Photochrome-mediated regulation of messenger RNAs for the small subunit of ribulose 1, 5-bisphosphate carboxylase and the light-harvesting chlorophyll a/b-protein in Lemna gibba

Analysis of Lhc family genes reveals development regulation and diurnal fluctuation expression patterns in Cyperus esculentus, a Cyperaceae plant

Sixteen Lhc genes representing 13 phylogenetic groups were identified from the full-length transcriptome of tigernut, exhibiting development regulation and diurnal fluctuation expression patterns in leaves. Nuclear encoded light-harvesting chlorophyll a/b-binding (Lhc) proteins play indispensable roles in oxygenic photosynthesis. In this study, we present the first transcriptome-based characterization of Lhc family genes in tigernut (Cyperus esculentus L.), a Cyperaceae C₄ plant producing oil in underground tubers. A number of 16 Lhc genes representing 13 phylogenetic groups identified from the full-length tigernut transcriptome are equal to that found in both Carex littledalei (another Cyperaceae plant) and papaya, slightly more than 15 members present in both rice and jatropha, but relatively less than 18, 20, and 21 members present in sorghum, cassava, and Arabidopsis, respectively. Nevertheless, nearly one-vs-one orthologous relationship was observed in most groups, though some of them are no longer located in syntenic blocks and species-specific expansion was frequently found in Lhcb1. Comparative genomics analysis revealed that the loss of two groups (i.e., Lhca2 and Lhca5) in C. littledalei is species-specific, sometime after the split with tigernut, and the expansion of Lhcb1 was mainly contributed by tandem duplication as observed in most species. Interestingly, a transposed duplication, which appears to be shared by monocots, was also identified in Lhcb1. Further transcriptome profiling revealed a predominant expression pattern of most CeLhc family genes in photosynthetic tissues and enhanced transcription during leaf maturation, reflecting their key roles in light absorption. Moreover, qRT-PCR analysis revealed an apparent diurnal fluctuation expression pattern of 11 dominant CeLhc genes. These findings not only highlight species-specific evolution of Lhc genes in the Cyperaceae family as well as the monocot lineage, but also provide valuable information for further functional analysis and genetic improvement in tigernut.

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.

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.

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.

shygrl1 is a mutant affected in multiple aspects of photomorphogenesis

We have used a counter-selection strategy based on aberrant phytochrome regulation of an Lhcb gene to isolate an Arabidopsis mutant designated shygrl1 (shg1). shg1 seedlings have reduced phytochrome-mediated induction of the Lhcb gene family, but normal phytochrome-mediated induction of several other genes, including the rbcS1a gene. Additional phenotypes observed in shg1 plants include reduced chlorophyll in leaves and additional photomorphogenic abnormalities when the seedlings are grown on medium containing sucrose. Mutations in the TATA-proximal region of the Lhcb1*3 promoter that are known to be important for phytochrome regulation affected reporter gene expression in a manner similar to the shg1 mutation. Our results are consistent with the possibility that the mutation either leads to defective chloroplast development or to aberrant phytochrome regulation. They also add to the evidence of complex interactions between light- and sucrose-regulated pathways.

The phytochrome response of the Lemna gibba NPR1 gene is mediated primarily through changes in abscisic acid levels

Two important signaling systems involved in the growth and development of plants, those triggered by the photoreceptor phytochrome and the hormone abscisic acid (ABA), are involved in the regulation of expression of the NPR1 gene of Lemna gibba. We previously demonstrated that phytochrome action mediates changes in ABA levels in L. gibba, correlating with changes in gene expression evoked by stimulation of the phytochrome system. We have now further characterized phytochrome- and ABA-mediated regulation of L. gibba NPR1 gene expression using a transient particle bombardment assay, demonstrating that regulatory elements controlling responses to both stimuli reside within 156 nucleotides upstream of the transcription start. Linker scan (LS) analysis of the region from -156 to -70 was used to identify two specific requisite and nonredundant cis-acting promoter elements between -143 to -135 (LS2) and -113 to -101 (LS5). Mutation of either of these elements resulted in a coordinate loss of regulation by phytochrome and ABA. This suggests that, unlike the L. gibba Lhcb2*1 promoter, in which phytochrome and ABA regulatory elements are separable, the phytochrome response of the L. gibba NPR1 gene can be attributed to alterations in ABA levels.

Chimeric Arabidopsis thaliana ribulose-1,5-bisphosphate carboxylase/oxygenase containing a pea small subunit protein is compromised in carbamylation

A cDNA of pea (Pisum sativum L.) RbcS 3A, encoding a small subunit protein (S) of ribulose-1,5-bisphosphate carboxylase/oxygenase (Rubisco), has been expressed in Arabidopsis thaliana under control of the cauliflower mosaic virus 35S promoter, and the transcript and mature S protein were detected. Specific antibodies revealed two protein spots for the four Arabidopsis S and one additional spot for pea S. Pea S in chimeric Rubisco amounted to 15 to 18% of all S, as judged by separation on two-dimensional isoelectric focusing/sodium dodecyl sulfate-polyacrylamide gel electrophoresis gels from partially purified enzyme preparations and quantitation of silver-stained protein spots. The chimeric enzyme had 11 +/- 1% fewer carbamylated sites and a 11 +/- 1% lower carboxylase activity than wild-type Arabidopsis Rubisco. Whereas pea S expression, preprotein transport, and processing and assembly resulted in a stable holoenzyme, the chimeric enzyme was reproducibly catalytically less efficient. We suggest that the presence of, on average, one foreign S per holoenzyme is responsible for the altered activity. In addition, higher-plant Rubisco, unlike the cyanobacterial enzyme, seems to have evolved species-specific interactions between S and the large subunit protein that are involved in carbamylation of the active site.

A chimeric Lhcb::Nia gene: an inducible counter selection system for mutants in the phytochrome signal transduction pathway

One approach towards understanding the transduction pathways of phytochromes is the selection of mutants impaired in various steps. We report here the construction of an inducible counter-selection system for such mutants employing the enzyme nitrate reductase. This enzyme can convert the benign substrate analogue chlorate to the toxic product chlorite, resulting in severe growth inhibition. An Arabidopsis thaliana nitrate reductase gene (Nial*2) was placed under the regulation of an Arabidopsis thaliana light-harvesting chlorophyll a/b protein (Lhcb1*3) promoter that is phytochrome-responsive. The chimeric Lhcb::Nia gene was transformed into A. thaliana. Homozygous transformant lines were selected and grown in the absence of nitrate and the presence of L-glutamine, conditions that substantially inhibited the expression of the endogenous nitrate reductase genes. In darkness seedlings of the transformed lines were resistant to chlorate; however, when seedlings were grown with intermittent red light, increased sensitivity to chlorate was observed. This sensitivity was correlated with an increase in both Nia1*2 RNA levels and nitrate reductase activity. The resistant seedlings were clearly distinguishable from the sensitive ones based on hypocotyl length, with no overlap in this parameter between the two populations. Thus, this system should allow for the selection of mutants that are impaired in phytochrome regulation of the transcription of Lhcb genes.

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

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

Cyclic temperature treatments of dark-grown pea seedlings induce a rise in specific transcript levels of light-regulated genes related to photomorphogenesis

Dark-grown pea seedlings exposed to cyclic heat shocks or daily temperature changes undergo a morphogenetic development similar to that induced by far red light. The morphological changes observed include expansion of the leaves, shortening of the stems and opening of the hooks. Compared with control etioplasts, plastids of heat-treated seedlings are as large as fully mature chloroplasts and contain well developed, unstacked membranes. These morphogenetic changes correlate with elevated levels of SSU and LHCP mRNAs which, under these conditions, fluctuate in a circadian manner. In contrast, the ELIP mRNA remains under strict light control and shows circadian fluctuations only if the plants are exposed to a short period of illumination. We propose that periodic temperature changes, like light treatment, might serve as a 'Zeitgeber' signal for circadian rhythm. The data indicate a correlation between the existence of circadian oscillations and morphogenetic development.

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

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

Cloning and nucleotide sequence analysis of genes coding for the major chlorophyll-binding protein of the moss Physcomitrella patens and the halotolerant alga Dunaliella salina

Two clones have been isolated from a genomic library of the moss Physcomitrella patens and a cDNA library of the halotolerant green alga Dunaliella salina. The isolates contain genes coding for the major light-harvesting chlorophyll-a/b-binding protein (CAB) in the photosystem II (PSII) light-harvesting complex (LHCII). The 2544-bp insert of the moss genomic clone contains the complete CAB-coding region and 5' and 3' flanking sequences. The coding region contains an intron of 359 bp which is spanned by a pair of 9-bp perfect direct repeats. There are two CCAAT boxes and five enhancer-like elements related to (G)TGGTTTAAA(G) (Weiher et al., 1983) residing in the intron. Comparisons of the moss cab gene with sequences of light-inducible genes of higher plants reveal homologous and repeated sequences similar to the enhancer element in the 5' region upstream from the TATA and CCAAT boxes thought to be responsive to light inducibility. The 1256-bp algal cDNA contains the complete CAB-coding sequence, a 170-bp 5'-nontranslated region, and a 264-bp 3'-nontranslated region. While the overall homology in the nontranslated regions is low between the cab gene of the moss and that of the alga, the 3'-nontranslated regions of the two contain some sequences that are conserved among the cab genes in higher plants. The deduced amino acid sequences of these two clones are highly conserved except for the N-terminal region. Their hydropathic plots are very similar and both possess three hydrophobic segments that are likely alpha-helical transmembrane segments. The proposed CAB transit peptide sequence of the alga is divergent from that of the moss or higher plants, suggesting that they may have evolved from different origins. Southern blot analysis shows that the cab genes in the moss and the alga, as in higher plants, are encoded by a number of homologous genes constituting a multigene family.

Isolation and characterization of a maize chlorophyll a/b binding protein gene that produces high levels of mRNA in the dark

A cDNA library prepared using mRNA isolated from red-light irradiated maize seedlings was screened by a difference procedure for clones that represent red-light regulated mRNA. Two such clones were found to represent mRNA for a chlorophyll a/b binding protein (CAB), and one of these (pAB1084) was used to screen a maize genomic library. One positive genomic clone (lambda AB1084) was isolated and sequenced. The gene represented by lambda AB1084, which we designate maize cab-1, contains extensive nucleotide homology within its protein coding region to CAB genes from other species. The boundaries of the transcribed region of the cab-1 gene were determined by S1 nuclease mapping. The 5' terminus of cab-1 mRNA is located 52-54 nucleotides (nt) upstream of the translation start site and 34 nt downstream of a TATA box. As in the case of petunia CAB genes, several poly(A) addition sites are present in mRNA from the cab-1 gene. The 5' flanking DNA of cab-1 contains sequences related to elements that have been implicated in the light-regulated expression of CAB and rbcS genes in other plant systems. Quantitative Northern blot hybridization analysis using a gene specific probe for cab-1 indicates that the mRNA for this gene is present at 0.4% of the total mRNA and up to 80% of the total CAB mRNA in the leaves of dark-grown seedlings. In consequence, although the degree of up-regulation by white light is only moderate (3- to 6-fold), cab-1 transcripts account for approximately 2% of the mRNA in the leaves of light-grown seedlings.

Structure of the Chlamydomonas reinhardtii cabII-1 gene encoding a chlorophyll-a/b-binding protein

Gene cabII-1 is a light regulated gene that encodes the precursor of a major chlorophyll-a/b-binding protein in Chlamydomonas reinhardtii. It is a member of a small gene family composed of about 3-7 members. Nucleotide sequencing data and S1 mapping reveal that the cabII-1 gene is interrupted by three introns. Except for the transit peptide and the N-terminus, the cabII-1 gene product is similar to cabII proteins in higher plants. The cabII-1 gene in C. reinhardtii appears to be an intermediate between type-I and type-II cabII genes described in higher plants.

Four genes in two diverged subfamilies encode the ribulose-1,5-bisphosphate carboxylase small subunit polypeptides of Arabidopsis thaliana

The multigene family encoding the small subunit polypeptides of ribulose-1,5-bisphosphate carboxylase/oxygenase in the crucifer Arabidopsis thaliana has been isolated and the organization and structure of the individual members determined. The family consists of four genes which have been divided into two subfamilies on the basis of linkage and DNA and amino acid sequence similarities. Three of the genes, designated ats1B, ats2B, and ats3B, reside in tandem on an 8 kb stretch of the chromosome. These genes share greater than 95% similarity in DNA sequence and encode polypeptides identical in length and 96.7% similar in amino acid sequence. The fourth gene, ats1A, is at least 10 kb removed from, or completely unlinked to the B subfamily. The B subfamily genes are more similar to each other than to ats1A in nucleotide and amino acid sequence. All four genes are interupted by two introns whose placement within the coding region of the genes is conserved. The introns of the B subfamily genes are similar in length and nucleotide sequence, but show no similarity to the introns of ats1A. Comparison of the DNA sequences within the immediate 5' and 3' flanking sequences among the genes revealed only limited regions of homology. S1 analysis shows that all four genes are expressed.

Photoregulation of psbA transcript levels in mustard cotyledons

We have investigated the photoreceptors potentially involved in the light regulation of the transcript levels of the psbA gene coding for D1, the 32 kD QB-binding protein of PSII. In cotyledons of 4 day old mustard seedlings, increasing fluence rates of continuous white light from ca. 0.1 to 250 μmol m(-2)s(-1) (400-700 nm) lead to a five-fold increase in transcript level from ca. 0.7 to 2.8 mg/g total RNA. The blue (<500 nm) component of this light did not contribute substantially to this effect, thus ruling out cryptochrome as the receptor responsible. Although phytochrome involvement was apparent from red/far-red reversibility, even multiple red pulses failed to elicit a comparable increase in transcript level to that seen under continuous white light. Although DCMU successfully inhibited delayed fluorescence quenching, it had no effect on transcript levels, thus ruling out photoregulation via electron transport and later components of the photosynthetic system. By contrast, Norflurazon, which leads to photobleaching of chlorophyll and hence disruption of thylakoid membrane assembly, completely abolished the light effect on psbA transcript level. We infer that photoregulation of the psbA transcript is principally related to thylakoid development, which is in turn critically dependent on photoconversion of protochlorophyllide to chlorophyll, but also associated with other processes such as phytochrome-regulated LHCP availability. Photocontrol of psbA expression is discussed in relation to that of the nuclear cab and rbcS genes.

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.

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.

Regulation of gene expression of ribulose bisphosphate carboxylase in greening pea leaves

Ribulose bisphosphate carboxylase/oxygenase (RuBisCO) is composed of two subunits, the chloroplastcoded large subunit (LS) and the nuclear-coded small subunit (SS). The effects of different light doses on the levels of the large subunit gene (rbcL), the rbcL and the rbcS mRNAs, and the rate of synthesis of RuBisCO were followed during greening. The rbcL gene dosage changed in response to light whereas the level of the rbcL mRNA changed independently of the gene dosage. This suggests that the expression of the rbcL gene is transcriptionally regulated and that the change in gene dosage only partially contributes to the increase in the mRNA. It appeared that the RuBisCO synthesis rate was proportional to the rbcS mRNA level rather than rbcL mRNA level. These results, taken together with the earlier observations of many researchers, suggest that RuBisCO synthesis in greening pea leaves is controlled primarily at the level of transcription of both genes and is fine-tuned at the post-transcriptional level in chloroplasts, so that the amount of LS is almost stoichiometric to that of SS.

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.

Molecular characterization of two clusters of genes encoding the Type I CAB polypeptides of PSII in Nicotiana plumbaginifolia

A Nicotiana plumbaginifolia genomic library in the phage Charon 34 was used to isolate and characterize 7 full-length genes and part of an 8th gene encoding chlorophyll a/b-binding (CAB) polypeptides. These genes are arranged in two clusters. All the genes within the clusters are arranged in opposite orientation to their neighbours. The nucleotide sequences of two genes, one from each cluster, show that both genes, designated Cab-E and Cab-C, encode very similar proteins (95.9% of homology) corresponding to type I photosystem II polypeptides. Southern blot analysis suggests that at least 19 CAB genes encoding type I PSII CAB polypeptides are present in the N. plumbaginifolia genome. We also describe the presence within the N. plumbaginifolia genome of CAB genes encoding PSII type II CAB polypeptides and PSI type I CAB polypeptides. The sequences of the 5' flanking region of three different CAB genes (Cab-E, Cab-C, and CAB-F) were determined. Two of them (Cab-C and Cab-F) share extensive homology, whereas the Cab-E promoter shows homology to Cab-C and Cab-F only in a unique region extending from the CAAT box to the TATA box. This conserved sequence is also found in the same position in promoters of CAB genes encoding type I PSII polypeptides from other plant species.

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.

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.

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.

Translational regulation of protein synthesis during light-induced chloroplast development in Euglena

Control of gene expression in Euglena was examined during light-induced chloroplast development. Greening was achieved under standard conditions which allowed the synthesis of all plastid proteins in both cytoplasmic and chloroplastic compartments, or under experimentally modified conditions inducing the preferential synthesis of the photosystem II (PSII) light-harvesting antenna or reaction centers. The relative composition of total mRNAs in cellular, cytoplasmic or chloroplastic fractions, as analyzed by their in-vitro translation products in cell-free systems did not significantly change during the in-vivo protein-synthesis processes which are specific to each greening system. By contrast, cytoplasmic polysomal mRNAs extracted during the selective recovery phase of PSII light-harvesting antennae provided a major in-vitro synthesis product of 28 kDa which could correspond to a precursor of the main 26-kDa apoprotein of the light-harvesting chlorophyll a/b protein complex. Similarly, the in-vivo selective synthesis of the 41-kDa and 51-kDa polypeptides of PSII reaction centers was concomitant with an enrichment of plastid polysomes in mRNA species coding for polypeptides of the same molecular weight. These observations confirm that protein synthesis during chloroplast development in Euglena is weakly regulated at the transcription level and they demonstrate that translational regulation occurs in both the cytoplasmic and the chloroplastic compartments.

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.

Photooxidative destruction of chloroplasts and its consequences for expression of nuclear genes

Expression of nuclear genes involved in plastidogenesis is known to be controlled by light via phytochrome. Examples are the small subunit (SSU) of ribulose-1,5-bisphosphate carboxylase and the light harvesting chlorophyll a/b binding protein of photosystem II (LHCP). In the present study we show that, beside phytochrome, the integrity of the plastid is essential for the expression of the pertinent nuclear genes as measured at the level of translatable mRNA. When the plastids are severely damaged by photooxidation in virtually carotenoid-free mustard (Sinapis alba L.) seedling cotyledons (made carotenoid-free by the application of Norflurazon, NF), almost no SSU, no SSU precursor, LHCP and LHCP precursor can be detected by immunological assays, and almost no translatable mRNA of SSU and LHCP can be found, although the levels and rates of phytochrome-mediated syntheses of representative cytoplasmic, mitochondrial and glyoxisomal enzymes are not adversely affected and morphogenesis of the mustard seedling proceeds normally (Reiß et al. 1983; Planta 159, 518-528). Norflurazon per se has no effect on the amount of translatable mRNA of SSU and LHCP as shown by irradiation of NF-treated seedlings with far-red light (FR) which strongly activates phytochrome but does not cause photooxidation in the plastids. It is concluded that a signal from the plastid is required to allow the phytochrome-mediated appearance of translatable mRNA for SSU and LHCP. Seedlings not treated with NF show a higher level of translatable mRNALHCP in red light (RL) compared to FR, whereas the mRNASSU levels are the same in RL and FR. These facts indicate that the level of translatable mRNALHCP is adversely affected if the apoprotein is not incorporated into the thylakoid membrane.

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.

Light regulation of plant gene expression by an upstream enhancer-like element

Light regulates many varied physiological and developmental phenomena during plant growth and differentiation, including the formation of a photosynthetically competent chloroplast from a proplastid. The expression of ribulose 1,5-bisphosphate carboxylase small subunit (rbcS) genes is regulated by light in a development- and tissue-specific manner2,3. In some plant species, phytochrome has been demonstrated to mediate this response, and photoregulation of rbcS expression occurs at least in part at the level of transcription. We have shown previously that a 5'-noncoding fragment (4-973 base pairs (bp) upstream of the messenger RNA cap site) of the pea rbcS ss3.6 gene contains all of the nucleotide sequence information necessary to direct the photoregulated expression of a bacterial chloramphenicol acetyltransferase (cat) gene in tobacco. Consistent with these findings, Morelli et al.11 have shown by deletion analysis of a second rbcS gene promoter, that the sequences required for photoregulated expression of rbcS E9 reside within the 5'-noncoding region. They identified an upstream region of approximately 700 bp needed for maximum transcription but not light-dark regulation, and a region from -35 to -2 bp which included the TATA box and contained the necessary information for light responsiveness. We now demonstrate that regulatory sequences 5' distal to the rbcS ss3.6 TATA box and transcriptional start site not only contain the information necessary for maximum expression, but also confer photoregulation. These upstream regulatory sequences function independently of orientation when fused to their homologous promoter or a heterologous promoter.

A shoot-specific mRNA from pea: nucleotide sequence and regulation as compared to light-induced mRNAs

The regulation of a mRNA encoding a shoot-specific polypeptide from developing pea seedlings was studied and compared to the regulation of mRNAs encoding two major light-induced nuclear-encoded polypeptides, the small subunit of the ribulose 1,5 biphosphate carboxylase (ssRuBPCase) and a polypeptide of the light-harvesting chlorophyll a/b complex (LHCP). By using cDNA clones as probes in Northern blottings of total cellular RNA it was found that both ssRuBPCase and LHCP mRNA could be induced in shoots by white and red light but to lower levels in roots and cotyledons. In contrast, the mRNA for the shoot-specific polypeptide was only found in shoots, and was present approximately two days after the start of germination. The shoot-specific mRNA sequence was predominantly found in stem tissue, irrespective of illumination, both in the young seedlings and adult plants. Only very low amounts could be detected in plumule and leaf. The shoot-specific sequence could also be detected in RNA isolated from developing shoots of another pea cultivar but not in those of other legumes and of cereals. The primary sequence of the complete coding portion and the deduced amino acid sequence of the mRNA encoding the shoot-specific polypeptide was determined. The observed codon usage is non-random and is consistent with data from other high plant genes. Possible polyadenylation signal sequences (AATAAG and AATAAT) were present at 55 and 124 bases 5' of the poly(A) tail. The polypeptide encoded by the shoot-specific mRNA consists of 196 amino acids with a calculated molecular weight of 21 898. It contains a four times reiterated highly conserved unit of 26 amino acids. The NH2-terminal end is highly hydrophobic and resembles a signal polypeptide.

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.

Ribulose bisphosphate carboxylase capacity and chlorophyll content in developing seedlings of Chenopodium rubrum L. growing under light of different qualities and fluence rates

In order to evaluate the aclimation of Chenopodium seedlings to different quantum fluence rates of R and BL, kinetics of Rubisco capacity, Chl content and chloroplast structure were studied. Under monochromatic light photoreceptors are stimulated selectively and their influence on biosynthetis capacities during chloroplast development can be studied.R irradiations saturate Rubisco capacity even at the lowest quantum fluence rates applied, whereas Chl a+b synthesis depends strongly upon fluence rate of R. Under BL irradiations, both Rubisco capacity and Chl content are fluence rate dependent. R irradiations favour Chl b synthesis relative to Chl a, whereas under BL Chl a content is high relative to Chl b. Under R irradiation Pfr is the main photoreceptor involved in regulation of Rubisco capacity whereas under BL a specific BL absorbing photoreceptor may control the response. From the fluence rate dependency under BL irradiations it is concluded that the blue region of the day light spectrum may be the sensor for monitoring fluence rate and causing the characteristic changes in shade and high/low WL adaptation with respect to Rubisco levels in Chenopodium.

Different Red Light Requirements for Phytochrome-Induced Accumulation of cab RNA and rbcS RNA

For several species of plants the abundance of those transcripts encoding the chlorophyll a/b binding protein (cab RNA) and the small subunit of ribulose-1,5-biphosphate carboxylase-oxygenase (rbcS RNA) has been established as being under the control of phytochrome. However, this conclusion does not take into account the various types of phytochrome control based on both the fluence of red light necessary to induce the response and the ability of far red light either to induce or to reverse the response. The fluence of red light necessary to induce the accumulation of rbcS RNA was found to be 10,000 times greater than that necessary to induce the accumulation of cab RNA. Furthermore, far red light alone was capable of inducing the accumulation of cab RNA. It is possible, therefore, that developing pea buds accumulate cab RNA before rbcS and that cab RNA is not subject to the normal end-of-day signals affecting many phytochrome responses.

Determination of the translation start site of the large subunit of ribulose-1,5-bisphosphate carboxylase from maize

Sequence studies of the gene for the large subunit of ribulose-1,5-bisphosphate carboxylase from maize indicate the presence of two translation start sites, 18 bp apart. Each site is preceded by a suitable ribosome binding region. By using a simplified E. coli-based in vitro system which measures fromation of the first dipeptide of the gene product, we have determined that only the second methionine initiates translation.

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.

An inverse control by phytochrome of the expression of two nuclear genes in barley (Hordeum vulgare L.)

During the light-dependent transformation of etioplasts to chloroplasts a rapid decrease of the NADPH-protochlorophyllide oxidoreductase is induced. At the same time the mRNA activity coding for this enzyme protein also declines rapidly under the influence of phytochrome (Pfr). On the other hand the apoprotein of the light-harvesting chlorophyll a/b protein and its mRNA activity are inversely affected by the same photoreceptor. Cloned cDNA sequences which are complementary to these mRNAs have been used to assess the effect of phytochrome (Pfr) on the concentration of the two transcripts. The phytochrome-induced changes of the two translatable mRNAs are paralleled by corresponding changes in the steady-state concentration of the mRNA sequences. This inverse relationship between the light-dependent regulation of the NADPH-protochlorophyllide oxidoreductase and the light-harvesting chlorophyll a/b protein suggests that a single reversible triggering event can increase the transcription of certain genes and decrease the transcription of others.