Diurnal and Circadian Rhythms in the Accumulation and Synthesis of mRNA for the Light-Harvesting Chlorophyll a/b-Binding Protein in Tobacco

Methods to optimize optical sensing of biotic plant stress - combined effects of hyperspectral imaging at night and spatial binning

In spatio-temporal plant monitoring, optical sensing (including hyperspectral imaging), is being deployed to, non-invasively, detect and diagnose plant responses to abiotic and biotic stressors. Early and accurate detection and diagnosis of stressors are key objectives. Level of radiometric repeatability of optical sensing data and ability to accurately detect and diagnose biotic stress are inversely correlated. Accordingly, it may be argued that one of the most significant frontiers and challenges regarding widespread adoption of optical sensing in plant research and crop production hinges on methods to maximize radiometric repeatability. In this study, we acquired hyperspectral optical sensing data at noon and midnight from soybean (Glycine max) and coleus wizard velvet red (Solenostemon scutellarioides) plants with/without experimentally infestation of two-spotted spider mites (Tetranychus urticae). We addressed three questions related to optimization of radiometric repeatability: (1) are reflectance-based plant responses affected by time of optical sensing? (2) if so, are plant responses to two-spotted spider mite infestations (biotic stressor) more pronounced at midnight versus at noon? (3) Is detection of biotic stress enhanced by spatial binning (smoothing) of hyperspectral imaging data? Results from this study provide insight into calculations of radiometric repeatability. Results strongly support claims that acquisition of optical sensing data to detect and characterize stress responses by plants to detect biotic stressors should be performed at night. Moreover, the combination of midnight imaging and spatial binning increased classification accuracies with 29% and 31% for soybean and coleus, respectively. Practical implications of these findings are discussed. Study results are relevant to virtually all applications of optical sensing to detect and diagnose abiotic and biotic stress responses by plants in both controlled environments and in outdoor crop production systems.

Calibration to maximize temporal radiometric repeatability of airborne hyperspectral imaging data

Many studies provide insight into calibration of airborne remote sensing data but very few specifically address the issue of temporal radiometric repeatability. In this study, we acquired airborne hyperspectral optical sensing data from experimental objects (white Teflon and colored panels) during 52 flight missions on three separate days. Data sets were subjected to four radiometric calibration methods: no radiometric calibration (radiance data), empirical line method calibration based on white calibration boards (ELM calibration), and two atmospheric radiative transfer model calibrations: 1) radiometric calibration with irradiance data acquired with a drone-mounted down-welling sensor (ARTM), and 2) modeled sun parameters and weather variables in combination with irradiance data from drone-mounted down-welling sensor (ARTM+). Spectral bands from 900-970 nm were found to be associated with disproportionally lower temporal radiometric repeatability than spectral bands from 416-900 nm. ELM calibration was found to be highly sensitive to time of flight missions (which is directly linked to sun parameters and weather conditions). Both ARTM calibrations outperformed ELM calibration, especially ARTM2+. Importantly, ARTM+ calibration markedly attenuated loss of radiometric repeatability in spectral bands beyond 900 nm and therefore improved possible contributions of these spectral bands to classification functions. We conclude that a minimum of 5% radiometric error (radiometric repeatability<95%), and probably considerably more error, should be expected when airborne remote sensing data are acquired at multiple time points across days. Consequently, objects being classified should be in classes that are at least 5% different in terms of average optical traits for classification functions to perform with high degree of accuracy and consistency. This study provides strong support for the claim that airborne remote sensing studies should include repeated data acquisitions from same objects at multiple time points. Such temporal replication is essential for classification functions to capture variation and stochastic noise caused by imaging equipment, and abiotic and environmental variables.

Draft genome of Puya raimondii (Bromeliaceae), the Queen of the Andes

Puya raimondii, the Queen of the Andes, is an endangered high Andean species in the Bromeliaceae family. Here, we report its first genome to promote its conservation and evolutionary study. Comparative genomics showed P. raimondii diverged from Ananas comosus about 14.8 million years ago, and the long terminal repeats were likely to contribute to the genus diversification in last 3.5 million years. The gene families related to plant reproductive development and stress responses significantly expanded in the genome. At the same time, gene families involved in disease defense, photosynthesis and carbohydrate metabolism significantly contracted, which may be an evolutionary strategy to adapt to the harsh conditions in high Andes. The demographic history analysis revealed the P. raimondii population size sharply declined in the Pleistocene and then increased in the Holocene. We also designed and tested 46 pairs of universal primers for amplifying orthologous single-copy nuclear genes in Puya species.

Tetrapyrrole Signaling in Plants

Tetrapyrroles make critical contributions to a number of important processes in diverse organisms. In plants, tetrapyrroles are essential for light signaling, the detoxification of reactive oxygen species, the assimilation of nitrate and sulfate, respiration, photosynthesis, and programed cell death. The misregulation of tetrapyrrole metabolism can produce toxic reactive oxygen species. Thus, it is not surprising that tetrapyrrole metabolism is strictly regulated and that tetrapyrrole metabolism affects signaling mechanisms that regulate gene expression. In plants and algae, tetrapyrroles are synthesized in plastids and were some of the first plastid signals demonstrated to regulate nuclear gene expression. In plants, the mechanism of tetrapyrrole-dependent plastid-to-nucleus signaling remains poorly understood. Additionally, some of experiments that tested ideas for possible signaling mechanisms appeared to produce conflicting data. In some instances, these conflicts are potentially explained by different experimental conditions. Although the biological function of tetrapyrrole signaling is poorly understood, there is compelling evidence that this signaling is significant. Specifically, this signaling appears to affect the accumulation of starch and may promote abiotic stress tolerance. Tetrapyrrole-dependent plastid-to-nucleus signaling interacts with a distinct plastid-to-nucleus signaling mechanism that depends on GENOMES UNCUOPLED1 (GUN1). GUN1 contributes to a variety of processes, such as chloroplast biogenesis, the circadian rhythm, abiotic stress tolerance, and development. Thus, the contribution of tetrapyrrole signaling to plant function is potentially broader than we currently appreciate. In this review, I discuss these aspects of tetrapyrrole signaling.

Measurement of luciferase rhythms

Firefly luciferase (LUC) is a sensitive and versatile reporter for the analysis of gene expression. Transgenic plants carrying CLOCK GENE promoter:LUC fusions can be assayed with high temporal resolution. LUC measurement is sensitive, noninvasive, and nondestructive and can be readily automated, greatly facilitating genetic studies. For these reasons, LUC fusion analysis is a mainstay in the study of plant circadian clocks.

Light-harvesting chlorophyll a/b-binding proteins, positively involved in abscisic acid signalling, require a transcription repressor, WRKY40, to balance their function

The light-harvesting chlorophyll a/b-binding (LHCB) proteins are the apoproteins of the light-harvesting complex of photosystem II. In the present study, we observed that downregulation of any of the six LHCB genes resulted in abscisic acid (ABA)-insensitive phenotypes in seed germination and post-germination growth, demonstrating that LHCB proteins are positively involved in these developmental processes in response to ABA. ABA was required for full expression of different LHCB members and physiologically high levels of ABA enhanced LHCB expression. The LHCB members were shown to be targets of an ABA-responsive WRKY-domain transcription factor, WRKY40, which represses LHCB expression to balance the positive function of the LHCBs in ABA signalling. These findings revealed that ABA is an inducer that fine-tunes LHCB expression at least partly through repressing the WRKY40 transcription repressor in stressful conditions in co-operation with light, which allows plants to adapt to environmental challenges.

Beyond Arabidopsis: the circadian clock in non-model plant species

Circadian clocks allow plants to temporally coordinate many aspects of their biology with the diurnal cycle derived from the rotation of Earth on its axis. Although there is a rich history of the study of clocks in many plant species, in recent years much progress in elucidating the architecture and function of the plant clock has emerged from studies of the model plant, Arabidopsis thaliana. There is considerable interest in extending this knowledge of the circadian clock into diverse plant species in order to address its role in topics as varied as agricultural productivity and the responses of individual species and plant communities to global climate change and environmental degradation. The analysis of circadian clocks in the green lineage provides insight into evolutionary processes in plants and throughout the eukaryotes.

Light-harvesting chlorophyll a/b-binding proteins are required for stomatal response to abscisic acid in Arabidopsis

The light-harvesting chlorophyll a/b binding proteins (LHCB) are perhaps the most abundant membrane proteins in nature. It is reported here that the down-regulation or disruption of any member of the LHCB family, LHCB1, LHCB2, LHCB3, LHCB4, LHCB5, or LHCB6, reduces responsiveness of stomatal movement to ABA, and therefore results in a decrease in plant tolerance to drought stress in Arabidopsis thaliana. By contrast, over-expression of a LHCB member, LHCB6, enhances stomatal sensitivity to ABA. In addition, the reactive oxygen species (ROS) homeostasis and a set of ABA-responsive genes are altered in the lhcb mutants. These data demonstrate that LHCBs play a positive role in guard cell signalling in response to ABA and suggest that they may be involved in ABA signalling partly by modulating ROS homeostasis.

Proteomic identification of rhythmic proteins in rice seedlings

Many aspects of plant metabolism that are involved in plant growth and development are influenced by light-regulated diurnal rhythms as well as endogenous clock-regulated circadian rhythms. To identify the rhythmic proteins in rice, periodically grown (12h light/12h dark cycle) seedlings were harvested for three days at six-hour intervals. Continuous dark-adapted plants were also harvested for two days. Among approximately 3000 reproducible protein spots on each gel, proteomic analysis ascertained 354 spots (~12%) as light-regulated rhythmic proteins, in which 53 spots showed prolonged rhythm under continuous dark conditions. Of these 354 ascertained rhythmic protein spots, 74 diurnal spots and 10 prolonged rhythmic spots under continuous dark were identified by MALDI-TOF MS analysis. The rhythmic proteins were functionally classified into photosynthesis, central metabolism, protein synthesis, nitrogen metabolism, stress resistance, signal transduction and unknown. Comparative analysis of our proteomic data with the public microarray database (the Plant DIURNAL Project) and RT-PCR analysis of rhythmic proteins showed differences in rhythmic expression phases between mRNA and protein, suggesting that the clock-regulated proteins in rice are modulated by not only transcriptional but also post-transcriptional, translational, and/or post-translational processes.

Characterization of two Myb-like transcription factors binding to CAB promoters in wheat and barley

The expression pattern and level of light-regulated genes are controlled by complex regulatory networks. Expression of genes encoding chlorophyll a/b-binding proteins of photosystem II is controlled by different photoreceptors and regulated primarily at the level of transcription. Light-dependent transcription of these genes is further modulated by the circadian system, affected by a developmental program and by a variety of environmental factors such as stress. Here we report the isolation of two Myb-like transcription factors from barley, HvMCB1 and HvMCB2, that bind specifically to defined regions of CAB promoters derived from wheat and barley. Deletion and mutation analysis of the wheat CAB1 promoter suggest that HvMCB1 and HvMCB2 are required for high-level but not for light- and circadian clock-regulated expression. Moreover, we demonstrate that the induction of HvMCB1 and HvMCB2 transcription is regulated differentially by environmental factors and plastid development. These observations indicate that HvMCB1 and HvMCB2, together with other, yet unknown regulatory factors, may mediate responsiveness of CAB gene transcription to a variety of environmental and developmental signals.

Cloning and characterisation of chlorophyll synthase from Avena sativa

The chlorophyll synthase gene from oat (Avena sativa) was cloned and expressed in Escherichia coli. The deduced amino acid sequence consists of 378 amino acids including a presequence of 46 amino acids. Deletion mutants show that a core protein comprising amino acid residues 88 to 377 is enzymatically active. The sequence of the mature protein shows 85% identity with the chlorophyll synthase of Arabidopsis thaliana and 62% identity with the chlorophyll synthase of Synechocystis PCC 6803. The gene is constitutively expressed as the same transcript level is found in dark-grown and in light-grown seedlings. The enzyme requires magnesium ions for activity; manganese ions can reconstitute only part of the activity. Diacetyl and N-phenylmaleimide (NPM) inhibit the enzyme activity. Site-directed mutagenesis reveals that, out of the 4 Arg residues present in the active core protein, Arg-91 and Arg-161 are essential for the activity. Five cysteine residues are present in the core protein, of which only Cys-109 is essential for the enzyme activity. Since the wild-type and all other Cys-mutants with the exception of the mutant C304A are inhibited by N-phenylmaleimide, we conclude that the inhibitor binds to a non-essential Cys residue to abolish activity. The role of the various Arg and Cys residues is discussed.

Complete 5' and 3' end maturation of group II intron-containing tRNA precursors

Higher plant chloroplasts provide the only experimentally validated example of functional tRNA genes that are disrupted by group II introns. Here, precursor transcripts for tRNA(Gly)(UCC), tRNA(Val)(UAC), and tRNA(Ala)(UGC) were investigated for processing of 5' leader and 3' trailer sequences in vivo. Use of intron-specific primer pairs and inclusion of a barley chloroplast splicing mutant specifically allowed us to evaluate the potential effect of intervening sequences that disrupt tRNA secondary and tertiary structures. The data suggest that (1) neither integrity of the dihydrouridine nor the anticodon domain is required for the nucleotidyltransferase-mediated addition of 3'-terminal CCA; (2) interruption of these two structural elements by group II introns does not interfere with nucleotide-specific 5' maturation by RNase P; (3) processing intermediates of chloroplast tRNAs can be 3' polyadenylated; and (4) plastid DNA-encoded proteins are not required for 3' and 5' maturation of plastid tRNAs.

A gene family encoding glutathione peroxidase homologues in Hordeum vulgare (barley)

We have isolated and characterised three barley cDNAs encoding glutathione peroxidase (GPX) homologues, designated HVGPH1, HVGPH2 and HVGPH3. HVGPH1 may represent a cytosolic form of GPX. The structure of the HVGPH2 N-terminal domain is typical for a plastid transit peptide. A potential peroxisomal targeting sequence occurs near the N-terminus of HVGPH3. Transcript levels of HVGPH1 and HVGPH2 were increased in leaves undergoing stress. In contrast, HVGPH3 mRNA accumulation showed a negative response to stress. Our data indicate that the barley genome bears a small gene family encoding GPX homologues differing in their function and cellular localisation.

Inter-organellar crosstalk in higher plants: impaired chloroplast development affects mitochondrial gene and transcript levels

Co-ordination of gene expression between the three genomes present in plastids, mitochondria and nucleus is of crucial importance for plant cells. Previous studies revealed that in white leaves of the albostrians (Hordeum vulgare cv. Haisa) mutant, photosynthesis-related plastid and nuclear genes are expressed only at an extremely low level. The plastids of this mutant lack ribosomes, photosynthetic activity and have only rudimentary membrane systems. Here we report on the expression of mitochondrial genes in albostrians barley. Steady-state RNA levels of the mitochondrial genes encoding cytochrome oxidase or ATPase subunits, coxII, coxIII, atpA, atp6, atp9 and cob, were observed to be consistently elevated in the white leaves but not in roots. Investigation of mitochondrial DNA revealed an about three-fold enhanced mitochondrial gene copy number in white compared to green leaf cells, but no differential amplification of mitochondrial genes. Analysis of plants in which the white albostrians plastids were combined with a new nuclear background showed that the enhanced transcript levels were a consequence of the impaired plastids and not of the nuclear albostrians allele. Furthermore, plants bleached by the carotenoid biosynthesis inhibitor norflurazon also showed an enhanced mitochondrial transcript level. These findings allow the conclusion that lack of chloroplast activity in an otherwise fully differentiated leaf leads to an increase in mitochondrial gene copy number and an elevated level of mitochondrial transcripts. Our results indicate an influence of plastids on the genetic apparatus of mitochondria in leaves but not in roots.

Subpopulations of chloroplast ribosomes change during photoregulated development of Zea mays leaves: ribosomal proteins L2, L21, and L29

Seedlings grown in darkness, i.e., etiolated seedlings, lack chlorophyll and most other components of the photosynthetic apparatus. On illumination, the plastids become photosynthetically competent through the production of chlorophylls and proteins encoded by certain chloroplast and nuclear genes. There are two types of photosynthetic cells in leaves of the C4 plant maize: bundle sheath cells (BSC) and adjacent mesophyll cells (MC). Some proteins of the maize photosynthetic machinery are solely or preferentially localized in MC and others in BSC. A particular gene may be photoregulated up in one cell type and down in the other. Transcripts of the nuclear gene rpl29, encoding the chloroplast ribosomal protein L29, increase in abundance about 17-fold during light-induced maturation of plastids. There is about 1.5 times more L29 protein in ribosomes of greening leaves than in ribosomes of unilluminated leaves; the L29 contents of MC and BSC are about the same. However, L21 is present about equally in plastid ribosomes of unilluminated and illuminated seedlings. In contrast to both L29 and L21, the fraction of the ribosome population containing L2 is about the same in MC and BSC of etiolated leaves but, on illumination, the proportion of the ribosome population with L2 increases in BSC but not in MC. The existence of different subpopulations of plastid ribosomes-e.g., those with and without L21 and/or L29 during development-evokes interesting, but as yet unanswered, questions about the roles of different types of ribosomes in differentiation.

Imbibition, but not release from stratification, sets the circadian clock in Arabidopsis seedlings

Circadian rhythms in the abundance of the CAT2 catalase mRNA were not seen in etiolated seedlings but developed upon illumination. These circadian oscillations were preceded by a rapid and transient induction of CAT2 mRNA abundance that varied strikingly according to the timing (circadian phase) of the onset of illumination. This variation oscillated with a circadian periodicity of approximately 28 hr, indicating that the circadian oscillator is running in etiolated seedlings and regulates (gates) the induction of CAT2 by light. Moreover, because we assayed populations of seedlings, we infer that the individual clocks among populations of etiolated seedlings were synchronized before the onset of illumination. What developmental or environmental signals synchronized the clocks among seedlings? Varying the phase of the onset of illumination relative to release from stratification failed to affect the acute induction of CAT2, indicating that the temperature step from 4 to 22 degrees C associated with release from stratification did not reset the circadian clock. However, the acute induction of CAT2 mRNA varied with time after imbibition, demonstrating that imbibition provides a signal capable of resetting the circadian clock and of synchronizing the clocks among populations of seedlings.

Endogenous fluctuations of DNA topology in the chloroplast of Chlamydomonas reinhardtii

DNA supercoiling in the chloroplast of the unicellular green alga Chlamydomonas reinhardtii was found to change with a diurnal rhythm in cells growing in alternating 12-h dark-12-h light periods. Highest and lowest DNA superhelicities occurred at the beginning and towards the end of the 12-h light periods, respectively. The fluctuations in DNA supercoiling occurred concurrently and in the same direction in two separate parts of the chloroplast genome, one containing the genes psaB, rbcL, and atpA and the other containing the atpB gene. Fluctuations were not confined to transcribed DNA regions, indicating simultaneous changes in DNA conformation all over the chloroplast genome. Because the diurnal fluctuations persisted in cells kept in continuous light, DNA supercoiling is judged to be under endogenous control. The endogenous fluctuations in chloroplast DNA topology correlated tightly with the endogenous fluctuations of overall chloroplast gene transcription and with those of the pool sizes of most chloroplast transcripts analyzed. This result suggests that DNA superhelical changes have a role in the regulation of chloroplast gene expression in Chlamydomonas.

Splicing and intron-internal RNA editing of trnK-matK transcripts in barley plastids: support for MatK as an essential splice factor

Group II introns frequently require assistance by specific factors, maturases, for folding and effective splicing in vivo. The only putative maturase of higher plant chloroplasts is encoded by matK, located in the intron of trnK. We show that in barley matK transcripts are modified at a first codon base by C-to-U RNA editing. The resulting H --> Y substitution restores a sequence motif that is present in maturases of yeast and plant mitochondria and of Lactococcus ltrA and that is positioned within the X domain. Processing of trnK-matK transcripts was further investigated in plastids lacking functional ribosomes due to a mutation. Absence of the intron-encoded matK gene product in these plastids is correlated with the accumulation of precursor transcripts for tRNALys(UUU)-matK, processed to different degrees, and by the lack of mature and spliced tRNA molecules. These results suggest an essential role of MatK for splicing of its own transcript in vivo. Processing of the 5' end of trnK exon 1 was found to proceed efficiently also in the mutant plastids although the two tRNA exons were separated by the 2481 nt intron. Consequently, presence of the intron does not interfere with the formation of mature 5' termini.

Conserved circadian elements in phylogenetically diverse algae

Circadian expression of the luciferin-binding protein (LBP) from the dinoflagellate Gonyaulax polyedra is regulated at the translational level. A small interval in the lbp 3'-untranslated region, which contains seven UG-repeats, serves as a cis-acting element to which a trans-acting factor (CCTR) binds in a circadian manner. Its binding activity correlates negatively with the circadian expression of LBP. Here I report the identification of a protein in the green alga Chlamydomonas reinhardtii that represents a CCTR analog. It binds both specifically and under control of the circadian clock to the UG-repeat region. The data show for the first time that circadian cis-elements implicated in translational regulation have been conserved during evolution.

The Chlamydomonas reinhardtii LI818 gene represents a distant relative of the cabI/II genes that is regulated during the cell cycle and in response to illumination

In the green unicellular alga Chlamydomonas reinhardtii, as in higher plants, the expression of the genes encoding the chlorophyll a/b-binding (CAB) polypeptides associated with photosystem I (PSI) and photosystem II (PSII) is regulated by endogenous (circadian clock) and exogenous signals (light and temperature). The circadian clock ensures that the oscillation in the levels of the different cab mRNAs is continuously kept in phase with light/dark (LD) cycles and is maximal by the middle of the day. On the other hand, light controls the amplitude of the oscillations. We report here the cloning and characterization of the C. reinhardtii LI818 gene, which identifies a CAB-related polypeptide and whose expression is regulated quite differently from the cab I/II genes. We show: (1) that in LD synchronized Chlamydomonas cells LI818 mRNA accumulation is subject to dual regulation that involves separable regulation by light and an endogenous oscillator; (2) that LI818 mRNA is fully expressed several hours before the cab I/II mRNAs and that the latter accumulate concomitantly; (3) that blocking the electron flow through PSII using DCMU prevents cells from accumulating cab I/II mRNAs but not LI818 mRNA and (4) that the accumulation of LI818 mRNA is abolished by blocking cytoplasmic protein synthesis, suggesting that these regulatory mechanisms are mediated by labile proteins.

Significance of circadian gene expression in higher plants

The significance of the circadian clock for living organisms is not fully understood. Recent findings demonstrate circadian control of transcription of quite a number of genes with individual maxima throughout the entire day. Evidence in favor of circadian-clock-controlled translation has also been documented. In this article, we want to promote the idea that in plants the clock functions as a regulator which coordinates critical cellular processes, such as cell division, nitrate reduction, or synthesis of chlorophyll-protein complexes, in such a way that the generation of dangerous, oxidative radicals or exposure to harmful light is minimized. This has been achieved by plant organisms either by confining gene expression to the dark phase or by a tight coordination of different tiers of gene expression during the light phase. This leads to the consequence for the researcher that the time of experimentation needs to be carefully considered and documented. It also follows that one might lose important findings if only a particular portion of the day is investigated.

Impaired splicing of the rps12 transcript in ribosome-deficient plastids

Analysis of RNA maturation in ribosome-deficient plastids of four non-allelic barley mutants revealed an increased accumulation and altered processing of transcripts of the ribosomal protein gene CS12 (rps12) compared to normal chloroplasts. The three exons of rps12 are part of two different polycistronic transcription units. Generation of mature rps12-mRNA involves both cis- and trans-splicing. In ribosome-deficient plastids, the cis-intron separating exons 2 and 3 remains entirely unspliced whereas the splicing of the bipartite rps12 trans-intron between exon 1 and exon 2 occurs, but at a reduced level. A comparison of the 3' and 5' ends of the two RNAs that are generally assumed to interact during trans-splicing showed a difference in the processing pathways of 3' rps12 transcripts between mutated and normal chloroplasts. Nonetheless, the final products were identical.

Expression of tobacco genes for light-harvesting chlorophyll a/b binding proteins of photosystem II is controlled by two circadian oscillators in a developmentally regulated fashion

Light-induced expression of genes encoding the light-harvesting chlorophyll a/b binding proteins of photosystem II (Cab) was shown to be controlled by a circadian oscillator coupled to the red-light-absorbing plant photoreceptor phytochrome. Here we show that a red-light-insensitive oscillator is also involved in regulating the expression of the Cab genes. We provide evidence that germination leads, in a light-independent manner, to the setting and/or synchronization of endogenous oscillators and that it induces the expression of Cab genes in a circadian fashion. This circadian oscillator is not coupled to phytochrome, as it cannot be reset by red light for at least 44 h after sowing. Short red light pulses given between 12 and 44 h after sowing, however, induce new rhythms without perturbing the already free-running red-light-independent circadian oscillation. At this stage of development, the phytochrome-coupled and uncoupled circadian rhythms coexist. Both circadian rhythms are expressed and exhibit period lengths close to 24 h but are phased differently. At later stages of development (60 h or later after sowing), red light treatments synchronized these free-running rhythms and led to the appearance of a single new circadian oscillation. These data indicate that during early development the expression of single tobacco Cab genes, particularly expression of the Cab21 and Cab40 genes, is controlled in a developmentally dependent manner by two circadian oscillators.

The steady-state mRNA levels for thylakoid proteins exhibit coordinate diurnal regulation

Steady-state mRNA levels for thylakoid proteins were analysed in spinach cotyledons under diurnally changing light conditions. Most fluctuate considerably throughout the day, while the levels of others show only low amplitude or no oscillation. Levels of mRNAs coding for proteins that belong to the same multiprotein complex generally oscillate in parallel and exhibit maxima that are specific for that complex: mRNAs for photosystem I proteins appear prior to those for photosystem II polypeptides and these again prior to mRNAs for the three polypeptides constituting the oxygen-evolving complex. For the mRNAs that change with high amplitudes (e.g. those for LHCP or the 20 kDa apoprotein of the CP24 complex) oscillations have also been found under constant conditions, indicating that a circadian oscillator is involved. Transgenic tobacco seedlings harbouring chimeric GUS gene fusions with 5'-flanking sequences from the spinach genes Lhcb, PsaF and AtpD (encoding a light-harvesting chlorophyll a/b apoprotein of photosystem II, subunit 3 of photosystem I and subunit delta of the plastid ATP synthase, respectively) confirm that the differences in the amplitudes as well as the timepoints of maximum mRNA accumulation are perceived via cis-regulatory elements upstream of the respective ATG codons.

Avenacosidase from oat: purification, sequence analysis and biochemical characterization of a new member of the BGA family of beta-glucosidases

A protein consisting of 60 kDa subunits (As-P60) was isolated from etiolated oat seedlings (Avena sativa L.) and characterized as avenacosidase, a beta-glucosidase that belongs to a preformed defence system of oat against fungal infection. The enzyme is highly aggregated; it consists of 300-350 kDa aggregates and multimers thereof. Dissociation by freezing/thawing leads to complete loss of enzyme activity. The specificity of the enzyme was investigated with para-nitrophenyl derivatives which serve as substrates, in decreasing order beta-fucoside, beta-glucoside, beta-galactoside, beta-xyloside. The corresponding orthonitrophenyl glycosides are less well accepted. No hydrolysis was found with alpha-glycosides and beta-thioglucoside. An anti-As-P60 antiserum was prepared and used for isolation of a cDNA clone coding for As-P60. A presequence of 55 amino acid residues was deduced from comparison of the cDNA sequence with the N-terminal sequence determined by Edman degradation of the mature protein. The presequence has the characteristics of a stroma-directing signal peptide; localization of As-P60 in plastids of oat seedlings was confirmed by western blotting. The amino acid sequence revealed significant homology (> 39% sequence identity) to beta-glucosidases that are constituents of a defence mechanism in dicotyledonous plants. 34% sequence identity was even found with mammalian and bacterial beta-glucosidases of the BGA family. Avenacosidase extends the occurrence of this family of beta-glucosidases to monocotyledonous plants.

Control of lhc gene transcription by the circadian clock in Chlamydomonas reinhardtii

Transcription of nuclear lhc genes has been shown to be under circadian clock control in angiosperms. but many aspects of this regulation have not been elucidated. Unicellular organisms, such as the green alga Chlamydomonas reinhardtii, offer significant advantages for the study of cellular clocks. Therefore, we have asked whether lhc gene expression is regulated by a circadian clock in C. reinhardtii. The mRNA for a photosystem I chlorophyll a/b apoprotein showed a strong diurnal rhythm in cells growing under 12 h/12 h light/dark (LD) cycles; the mRNA accumulated and then declined during the light period reaching very low levels at mid-dark. A similar diurnal pattern was documented for rbcS mRNA. In LD-grown cells shifted to continuous light, the ca. 24 h rhythm of lhca1 mRNA continued for at least 2 cycles. In LD-grown cells shifted to continuous darkness the rhythm of lhca1, but not rbcS2, mRNA also continued, although at lower absolute levels than in LD-grown cells. Also, in the cells shifted to continuous dark, the lhca1 mRNA rhythm persisted in the absence of significant cell division. Pulse-labelling with 32PO4 and sensitivity to actinomycin D demonstrated that control of lhca1 (and rbcS) is mainly transcriptional. However, it was also shown that the half-life of lhca1 mRNA (and rbcS2) is short (1-2 h) and may also vary somewhat during a cycle. We conclude that a cellular, circadian clock regulates lhca1 transcription in C. reinhardtii.

Automated sampling and RNA isolation at room temperature for measurements of circadian rhythms in Chlamydomonas reinhardtii

The development of techniques allowing the unattended collection of RNA from cell samples at room temperature makes practical accurate and facile monitoring of circadian rhythms in Chlamydomonas reinhardtii. The utility of these methods was demonstrated by collecting RNA samples for three days from cells maintained in continuous darkness. Every hour, cells were automatically collected and lysed with buffer containing SDS and proteinase K. Samples were maintained at room temperature with little or no evidence of degradation of RNA. Strong, non-damping circadian rhythms of cab mRNA abundance were measured. Free-running rhythms of about 24 h were measured from cultures maintained at 16, 20, 25 and 30 degrees C, thus demonstrating temperature compensation of circadian period. Simultaneous collections from cultures previously entrained to 12 h light/12 h dark cycles of opposite phase displayed circadian rhythms of cab mRNA abundance that were in phase with their previous entraining light cycles. Thus, this result suggests that the measured circadian rhythms of cab mRNA abundance was not an artifact of the collection procedure.

Destabilization of rbcS sense transcripts by antisense RNA

Steady-state rbcS mRNA levels are drastically reduced in transgenic tobacco plants that express rbcS antisense RNAs. We have found that these reductions are not due to an effect of the antisense RNA at the level of rbcS transcription; rather, the sense mRNAs are more actively degraded in the mutant than wild-type plants. We have examined the kinetics of this turnover process by inhibiting transcription with cordycepin, and have found that rbcS sense mRNA decay is accelerated about five-fold in the antisense plants. This provides direct evidence that antisense RNAs can serve to destabilize sense transcripts in plants.

Ribosome-deficient plastids affect transcription of light-induced nuclear genes: genetic evidence for a plastid-derived signal

Transcription of ten nuclear genes was analysed in the albostrians mutant of barley (Hordeum vulgare L.). The lack of plastid ribosomes in white seedlings of this mutant results in a complex alteration of nuclear gene expression at the transcriptional level. We found a strong reduction in the accumulation of mRNAs transcribed from nuclear genes encoding chloroplast enzymes involved in the Calvin cycle, the chlorophyll a/b binding protein, and the cytosolic enzyme nitrate reductase. In contrast, the levels of transcripts of the genes encoding the cytosolic glycolytic enzymes glyceraldehyde phosphate dehydrogenase and phosphoglycerate kinase were slightly enhanced. Accumulation of chalcone synthase mRNA even reaches much higher levels in white than in green leaves. Ribosome-deficient plastids were combined by crossing with a nuclear genotype heterozygous for the albostrians allele. Analysis of transcript levels in F1 plants having the same nuclear genotype and differing only with respect to their content of normally developed chloroplasts versus undifferentiated mutant plastids, provided strong genetic evidence for the plastid being the origin of a signal (chain) involved in regulation of nuclear gene expression. Results of run-on transcription in isolated nuclei demonstrated that the plastid signal acts at the level of transcription; it does not interfere with gene regulation in general. Mechanisms triggering nuclear gene expression in response to light operate in white mutant leaves: the very low levels of mRNAs derived from nuclear genes encoding chloroplast proteins and the strongly enhanced level of chalcone synthase mRNA were both light inducible. Also the negative regulation of leaf thionein gene expression by light is observed in white albostrians seedlings.(ABSTRACT TRUNCATED AT 250 WORDS)

Circadian rhythmicity in the expression of a novel light-regulated rice gene

We have identified and analyzed cDNAs corresponding to a single-copy gene from rice, designated lir1, whose expression exhibits dramatic diurnal fluctuations. The cDNAs encode a putative protein of 128 amino acids with no homology to known proteins. Lir1 mRNA accumulates in the light, reaching maximum and minimum steady-state levels at the end of the light and dark period, respectively. The oscillations of lir1 mRNA abundance persist after the plants have been transferred to continuous light or darkness. Plants germinated in the dark have very low levels of lir1 mRNA, whereas plants germinated in continuous light express lir1 at an intermediate but constant level. These results indicate that lir1 expression is controlled by light and a circadian clock.

Light-regulated and endogenous fluctuations of chloroplast transcript levels in Chlamydomonas. Regulation by transcription and RNA degradation

Changes in the relative sizes of pools of transcripts of organelle genes during plastid development are common in flowering plants, but technical difficulties have prevented direct determinations of the effects of changes in rates of transcription and degradation on such fluctuations. It has been possible to follow both rates in Chlamydomonas reinhardtii. In synchronous or asynchronous cultures of cells grown in 12 h light/12 h dark periods, sizes of pools of transcripts of the chloroplast genes atpA, atpB, tufA, and psaB fluctuate. Differences in chloroplast transcript abundances in light/dark cycles were found to be cell cycle-independent but controlled by either an endogenous rhythm (atpA, atpB, and tufA) or by light (psaB). In vivo labeling experiments showed that transcriptional regulation and light/dark-regulated degradation both contribute, in gene-specific manners, to the level of transcripts of individual C. reinhardtii chloroplast genes in cells grown in alternating light/dark cycles.

Nucleotide sequence of a tobacco cDNA encoding plastidic glutamine synthetase and light inducibility, organ specificity and diurnal rhythmicity in the expression of the corresponding genes of tobacco and tomato

A full-length cDNA encoding glutamine synthetase (GS) was cloned from a lambda gt10 library of tobacco leaf RNA, and the nucleotide sequence was determined. An open reading frame accounting for a primary translation product consisting of 432 amino acids has been localized on the cDNA. The calculated molecular mass of the encoded protein is 47.2 kDa. The predicted amino acid sequence of this precursor shows higher homology to GS-2 protein sequences from other species than to a leaf GS-1 polypeptide sequence, indicating that the cDNA isolated encodes the chloroplastic isoform (GS-2) of tobacco GS. The presence of C- and N-terminal extensions which are characteristic of GS-2 proteins supports this conclusion. Genomic Southern blot analysis indicated that GS-2 is encoded by a single gene in the diploid genomes of both tomato and Nicotiana sylvestris, while two GS-2 genes are very likely present in the amphidiploid tobacco genome. Western blot analysis indicated that in etiolated and in green tomato cotyledons GS-2 subunits are represented by polypeptides of similar size, while in green tomato leaves an additional GS-2 polypeptide of higher apparent molecular weight is detectable. In contrast, tobacco GS-2 is composed of subunits of identical size in all organs examined. GS-2 transcripts and GS-2 proteins could be detected at high levels in the leaves of both tobacco or tomato. Lower amounts of GS-2 mRNA were detected in stems, corolla, and roots of tomato, but not in non-green organs of tobacco. The GS-2 transcript abundance exhibited a diurnal fluctuation in tomato leaves but not in tobacco leaves. White or red light stimulated the accumulation of GS-2 transcripts and GS-2 protein in etiolated tomato cotyledons. Far-red light cancelled this stimulation. The red light response of the GS-2 gene was reduced in etiolated seedlings of the phytochrome-deficient aurea mutant of tomato. These results indicate a phytochrome-mediated light stimulation of GS-2 gene expression during greening in tomato.

Low temperature interrupts circadian regulation of transcriptional activity in chilling-sensitive plants

Impaired chloroplast function is responsible for nearly two-thirds of the inhibition to net photosynthesis caused by dark chilling in tomato (Lycopersicon esculentum Mill.), yet it has not been possible to localize the dysfunction to specific chloroplast reactions. We report here on an effect that low-temperature exposure has in tomato on the expression of certain nuclear-encoded chloroplast proteins, which may be directly related to the chilling sensitivity of photosynthesis. Transcriptional activity of genes for both the chlorophyll a/b binding protein of photosystem II (Cab) as well as for ribulose 1,5-bisphosphate carboxylase/oxygenase (Rubisco) activase was found to be controlled by an endogenous rhythm. For Cab this rhythm was also visible at the level of newly synthesized protein, indicating that the circadian control of transcriptional activity normally ensures that this protein is synthesized only during daylight hours. However, low-temperature treatment suspended the timing of the rhythm in tomato so that, upon rewarming, the circadian control was reestablished but was displaced from the actual time of day by the length of the chilling exposure. In addition, we found that the normal turnover of Cab and Rubisco activase mRNA was suspended during the low-temperature treatment, but, upon rewarming, this stabilized message was not translated into protein. We believe that the low-temperature-induced mistiming of gene expression together with its effect on the translatability of existing transcripts may be an important clue in unraveling the basis for the chilling sensitivity of photosynthesis in tomato.

Control of cab gene expression in synchronized Chlamydomonas reinhardtii cells

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

Circadian Control of cab Gene Transcription and mRNA Accumulation in Arabidopsis

An intriguing property of many organisms is their ability to exhibit rhythmic cellular events that continue independently of environmental stimuli. These rhythmic processes are generated by an endogenous mechanism known as the biological clock. We wished to determine whether Arabidopsis thaliana will serve as a model plant system for a molecular genetic dissection of the circadian clock. To this end, we investigated the expression of Arabidopsis chlorophyll a/b-binding protein (cab) genes throughout the circadian cycle. Steady-state mRNA levels of the cab2 and cab3 genes showed a dramatic circadian cycling in plants shifted from light/dark cycles to constant darkness, whereas the cab1 mRNA level exhibited little or no cycling under the same conditions. Analysis of cab promoter fusions in transgenic tobacco revealed that both the cab1 and cab2 5[prime] upstream regions confer circadian-regulated expression on a chloramphenicol acetyltransferase (cat) reporter gene. In vitro nuclear run-on transcription assays also indicated that the transcription of the cab1 and cab2 genes is circadian regulated in Arabidopsis. Taken together, these data suggest that a post-transcriptional mechanism influences cab1 mRNA levels in Arabidopsis. The identification of circadian-regulated cis-acting elements in the cab1 and cab2 upstream regions will provide powerful tools for both molecular and genetic analysis of the higher plant circadian clock.

Differential expression of the two Arabidopsis nitrate reductase genes

The differential regulation of the two nitrate reductase (NR, EC 1.6.6.1) genes of Arabidopsis thaliana L. Heynh was examined. cDNAs corresponding to each of the NR genes (NR1 and NR2) were used to measure changes in the steady-state levels of NR mRNA in response to nitrate, light, circadian rhythm, and tissue specificity. Although nitrate-induction kinetics of the two genes are very similar, NR1 is expressed in the absence of nitrate at a higher basal level than NR2. Nitrate induction is transient both in the roots and leaves, however the kinetics are different: the induction and decline in the roots precede that in the leaves. Light induces the expression of each of the genes with significantly different kinetics: NR2 reached saturation more rapidly than did NR1. Both genes showed similar diurnal patterns of circadian rhythm, with NR2 mRNA accumulating earlier in the morning.

Circadian Control of cab Gene Transcription and mRNA Accumulation in Arabidopsis

An intriguing property of many organisms is their ability to exhibit rhythmic cellular events that continue independently of environmental stimuli. These rhythmic processes are generated by an endogenous mechanism known as the biological clock. We wished to determine whether Arabidopsis thaliana will serve as a model plant system for a molecular genetic dissection of the circadian clock. To this end, we investigated the expression of Arabidopsis chlorophyll a/b-binding protein (cab) genes throughout the circadian cycle. Steady-state mRNA levels of the cab2 and cab3 genes showed a dramatic circadian cycling in plants shifted from light/dark cycles to constant darkness, whereas the cab1 mRNA level exhibited little or no cycling under the same conditions. Analysis of cab promoter fusions in transgenic tobacco revealed that both the cab1 and cab2 5[prime] upstream regions confer circadian-regulated expression on a chloramphenicol acetyltransferase (cat) reporter gene. In vitro nuclear run-on transcription assays also indicated that the transcription of the cab1 and cab2 genes is circadian regulated in Arabidopsis. Taken together, these data suggest that a post-transcriptional mechanism influences cab1 mRNA levels in Arabidopsis. The identification of circadian-regulated cis-acting elements in the cab1 and cab2 upstream regions will provide powerful tools for both molecular and genetic analysis of the higher plant circadian clock.

Diurnal Fluctuations in the Content and Functional Properties of the Light Harvesting Chlorophyll a/b Complex in Thylakoid Membranes : Correlation with the Diurnal Rhythm of the mRNA Level

Diurnal fluctuations were observed in the content and some structural and functional properties of the light-harvesting chlorophyll (Chl) a/b pigment-protein complex of photosystem II (LHCII) in young developing wheat (Triticum aestivum) leaves grown under 16 hours light/8 hours dark illumination regime. The fluctuations could be correlated with the diurnal oscillation in the level of mRNA for LHCII. The most pronounced changes occurred in the basal segments of the leaves. They were weaker or hardly discernible in the middle and tip segments. As judged from the diurnal variations of the Chl-a/Chl-b molar ratio, the LHCII content of the thylakoid membranes peaked around 2 pm. This can be accounted for by the cumulative effect of the elevated level of mRNA in the morning and early afternoon. In the basal segment, the extent of the fluctuation in the LHCII content was approximately 25%, as determined from gel electrophoresis ("green gels"). The amplitude of the principal bands of the circular dichroism (CD) spectra of isolated chloroplasts paralleled the changes in the LHCII content. Our circular dichroism data suggest that the newly synthesized LHCII complexes are incorporated into the existing helically organized macrodomains of the pigment-protein complexes or themselves form such macrodomains in the thylakoid membranes. Chl-a fluorescence induction kinetics also showed diurnal variations especially in the basal segments of the leaves. This most likely indicates fluctuations in the ability of membranes to undergo "state transitions." These observations suggest a physiological role of diurnal rhythm of mRNA for LHCII in young developing leaves.

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.

Effect of light/dark cycles on expression of nitrate assimilatory genes in maize shoots and roots

The level of nitrate reductase (NR) and nitrite reductase (NiR) varied in both shoot and root tissue from nitrate-fed Zea mays L. grown under a 16-hour light/8-hour dark regime over a 10-day period postgermination, with peak activity occurring in days 5 to 6. To study the effect of different light regimes on NR and NiR enzyme activity and mRNA levels, 6-day-old plants were grown in the presence of continuous KNO(3) (10 millimolar). Both shoot NRA and mRNA varied considerably, peaking 4 to 8 hours into the light period. Upon transferring plants to continuous light, the amplitude of the peaks increased, and the peaks moved closer together. In continuous darkness, no NR mRNA or NR enzyme activity could be detected by 8 hours and 12 hours, respectively. In either a light/dark or continuous light regime, root NRA and mRNA did not vary substantially. However, when plants were placed in continuous darkness, both declined steadily in the roots, although some remained after 48 hours. Although there was no obvious cycling of NiR enzyme activity in shoot tissue, changes in mRNA mimicked those seen for NR mRNA. The expression of NR and NiR genes is affected by the light regime adopted, but light does not have a direct effect on the expression of these genes.

Diurnal Rhythmicity in the Pattern of mRNAs in the Leaves of Sinapis alba

Previous studies have shown that certain specific leaf mRNAs exhibit a diurnal rhythmicity in their quantity in higher plants. To determine whether this situation is restricted to a few mRNAs, or affects a large number, we have used in vitro translation and two-dimensional polyacrylamide gel electrophoresis to analyze the mRNA complement in leaves of Sinapis alba at different times during an 8-hour/16-hour day/night cycle. A method for the visual analysis of two-dimensional polyacrylamide gel electrophoresis was also developed. This method selected, at each sampling time, spots that were significant. It then selected, between two sampling times, intensity changes that were significant at the 0.02 confidence level. During a day/night cycle, complex rhythmic changes affected about 10% of the mRNAs. Nineteen different rhythm patterns were found. These 19 patterns fell into four main classes: mRNAs that increase during the light period and decrease during the dark, mRNAs that increase and then decrease during the light period, mRNAs that decrease during the light period and increase during the dark period, and mRNAs that increase and then decrease during the dark period.

Analysis of the diurnal expression patterns of the tomato chlorophyll a/b binding protein genes. Influence of light and characterization of the gene family

Steady-state mRNA levels of the chlorophyll a/b binding (cab) proteins oscillate substantially during a diurnal cycle in tomato leaves. This accumulation pattern is also observed in complete darkness, supporting the hypothesis that the expression of cab genes is at least partially regulated by an endogenous rhythm ("biological clock"). The amplitude of the cab mRNA accumulation is dependent on the duration of illumination and the circadian phase in which light was applied to the tomato plants. These results at the molecular level correlate well with the photoperiodic phenomenon. The characterization of the expression pattern of individual members of the cab gene family was attempted. Distinct primer extension products were detected using specific oligonucleotides homologous to the cab 1, cab 4, cab 5 and cab 8 genes. Based on this analysis the transcription start sites of these genes were determined to be between position -70 and -9 upstream of the ATG codon. During the diurnal cycle the cab 1 and cab 4 genes exhibit the same expression pattern; no transcripts detected at 3 and 6 a.m., maximum mRNA levels were measured at noon and decreasing levels in the afternoon.