translational control

Lemna gibba L. G-3 plants grown heterotrophically in the dark with intermittent red light (2 min every 8 h) contain a substantial amount of translatable mRNA encoding the light-harvesting chlorophyll (Chl)a/b-protein. However, very little [(35)S]methionine is incorporated into the apoproteins during a 1-h labeling period in the dark in these plants compared to plants grown in continuous white light. The Chla/b-protein mRNA is found to be associated with functioning polysomes in plants grown in the dark with intermittent red illumination (R plants). The small amounts of the apoproteins which are synthesized by these plants are found in the membrane fraction; neither the mature apoproteins nor their precursor(s) can be detected immunologically in the soluble fraction. The protein does not accumulate in these plants. Pulse-chase experiments with the R plants demonstrate that the newly synthesized apoproteins have a half-life of about 10 h in the dark. This turnover is not sufficient to explain the observed 20-fold difference in [(35)S]methionine incorporation into the apoprotein between white-light-grown and R plants. We therefore suggest that the synthesis of the Chla/b-apoproteins can be regulated by a light-dependent step at the level of translation, and that this regulation occurs after the initiation of translation.

Evidence against the involvement of DNA synthesis in phytochrome-mediated photomorphogenesis

In order to clarify the relationship between photomorphogenesis and DNA replication we investigated the effect of continuous far-red or white light on the synthesis of DNA in the cotyledons and the hypocotyl of mustard seedlings between 36 and 108 h after sowing. The total DNA content of the cotyledons (about 2.2 pg cell(-1)) did not significantly change during this period although long-term labeling experiments revealed newly synthesized DNA of nuclear, plastid, and mitochondrial origin. Light had no detectable effect on total DNA content and on the labeling of either DNA fraction. Histoautoradiography indicated that nuclear DNA synthesis was exclusively localized in dividing stomatal cells and in sieve tube companion cells undergoing endopolyploidization. The DNA content of the hypocotyl increased continuously but likewise showed no detectable effect of light. It is concluded that cell growth and differentiation during photomorphogenesis is independent of DNA synthesis.

Control by Phytochrome of Cytoplasmic Precursor rRNA Synthesis in the Cotyledons of Mustard Seedlings

The influence of phytochrome (high irradiance reaction; operationally, continuous far red light) on the incorporation of [(3)H]uridine into the cytoplasmic 2.5 megadalton precursor rRNA in the cotyledons of mustard (Sinapis alba L.) seedlings has been investigated. After irradiating 36-hour-old etiolated seedlings with 12 hours of far red light, the rate of incorporation is stimulated about 2-fold, leading to 50% labeling of the precursor rRNA pool about 15 minutes after the tracer has reached the nucleotide precursor pool. In the dark control, there is a significantly smaller pool of precursor rRNA which is half-saturated with label only after about 27 minutes. Since neither the specific radioactivity of the UTP pool nor the processing of the precursor rRNA demonstrate a corresponding light-dependent change, it is concluded that phytochrome mediates an increase of the transcription of the rRNA genes. This gene activation accounts for the increased accumulation of mature cytoplasmic rRNA during the course of photomorphogenesis of the cotyledons.

Biosynthetic pathways of two polypeptide subunits of the light-harvesting chlorophyll a/b protein complex

We have used an in vitro reconstitution system, consisting of cell-free translation products and intact chloroplasts, to investigate the pathway from synthesis to assembly of two polypeptide subunits of the light-harvesting chlorophyll-protein complex. These polypeptides, designated 15 and 16, are integral components of the thylakoid membranes, but they are products of cytoplasmic protein synthesis. Double immunodiffusion experiments reveal that the two polypeptides share common antigenic determinants and therefore are structurally related. Nevertheless, they are synthesized in vitro from distinct mRNAs to yield separate precursors, p15 and p16, each of which is 4,000 to 5,000 daltons larger than its mature form. In contrast to the hydrophobic mature polypeptides, the precursors are soluble in aqueous solutions. Along with other cytoplasmically synthesized precursors, p15 and p16 are imported into purified intact chloroplasts by a post-translational mechanism. The imported precursors are processed to the mature membrane polypeptides which are recovered exclusively in the thylakoids. The newly imported polypeptides are assembled correctly in the thylakoid lipid bilayer and they bind chlorophylls. Thus, these soluble membrane polypeptide precursors must move from the cytoplasm through the two chloroplast envelope membranes, the stroma, and finally insert into the thylakoid membranes, where they assemble with chlorophyll to form the light-harvesting chlorophyll protein complex.

The protochlorophyllide holochrome of barley (Hordeum vulgare L.). Phytochrome-induced decrease of translatable mRNA coding for the NADPH: protochlorophyllide oxidoreductase

During the illumination of dark-grown barley plants light induces a rapid decrease of a translatable mRNA which codes for a polypeptide of Mr 44000. This component was identified as a precursor of the NADPH:protochlorophyllide oxidoreductase. The precursor has an Mr larger than the authentic protein by approximately 8000. The light-induced change in the level of translatable mRNA can be induced by a 15-s red-light pulse followed by 5 h of darkness. The red-light effect is reversed by a subsequent far-red-light treatment. It is concluded that the light-induced decline of translatable mRNA for the NADPH:protochlorophyllide oxidoreductase is controlled by phytochrome. The significance of this finding for present concepts of light-dependent control of chloroplast development and chlorophyll synthesis is discussed.

Biosynthesis of the light-harvesting chlorophyll a/b protein. Polypeptide turnover in darkness

1. When etiolated pea seedlings were exposed to continuous light for 24 h and then returned to darkness, 38% of the chlorophyll a, 74% of the chlorophyll b and 84% of the light-harvesting chlorophyll a/b protein that had accumulated under illumination proved to be unstable in darkness. The unstable chlorophyll displayed a half-life of about 90 min. In contrast, alpha and beta subunits of the chloroplast coupling factor and the large and small subunits of ribulose 1,5-biphosphate carboxylase continued to accumulate in darkness, although at a slower rate than in plants maintained under light. 2. Short-term labelling in vivo with L-[35S]methionine showed that leaves continued to synthesize the light-harvesting protein and the small subunit of ribulose 1,5-biphosphate carboxylase for up to 48 h after transfer of plants from light and darkness. However, after long-term labelling (16 h), the light-harvesting chlorophyll a/b protein was found to be labelled to high specific activity only in illuminated leaves. 3. I conclude that the light-harvesting chlorophyll a/b protein is subject to turnover after transfer of plants from light to darkness. The site of breakdown appears to be the photosynthetic membrane. I suggest that turnover of the protein is part of the normal physiological mechanism for co-ordinating the accumulation of the pigment and protein components of the light-harvesting chlorophyll a/b complex.