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

Adventures in Life and Science, from Light to Rhythms

The author describes her life's pathway from her beginnings at a time when women were not well represented in the sciences. Her grandparents were immigrants to the United States. Although her parents were not able to go to college because of the Great Depression, they supported her education and other adventures. In addition to her interest in science, she describes her interest and involvement in politics. Her education at Oberlin, Stanford, and Harvard prepared her for her independent career at the University of California, Los Angeles, where she was an affirmative action appointment. Her research initially centered on the plant photoreceptor phytochrome, but later in her career she investigated circadian rhythms in plants, discovering and characterizing one of the members of the central oscillator.

My Path from Chemistry to Phytochrome and Circadian Rhythms

I summarize my scientific journey from my first interest in science to my career investigating how plants use the phytochrome photoreceptor to regulate what genes they express. I then describe how this work led to an understanding of how circadian rhythms function in plants and to the discovery of CCA1, a component of the plant central oscillator.

Molecular cloning of cDNA for Avena phytochrome

We have isolated several cDNA clones for phytochrome, a plant regulatory photoreceptor. A cDNA library was constructed by using etiolated Avena poly(A)(+) RNA enriched for phytochrome mRNA by size fractionation. Replicate arrays of colonies were differentially screened with cDNA probes made from poly(A)(+) RNA that had been either enriched in or depleted of phytochrome mRNA. Of the colonies hybridizing preferentially with the enriched probe, several contained plasmids that specifically selected phytochrome mRNA when assayed by hybridization-selection and translation. The largest such plasmid, pAP-2, was used to isolate clones from an Avena genomic library. One of these genomic clones was then used to screen a second cDNA library in an attempt to identify full-length phytochrome clones. The largest of the plasmids thus obtained, pAP-3, contains a 3.4-kilobasepair (kbp) insert, verified to contain phytochrome sequences by hybridization-selection and translation. Sequence analysis of pAP-2 and pAP-3 revealed that the two clones are identical in sequence through a 2.4-kbp region in which they overlap. However, the pAP-2 insert contains, in addition, 1.5 kbp of sequence of unknown origin, the apparent result of a recombination event. Blots of poly(A)(+) RNA hybridized with (32)P-labeled pAP-2 or pAP-3 show a single mRNA band at 4.2 kilobases. Blot analysis of RNA from dark-grown and from red-irradiated tissue demonstrates that a previously reported light-induced decrease in translatable phytochrome mRNA results from a decrease in physical abundance of this mRNA.

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.

Photosynthesis-associated gene families: differences in response to tissue-specific and environmental factors

The endogenous small subunit of the ribulose-1,5-bisphosphate carboxylase gene rbcS and the light-harvesting chlorophyll a/b-binding protein gene (LHCP) of pea are expressed in a light-inducible manner and are active mainly in green chloroplast-containing tissue. Chimeric genes under control of the 5'-flanking sequences of the rbcS ss3.6 or LHCP AB80 genes from pea were used to study the factors relating to the issue-specific and lightinducible expression of these nuclear-encoded genes in transgenic tobacco plants. The results show that plastid development plays a crucial role in the activation of expression of these chimeric genes. Particular members of each of the above gene families respond differently to tissue-specific and environmental factors. Furthermore, the light-inducible expression directed by the 5'-flanking sequence of ss3.6 rbcSgene is not exclusively mediated by phytochrome, but probably is controlledin large part by another photoreceptor.

Organ-specific and light-induced expression of plant genes

Light plays a pivotal role in the development of plants. The photoregulation of plant genes involves recognition of light quality and quantity by phytochrome and other light receptors. Two gene families, rbcS and Cab, which code for abundant proteins active in photosynthesis, the small subunit of ribulose bisphosphate carboxylase and the chlorophyll a/b binding protein, show a 20-to 50-fold increase in transcript abundance in the light. Analyses in calli and transgenic plants of deletions of the rbcS gene and of chimeric constructions has allowed localization of two regions involved in light-induced transcription. One element is confined to a 33-base pair region surrounding the TATA box. In addition, an enhancer-like element contained within a 240-base pair fragment can confer phytochrome-induced transcription and organ specificity on nonregulated promoters.

Temporal pattern of jasmonate-induced alterations in gene expression of barley leaves

Leaf tissues of barley (Hordeum vulgare L. cv. Salome) respond to methyl jasmonate (JaMe) treatment with a characteristic pattern of gene expression. Jasmonate-induced proteins (JIPs), such as leaf thionins (jip15 gene product) and ribosome-inactivating proteins (jip60 gene product), rapidly accumulate. Their genes are transiently transcriptionally activated, as shown here by the determination of in-vitro transcription rates in run-off assays. In contrast to jip genes, expression of photosynthetic genes encoding the small subunit of ribulose-1,5-bisphosphate carboxylase/oxygenase (rbcS gene product) and a type III light-harvesting chlorophyll-a/b-binding protein (LHCP; lhbC1 gene product), for example, was rapidly down-regulated in JaMe-treated barley leaves. Despite decreasing rates of rbcS and lhbC1 gene transcription, their transcripts were maintained in JaMe-treated leaf tissues for at least 36 h. Only at a later stage, was there a decline in the levels of rbcS and lhbC1, but not jip, transcripts, suggesting a selective destabilization of photosynthetic mRNAs in JaMe-treated leaf tissues.

Differential Synthesis of Photosystem Cores and Light-Harvesting Antenna during Proplastid to Chloroplast Development in Spirodela oligorrhiza

Proplastids and etioplasts are common starting points for monitoring chloroplast development in higher plants. Although proplastids are the primary precursor of chloroplasts, most proplastid to chloroplast systems are cumbersome to study temporally. Conversely, the etioplast to chloroplast transition is initiated by light and is readily examined as a function of time. Etioplasts, however, are found mostly in plants germinated in the dark and are not an obligatory step in chloroplast development. We have chosen to study chloroplast ontogeny in Spirodela oligorrhiza (Kurtz) Hegelm (a C(3)-monocot) because of its unique ability to grow indefinitely in the dark. Ultrastructural, physiological, and molecular evidence is presented in support of a temporal, light-triggered proplastid to chloroplast transition in Spirodela. The dark-grown plants are devoid of chlorophyll, and upon illumination synchronously green over a 3- to 5-day period. Synthesis of chloroplast proteins involved in photosynthesis is coincident with thylakoid assembly, chlorophyll accumulation, and appearance of CO(2) fixation activity. Interestingly, the developmental sequence in Spirodela was slow enough to reveal that biosynthesis of the D1 photosystem II reaction center protein precedes biosynthesis of the major light-harvesting antenna proteins. This, coupled with the high chlorophyll a/b ratio observed early in development, indicated that reaction center assembly occurred prior to accumulation of the light-harvesting complexes. Thus, with Spirodela one can study proplastid to chloroplast conversions temporally in higher plants and follow the process on a time scale that enables a detailed dissection of plastid maturation processes.

Carbon metabolism enzymes and photosynthesis in transgenic tobacco (Nicotiana tabacum L.) having excess phytochrome

J.M. Keller et al. (1989, EMBO J. 8, 1005-1012) introduced a phytochrome gene controlled by a cauliflower mosaic virus 35S promoter into tobacco (Nicotiana tabacum L.) providing material to test whether several photosynthesis enzymes can be increased by one modification to the plant. We report here that this transgenic tobacco had greater amounts of all enzymes examined as well as greater amounts of total protein and chlorophyll per unit leaf area. Fructose bisphosphatase (E.C. 3.1.3.11), glyceraldehyde 3-phosphate dehydrogenase (E.C. 1.2.1.12), and sucrose-phosphate synthase (E.C. 2.4.1.14) were also higher when expressed per unit protein. However, ribulose-1,5-bisphosphate carboxylase (E.C. 4.1.1.39) amount per unit leaf protein was the same in transgenic and wild-type (WT) plants. Photosynthesis in the transgenic plants was lower than in WT at air levels of CO2, but higher than in WT above 1000 μbar CO2. The photosynthesis results indicated a high resistance to CO2 diffusion in the mesophyll of the transgenic plants. Examination of electron micrographs showed that chloroplasts in the transgenic plants were often cup-shaped, preventing close association between chloroplast and cell surface. Chloroplast cupping may have caused the increase in the mesophyll resistance to CO2 diffusion. We conclude that it is possible to affect more than one enzyme with a single modification, but unexpected physical modifications worsened the photosynthetic performance of this plant.

Post-transcriptional regulation of organ-specific expression of individual rbcS mRNAs in Lemna gibba

Many studies of nuclear genes encoding chloroplast proteins have focused on the transcriptional regulation of their expression. The genes (rbcS) encoding the small subunit (SSU) of ribulose-1,5-bisphosphate carboxylase/oxygenase, a major stromal protein, comprise one such group. We have examined the role played by post-transcriptional events in determining the relative levels of individual rbcS mRNAs in different organs of the aquatic monocot Lemna gibba. L. gibba is unusual among angiosperms in that its roots are normally exposed to light during growth and contain chloroplasts. We have found that such roots transcribe rbcS genes and contain rbcS mRNA. We have used sequence-specific probes from the 3'-untranslated region of six rbcS genes from L. gibba to analyze the expression of the individual genes in different organs. All six genes were expressed in steady-state mRNA in fronds grown in constant white light. However, only five of these were easily detectable in steady-state mRNA isolated from roots of the same plants, and the relative expression of each gene varied between the roots and the fronds. In steady-state mRNA, SSU1 was found to be highly expressed in both roots and fronds, whereas SSU40B was expressed at low levels in the roots as compared with the fronds, and SSU5B RNA was barely detectable in the roots. The extremely low level of SSU5B RNA in steady-state root mRNA is likely to be a consequence of post-transcriptional events because this gene was transcribed at comparable rates in vitro in nuclei isolated from either roots or fronds. Localization of individual gene transcripts by in situ hybridization showed that SSU1 and SSU5B are expressed in the same cells in the fronds. Thus, the mechanism of differential expression is likely to involve an organ-specific post-transcriptional mechanism.

Transcriptional and post-transcriptional processes regulate expression of RNA encoding the small subunit of ribulose-1,5-biphosphate carboxylase differently in petunia and in soybean

The effects of white light, far-red light and darkness on the in vitro transcription and RNA levels of the small subunit of ribulose-1,5-bisphosphate carboxylase (rbcS) were investigated in petunia and in soybean. In petunia plants treated with 48 hours of darkness the in vitro transcription rate of two of the rbcS subfamilies of petunia, rbcS A and rbcS C, declined 32- and 8-fold respectively, whereas treatment of dark-adapted plants with light caused the in vitro transcription rate of these subfamilies to return to their light-grown levels. Relative RNA levels of rbcS A and rbcS C declined in parallel with in vitro transcription rate changes upon treatment of petunia plants with darkness. However, while relative RNA levels of rbcS C changed in parallel with in vitro transcription rate under all conditions of far-red light and white light tested, there were differences between the changes in rbcS A in vitro transcription rate and RNA levels which were consistent with post-transcriptional regulation of rbcS A RNA. In addition we observed that nuclei isolated from the leaves of plants which were exposed to darkness for periods of 72 hours or longer were transcriptionally inactive. Similar experiments on the in vitro transcription and relative levels of the rbcS RNA in soybean seedlings have lead to the hypothesis that rbcS RNA is less stable in light than in darkness. In contrast, small decreases in rbcS in vitro transcription rate in mature soybean plants treated with darkness were accompanied by large decreases in rbcS RNA, suggesting that rbcS RNA was degraded more rapidly in darkness than in light in these plants. We have shown that differences in the modulation of rbcS RNA levels by post-transcriptional mechanisms exist between plants which belong to different orders, and between different developmental states of the same plant species.

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.

Appearance of nitrite-reductase mRNA in mustard seedling cotyledons is regulated by phytochrome

Nitrate reductase (NR, EC 1.6.6.1) and nitrite reductase (NIR, EC 1.7.7.1) are the key enzymes of nitrate reduction. It is well established that the appearance of these enzymes is "induced" by nitrate, and it is generally believed that NR is cytosolic while NIR is plastidic. In mustard (Sinapis alba L.) cotyledons we observed two isoforms of NIR (NIR1 and NIR2) using a chromato-focusing technique. Only one of them (NIR2) disappeared when the plastids were damaged by photooxidation in the presence of Norflurazon. It is concluded that NIR2 is plastidic while NIR1 is extraplastidic and not affected by photooxidation of the plastids. Both isoforms appear to have the same molecular weight (60 kilodaltons, kDa). Two distinct translation products which could be immunoprecipitated with NIR antiserum produced against total NIR from mustard were observed which differed slightly in molecular weight (60 versus 63 kDa). The 63-kDa polypeptide was considered to be the precursor of NIR2. While synthesis of NIR protein depended largely on nitrate, the levels of in-vitro-translatable NIR mRNAs were found to be either independent of nitrate and light (NIR1) or controlled by phytochrome only (NIR2). It appears that phytochrome strongly stimulates the level of mRNA while significant enzyme synthesis (NIR2) takes place only in the presence of relatively large amounts of nitrate. Since an increased enzyme level was strictly correlated with an increase of immunoresponsive NIR protein it is improbable that activation of a precursor plays a role. Rather, it is concluded that, in situ, nitrate controls translation.

Light effects on several chloroplast components in norflurazon-treated pea seedlings

Changes occurring in several chloroplast components during Norflurazon-induced photobleaching of Pisum sativum seedlings were investigated. mRNA steady state levels of the chlorophyll a/b-binding protein of photosystem II, ferredoxin I, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 and pEA207, two other light-responsive genes, were determined during chlorophyll photooxidation. Relative transcription rates were assayed in isolated nuclei. The results illustrate a complex set of interactions regulating expression of the nuclear and chloroplast genomes. Photobleaching was found to affect the expression of the various genes in different ways. While transcript levels of the chlorophyll a/b-binding protein decreased by more than 80% under photooxidative light conditions in carotenoid-deficient peas, levels of ferredoxin, the small and large subunits of ribulose 1,5-bisphosphate carboxylase, and pEA214 mRNAs were reduced by less than 50%. pEA207 mRNA levels, on the other hand, were resistant to the effects of photobleaching. Analyses of chlorophylls a and b and the chlorophyll a/b-binding protein suggest that accumulation of the protein and its mRNA are coordinated with chlorophyll abundance at several steps. In addition to post-transcriptional regulation at the level of mRNA and protein stability, there may exist coordination at the transcriptional stage.

Characterization of a negatively light-regulated mRNA from Lemna gibba

We have isolated a cDNA clone, called pLg106, which corresponds to a negatively light-regulated mRNA in the aquatic monocot Lemna gibba. Lg106 mRNA is more abundant in dark-treated plants than in plants grown under continuous white light. The levels of Lg106 mRNA reached a maximum 12-24 hours after plants had been placed in the dark. In vitro-labelled transcripts from nuclei isolated from white light-grown and darktreated Lemna hybridized equally to Lg106 DNA, indicating that transcription of the Lg106 gene was similar in both white light and darkness. Therefore, the higher level of Lg106 mRNA in the dark was not attributable to a change in transcription. We suggest that the stability of Lg106 mRNA is affected by changes in illumination. The steady-state level of Lg106 did not appear to be under phytochrome regulation, as the abundance of Lg106 mRNA from plants grown in intermittent red light or intermittent red followed immediately by far-red light was not significantly different from that of dark-treated plants. The size of the mRNA was estimated to be 650-700 nt. Genomic Southern blots indicated the presence of a single gene for Lg106. The Lg106 cDNA was sequenced and examined for similarities to nucleotide sequences in GenBank.

Cytokinin modulation of LHCP mRNA levels: the involvement of post-transcriptional regulation

When white-light-grown Lemna gibba plants are placed in the dark, the levels of mRNAs for two nuclear-encoded chloroplast proteins, the small subunit of ribulose-1,5-bisphosphate carboxylase (SSU) and the major chlorophyll a/b-binding protein of light-harvesting complex II (LHCP), decline to a small fraction of their previous level. We have reported [4] that red light (R), acting through phytochrome, and benzyladenine (BA), a synthetic cytokinin, independently stimulate accumulation of both mRNAs in the dark. Here, we have analyzed the products of transcription in isolated nuclei to determine if cytokinins act primarily through stimulation of transcription or if post-transcriptional processes are involved. We find that BA pretreatment may slightly stimulate transcription of LHCP RNA either with or without a red-light treatment. However, the effects of BA on the LHCP RNA accumulation were much greater than on transcription. Two naturally occurring cytokinins are also effective in increasing the mRNA abundance. We therefore conclude that, in Lemna, post-transcriptional processes are important in regulation of the LHCP RNA by cytokinins.

Control by phytochrome of the appearance of ribulose-1,5-bisphosphate carboxylase and the mRNA for its small subunit

We have measured levels of ribulose-1,5-bisphosphate carboxylase (RuBPCase) and levels of in-vitro-translatable mRNA for the small subunit (SSU) of RuBPCase up to 96 h after sowing in mustard (Sinapis alba L.) cotyledons, in order to investigate to what extent the rate of enzyme synthesis is related to the level of SSU-mRNA. Both enzyme and mRNA level are controlled strongly by phytochrome, but the rate of RuBPCase accumulation was found to be unrelated to the level of translatable SSU-mRNA. As an example, it was found that the amount of SSU-mRNA in far-red light (FR)-grown mustard seedlings doubles between 54 and 84 h after sowing while the rate of RuBPCase accumulation remains constant over this period. Since the holoenzyme shows zero turnover during this period it is concluded that the rate of enzyme synthesis remains constant although the level of SSU-mRNA increases strongly. Following an FR→dark transition, with different levels of physiologically active phytochrome (Pfr) established at the end of the light period, no correlation was found between the time course of mRNA levels in darkness and the rate of enzyme synthesis. Rather, the data indicate that there is at least one translational or post-translational regulatory step which is also phytochrome-dependent. It is concluded that coarse control of the appearance of translatable SSU-mRNA is essential for RuBPCase to appear at a high rate but that fine tuning by phytochrome of the actual appearance of RuBPCase is not transcriptional.

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.

The early light-inducible proteins of barley. Characterization of two families of 2-h-specific nuclear-coded chloroplast proteins

Within 1-2 h of illumination of etiolated barley plants the mRNAs of seven nuclear-coded proteins are transiently induced. It is proposed that at least some of these proteins are precursors to chloroplast membrane proteins since after posttranslational transport 2-h-specific bands of 18.5 kDa, 18 kDa and 13.5 kDa have been found bound to thylakoid membranes. cDNA clones for these early light-inducible proteins (ELIPs) have been isolated. Hybrid-release translation shows that part of their information must be homologous since the complete set of early light-inducible translation products is obtained with all investigated clones although the proportions of the translated bands vary for individual clones. From hybridization data it is concluded that two ELIP families of high (24-27 kDa) and of low (16-18 kDa) molecular mass exist which are induced in parallel. Induction of ELIPs occurs even at very low light intensities and is saturated at about 1000 lx. Therefore, ELIPs are not considered to represent light stress proteins but to play a regulatory role during development.

Coordinate, Organ-Specific and Developmental Regulation of Ribulose 1,5-Bisphosphate Carboxylase Gene Expression in Amaranthus hypochondriacus

The expression of the genes encoding the large subunit (LSU) and small subunit (SSU) of ribulose 1,5-bisphosphate carboxylase (RuBPCase) was examined in roots, stems, cotyledons, and leaves of amaranth during the development of these tissues. The highest accumulation of LSU and SSU polypeptides occurred in cotyledons and leaves. Their steady state levels were approximately 20-fold lower in stems, while in roots neither LSU and SSU polypeptides nor their respective mRNAs could be detected. In cotyledons and leaves accumulation of these two polypeptides reached peak levels during the expansion stage of each tissue and then declined, reflecting changes in the synthesis, not turnover, of these proteins. In cotyledons and stems, the rates of synthesis of LSU and SSU polypeptides correlated with the levels of their respective mRNA, suggesting regulation primarily at the transcriptional level. In contrast, the dramatic and specific decrease in the synthesis of these two proteins during the last stages of development of the leaves could only partially be accounted for by the modest reduction in their mRNAs. Neither the translatability of these mRNAs, as assayed in cell-free systems, nor the stability of LSU and SSU polypeptides were altered, thus implying that control was being exerted at the translational level. During the development of these different organs, the expression of the LSU and SSU genes were generally coordinately regulated both at the levels of protein synthesis and mRNA accumulation.

Light-dependent accumulation and localization of photosystem II proteins in maize

We have raised antibodies against several major components of photosystem II. These antisera, which are directed against the apoproteins of two chlorophyll-binding proteins (CPa-1 and CPa-2), the apoprotein of light-harvesting complex II and the 33-kDa extrinsic protein of the oxygen-evolving complex, were used to examine the light regulation of photosystem II assembly in maize. The principal findings of this study are as follows. The 33-kDa protein is present in dark-grown maize and the content increases 5-10-fold upon illumination. The level of the protein is mediated at least in part by phytochrome and is independent of the accumulation of chlorophyll. In contrast, none of the three chlorophyll-binding proteins examined was detectable in leaves of maize grown in darkness or under other light regimes where chlorophyll does not accumulate. Even in the absence of photosystem II assembly, the 33-kDa protein is properly transported across the thylakoid into the lumen. However, the protein does not attach in the normal way to the inner surface of the membrane under these conditions.

Comparison of the effects of exogenous native phytochrome and in-vivo irradiation on in-vitro transcription in isolated nuclei from barley (Hordeum vulgare)

In barley seedlings the transcription of genes coding for the light-harvesting chlorophyll a/b protein (LHCP) is stimulated and the transcription of genes coding for the NADPH-protochlorophyllide oxidoreductase (reductase) is repressed by light working via the phytochrome system. This phytochrome-mediated control of gene expression has been studied by monitoring in-vitro transcription in isolated nuclei. Two different experimental approaches have been used to elucidate the function of phytochrome (Pfr) during the transduction of the light signal. Concentrations of phytochrome were varied experimentally either by illuminating intact plants or macerated plant material prior to the isolation of nuclei or by adding purified phytochrome (Pfr) in its native 124-kDa form to the isolated nuclei. Our results indicate that there are at least two different steps involved in the phytochrome control of specific gene expression. (i) There is a rapid and transient change in the transcription rate which is saturated by very low levels of Pfr. (ii) There is a change in the duration and the maximum range of the transient change; this step requires relatively high Pfr concentrations and thus reacts very sensitively and rapidly to changes in Pfr levels as induced by secondary irradiations. This second step, but not the first one, could be triggered by the addition of purified oat phytochrome to a reconstituted nuclear system. This effect of purified phytochrome could only be shown if nuclei isolated from red-light (R)-irradiated seedlings were used. It was thus possible to simulate the effect of an in-vivo-applied second R pulse by the addition of Pfr to nuclei isolated from R-preirradiated plants.

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.

Nucleotide sequence and characterization of a gene encoding the phytochrome polypeptide from Avena

We have isolated and characterized a gene encoding the phytochrome polypeptide of Avena. Based on nucleotide sequence identity with previously sequenced cDNA clones this gene is designated as type 3 (phy3). The gene is about 5.9 kb long with six exons and five introns, one each of the latter in the 5' and 3'-untranslated regions. The largest exon encodes the entire 74-kDa, chromophore-bearing, N-terminal domain of the photo-receptor postulated to be directly involved in its mechanism of action. The transcription start point, identified by mung-bean nuclease digestion, is located 24 to 35 bp downstream from a tandem TATA box. Sequence elements homologous to a number of motifs implicated as upstream regulatory elements in other genes are present in the 5'-flanking DNA of phy3. Particularly intriguing are three elements at positions -140, -470 and -650. These elements share homology with the 'GT' motif postulated to be a component of the light-regulatory element of genes encoding the small subunit of ribulose bisphosphate carboxylase.

Phytochrome regulation of mRNA levels of ribulose-1,5-bisphosphate carboxylase in etiolated rye seedlings (Secale cereale)

The effect of red light and far-red light on the appearance of mRNA for the small and large subunit of ribulose-1,5-bisphosphate carboxylase in rye seedlings has been analysed. Irradiation of etiolated seedlings with a pulse of red light increased the mRNA level of the small subunit by a factor of 7-10 and that of the large subunit by a factor of 3. A pulse of far-red light resulted in a much lower, but measurable increase. The effect of red light is reverted by an immediate far-red pulse, demonstrating the classical phytochrome response.In vitro transcription experiments with nuclei isolated from red light-treated seedlings showed that the transcription rate of the small subunit mRNA was increased only by a factor of 1.5-2.5, indicating posttranscriptional as wells as transcriptional regulations of the small subunit of ribulose-1,5-bisphosphate carboxylase.

Expression of two nuclear genes encoding chloroplast proteins during early development of cucumber seedlings

Cloned complementary DNA probes have been used to measure steady-state transcript levels for the small subunit of ribulose bisphosphate carboxylase-oxygenase (SSU) and the chlorophyll a/b-binding protein (LHCP) in cotyledons during early development of cucumber seedlings. Initial accumulation of trancripts to SSU occurs 2d after germination and is independent of light and developmentally programmed. Although transcripts accumulate in dark-grown tissues, their levels increase rapidly in light-grown cotyledons from day 4, coinciding with emergence above the soil, so that by day 6 levels are 2.4 times higher in light-grown compared with dark-grown cotyledons. In contrast, accumulation of transcripts to LHCP occurs only in light-grown cotyledons. Southern blot analysis of genomic DNA indicates that in cucumber there are one and two genes encoding SSU and LHCP, respectively, considerably fewer than in those other plant species that have been examined. Both LHCP genes are expressed in light-grown cotyledons.

Transcriptional and post-transcriptional regulation of chloroplast gene expression in Petunia hybrida

To study the control of differential gene expression during plastid biogenesis in Petunia hybrida, we have investigated the in vivo translation and transcription of the rbc L gene, coding for the large subunit of ribulose bisphosphate carboxylase (LSU), and the psa A gene, coding for P700 chlorophyll-a apoprotein (AP700). Differential expression of these plastid-encoded genes was studied in two developmentally different plastid systems, proplastid-like organelles from the green cell suspension AK2401 and mature chloroplasts from green leaves. In vivo translation of rbc L and psa A transcripts was analysed using specific antibodies. Specific transcript levels were analysed using internal fragments of the rbc L and psa A genes. A standardization procedure was used so that a direct correlation could be made between the amount of products and gene copy number. In Petunia hybrida the amount of LSU polypeptides present in both plastid types does not correspond to the amount of specific mRNA for the gene. Although the rbc L transcripts are present in both plastid types, the LSU protein is only present in green leaf plastids and not in cell culture plastids. In vitro translation of isolated rbc L transcripts give similar results, thereby suggesting that differences in the primary structure of the transcripts are responsible for the observed discrepancy. In contrast to this, the amount of AP700 polypeptides does correspond to the amount of the psa A transcripts. Therefore, our results indicate that the expression of chloroplast genes during plastid biogenesis takes place on at least two different levels: expression of the rbc L gene is regulated post-transcriptionally while expression of the psa A gene is regulated at the transcriptional level.

Two soybean ribulose-1,5-bisphosphate carboxylase small subunit genes share extensive homology even in distant flanking sequences

Soybean contains a multigene family which encodes the small subunit of ribulose-1,5-bisphosphate carboxylase (RuBPCss). A member of this gene family, SRS4, has been isolated from a soybean genomic DNA library. Its nucleotide sequence has been determined and compared to the sequence of SRS1, a previously characterized RuBPCss gene from soybean. Relevant regulatory sequences such as the PuPuCCAAT boxes, TATA box, the actual start of transcription and poly A addition sites are conserved between the two genes. Using a gene specific synthetic probe to the 3' flanking region the steady state mRNA levels of SRS4, like SRS1, are shown to be very high in light grown soybean seedlings and low in seedlings grown in darkness. SRS1 and SRS4 are very closely related, the three exons being 96%, 93% and 96.5% homologous in nucleotide sequence. The polypeptide sequences are nearly identical with only one amino acid change in each of the three exons encoding the 178 amino acid precursor polypeptide. The two introns are about 75% homologous and the flanking regions are more than 85% homologous (700 base pairs on the 5' end and 300 base pairs on the 3' end). Furthermore, hybridization studies between lambda clones containing the SRS1 and SRS4 genes reveal that a region of strong homology extends at least 4 kb on the 5' end and about 1.1 kb on the 3' end. We propose that these two genes may be alloalleles or homeologous alleles. This proposal is consistent with soybean having an allotetraploid origin, and would imply that the divergence of two ancient Papilionoidae species gave rise to these two genes.

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.

Benzyladenine modulation of the expression of two genes for nuclear-encoded chloroplast proteins in Lemna gibba: Apparent post-transcriptional regulation

Cytokinins and phytochrome have both been reported to promote chloroplast development, and possible interactions between the two have been suggested. We have examined the effects of red light (R) and a cytokinin, benzyladenine (N(6)-benzylaminopurine; BA), on the levels of four mRNAs coding for chloroplast proteins in Lemna gibba L. The amounts of hybridizable RNA coding for both the major chlorophyll a/b-binding protein and for the small subunit of ribulose-1,5-bisphosphate (RuBP) carboxylase decrease to a low level when white-light-grown L. gibba plants are placed in the dark. We have previously shown that a subsequent R treatment causes a several-fold increase in the levels of these two messages, and this increase is phytochrome-mediated. We have now found that addition of submicromolar concentrations of BA to plants kept in total darkness also results in an increase in levels of these two mRNAs. Furthermore, BA treatment magnifies the extent of the response to R treatment. However, the levels of mRNAs encoding the large subunit of RuBP carboxylase and the 32-kDa herbicide-binding protein, which are both chloroplastsynthesized messages, are not significantly altered by either R or BA treatment during the same time period. The relative amount of β-actin mRNA, a nuclear-encoded message for a cytoplasmic protein, is also not altered either by R or BA treatment. Thus, BA treatment does not simply alter the proportion of mRNA to total RNA. This conclusion is also supported by the observation that levels of mRNA hybridizing to a sequence abundant in dark-treated plants are not altered by BA treatment. The amplification by BA of the R-induced increase in the level of chlorophyll a/b-binding protein mRNA, consistently seen in total RNA, is not observed in RNA isolated from nuclei from plants receiving the same treatments. We therefore suggest that cytokinin is regulating expression of this message at a post-transcriptional level, possibly by affecting the stability of the RNA.

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.

A simple gene-expression system for the small subunit of ribulose bisphosphate carboxylase in leaves ofNicotiana sylvestris

InNicotiana sylvestris only four transcripts coding for the small subunit of RUBISCO are present in leaves. They are very closely related as they are identical in the nucleotide sequence of the non-coding regions and show only three silent point differences in the region coding for the mature peptide.The main difference among these four transcripts lies in the length of the non-coding regions. Half of the SmRNA population as confirmed by direct RNA sequencing has an additional nucleotide sequence in the leader region. Two cDNAs have an additional nucleotide sequence at the end of the 3' non-coding region. Based on these criteria the transcripts were classified into two groups:.group I has a 73-nucleotide-long leader sequence and the nucleotides T, A and C at position 327, 432 and 519 in the coding region..group II has a 60-nucleotide-long leader sequence and the nucleotides C, G and T at these positions in the coding region.The two cDNAs showing a difference in the length of the 3' non-coding region belong to group II.The study of all these transcripts argues for the possibility that only two families of genes are expressed in leaves ofN. sylvestris.

Phytochrome-controlled expression of a wheat Cab gene in transgenic tobacco seedlings

We have monitored changes in the chlorophyll a/b-binding protein (Cab) mRNA levels in etiolated wheat leaves exposed to light of different wavelengths by Northern blot hybridizations and 5' S1 nuclease protection assays. Accumulation of the Cab mRNA and the specific Cab-1 transcript is regulated by phytochrome. Transcript levels are elevated by red light and the red enhancement can be partially reversed by far-red light. Moreover, far-red light alone can elicit a small increase in the transcript levels. These characteristic features of the wheat Cab-1 phytochrome response can be recapitulated in etiolated seedlings of transgenic tobacco containing the Cab-1 gene. Analyses of a chimeric construct revealed that a 1.8-kb 5'-flanking fragment (-1816 to +31) of the Cab-1 gene can confer phytochrome response as well as leaf-specific expression on a heterologous coding sequence.

The two genes for the small subunit of RuBP Carboxylase/oxygenase are closely linked in Chlamydomonas reinhardtii

Ribulose bisphosphate carboxylase-oxygenase (Rubisco) is a key enzyme in the photosynthetic fixation of CO2 by the chloroplast. The synthesis of the enzyme is an example of the cooperation between the chloroplast and the nucleocytoplasmic compartments, as it is assembled from subunits encoded in the two respective genomes. I have used a synthetic oligonucleotide probe to isolate the nuclear Rubisco small subunit genes (rbcS) directly from a genomic library of Chlamydomonas reinhardtii DNA. They constitute only a small family: there are two rbcS genes, and an additional related sequence, in the C. reinhardtii genome. All three are clustered within 11kb at a single locus, and should thus be particularly well suited for genetic manipulation. The pattern of expression of rbcS RNA is dependent on the growth conditions.

Analysis of cloned cDNA and genomic sequences for phytochrome: complete amino acid sequences for two gene products expressed in etiolated Avena

Cloned cDNA and genomic sequences have been analyzed to deduce the amino acid sequence of phytochrome from etiolated Avena. Restriction endonuclease site polymorphism between clones indicates that at least four phytochrome genes are expressed in this tissue. Sequence analysis of two complete and one partial coding region shows approximately 98% homology at both the nucleotide and amino acid levels, with the majority of amino acid changes being conservative. High sequence homology is also found in the 5'-untranslated region but significant divergence occurs in the 3'-untranslated region. The phytochrome polypeptides are 1128 amino acid residues long corresponding to a molecular mass of 125 kdaltons. The known protein sequence at the chromophore attachment site occurs only once in the polypeptide, establishing that phytochrome has a single chromophore per monomer covalently linked to Cys-321. Computer analyses of the amino acid sequences have provided predictions regarding a number of structural features of the phytochrome molecule.

Structure and developmental regulation of a wheat gene encoding the major chlorophyll a/b-binding polypeptide

A genomic clone for a major chlorophyll a/b-binding polypeptide of the light-harvesting complex has been sequenced from wheat. This gene, whAB1.6, encodes a 70-nucleotide 5'-nontranslated spacer, a 34-amino-acid NH2-terminal extension, i.e., the transit peptide, and a mature coding protein of 232 amino acid residues. The exact molecular weight of the precursor polypeptide is 28,560. The transit peptide is basic and is rich in serines. No intervening sequences are found in this gene. The transcription start site of the whAB1.6 gene occurs at AAAC as determined by S1 nuclease analysis. Putative regulatory sequences occur upstream of the gene at -25 (TTTAAATA) and at -72 (CCAACCA). Northern blots show a single RNA species estimated to be 1,100 nucleotides. Heterogeneity of the RNA population is demonstrated in S1 nuclease analyses with a 5'-end-labeled fragment that extends 191 nucleotides into the mature protein coding sequence. At least seven different transcripts can be recognized. The highest levels of RNA transcribed from the whAB1.6 gene are found in the basal segments of the wheat leaf, whereas other chlorophyll a/b-binding transcripts in the cell show a different pattern of abundance. As a control, we show that roots do not contain chlorophyll a/b-binding RNA. The most abundant RNA species shows an interrupted homology with the whAB1.6 gene at the start of the mature protein coding sequence; another species shows homology beginning at the start of the transit peptide and does not include the nontranslated region. Chlorophyll a/b-binding polypeptides accumulate toward the tip of the leaf as shown by Western blot analysis of total thylakoid proteins.

Arabidopsis thaliana and Plant Molecular Genetics

Arabidopsis thaliana is a small flowering plant with various properties that make it an excellent organism for experiments in molecular genetics. These properties include having a small nuclear genome, a near absence of dispersed repetitive DNA, and a generation time of 4 to 5 weeks. In addition, mutations that affect hormone synthesis and response, many different enzyme activities, and numerous developmental processes have been identified and characterized.

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.

Molecular cloning of a pea mRNA encoding an early light induced, nuclear coded chloroplast protein

cDNA clones were isolated for a chloroplast protein, the mRNA of which is induced to maximum levels within 2-4 h after onset of illumination in five day old, etiolated pea seedlings.The cDNA library was constructed from poly(A)(+)-mRNA which was isolated from 4 h illuminated seedlings. The extremely short induction period of the early light induced protein(ELIP)-mRNA established the basis of our screening procedure. Colony hybridization experiments were performed with(32)P-labelled cDNA probes, synthesized from RNA of seedlings which had been exposed to different programs of illumination. Plasmid DNAs were isolated from colonies showing strong hybridization signals exclusively with cDNA corresponding to the 4 h-mRNA. Hybrid released translation of preselected plasmids p 17/C2 and p17/C4 revealed a peptide of Mr 24 000. After posttranslational importin vitro, the processed product of Mr 17 000 appears in the chloroplast. Using these clones, the expression of the ELIP-mRNA was investigated by DOT-hybridization. The ELIP-mRNA reaches maximum levels within 2-4 hours after onset of illumination. Our results correspond precisely to thein vivo characteristics and indicate positive identification of the sought clones.

Structure and developmental regulation of a wheat gene encoding the major chlorophyll a/b-binding polypeptide

A genomic clone for a major chlorophyll a/b-binding polypeptide of the light-harvesting complex has been sequenced from wheat. This gene, whAB1.6, encodes a 70-nucleotide 5'-nontranslated spacer, a 34-amino-acid NH2-terminal extension, i.e., the transit peptide, and a mature coding protein of 232 amino acid residues. The exact molecular weight of the precursor polypeptide is 28,560. The transit peptide is basic and is rich in serines. No intervening sequences are found in this gene. The transcription start site of the whAB1.6 gene occurs at AAAC as determined by S1 nuclease analysis. Putative regulatory sequences occur upstream of the gene at -25 (TTTAAATA) and at -72 (CCAACCA). Northern blots show a single RNA species estimated to be 1,100 nucleotides. Heterogeneity of the RNA population is demonstrated in S1 nuclease analyses with a 5'-end-labeled fragment that extends 191 nucleotides into the mature protein coding sequence. At least seven different transcripts can be recognized. The highest levels of RNA transcribed from the whAB1.6 gene are found in the basal segments of the wheat leaf, whereas other chlorophyll a/b-binding transcripts in the cell show a different pattern of abundance. As a control, we show that roots do not contain chlorophyll a/b-binding RNA. The most abundant RNA species shows an interrupted homology with the whAB1.6 gene at the start of the mature protein coding sequence; another species shows homology beginning at the start of the transit peptide and does not include the nontranslated region. Chlorophyll a/b-binding polypeptides accumulate toward the tip of the leaf as shown by Western blot analysis of total thylakoid proteins.