Rhythmic regulation of the light-harvesting chlorophyll a/b protein and the small subunit of ribulose-1,5-bisphosphate carboxylase mRNA in rye seedlings

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.

Ribosome and transcript copy numbers, polysome occupancy and enzyme dynamics in Arabidopsis

Plants are exposed to continual changes in the environment. The daily alternation between light and darkness results in massive recurring changes in the carbon budget, and leads to widespread changes in transcript levels. These diurnal changes are superimposed on slower changes in the environment. Quantitative molecular information about the numbers of ribosomes, of transcripts for 35 enzymes in central metabolism and their loading into polysomes is used to estimate translation rates in Arabidopsis rosettes, and explore the consequences for important sub-processes in plant growth. Translation rates for individual enzyme are compared with their abundance in the rosette to predict which enzymes are subject to rapid turnover every day, and which are synthesized at rates that would allow only slow adjustments to sustained changes of the environment, or resemble those needed to support the observed rate of growth. Global translation rates are used to estimate the energy costs of protein synthesis and relate them to the plant carbon budget, in particular the rates of starch degradation and respiration at night.

Cloning and use of a coral 36B4 gene to study the differential expression of coral genes between light and dark conditions

This paper aims to validate reference genes for gene expression studies between light and dark conditions in the scleractinian coral Stylophora pistillata for future gene expression studies of the "light-enhanced calcification" phenomenon. For this purpose, we cloned, sequenced, and characterized a candidate reference gene, the 36B4 gene from the coral S. pistillata, and validated 36B4 and beta-actin as reference genes. To illustrate the future applications of these reference genes, we tested the dark and light expression of two photosynthetic genes (Rubisco and D1 protein of the photosystem II) and two genes encoding proteins involved in calcium transport for coral calcification (a calcium ATPase and a calcium channel). Results show that both photosynthetic genes are enhanced during the light when standardized against 36B4 and beta-actin, whereas the two genes encoding proteins involved in calcium transport are not differentially expressed between light and dark conditions. The characterization of a coral 36B4 and the establishment of such valid reference genes will be useful for future gene expression studies between diverse conditions (aposymbiotic/symbiotic, stress/control, light/dark conditions) in scleractinian corals.

Microarray analysis of diurnal and circadian-regulated genes in Arabidopsis

Plants respond to day/night cycling in a number of physiological ways. At the mRNA level, the expression of some genes changes during the 24-hr period. To identify novel genes regulated in this way, we used microarrays containing 11,521 Arabidopsis expressed sequence tags, representing an estimated 7800 unique genes, to determine gene expression levels at 6-hr intervals throughout the day. Eleven percent of the genes, encompassing genes expressed at both high and low levels, showed a diurnal expression pattern. Approximately 2% cycled with a circadian rhythm. By clustering microarray data from 47 additional nonrelated experiments, we identified groups of genes regulated only by the circadian clock. These groups contained the already characterized clock-associated genes LHY, CCA1, and GI, suggesting that other key circadian clock genes might be found within these clusters.

Circadian expression of the light-harvesting complex protein genes in plants

Photosynthesis is one of the important processes that enable life on earth. To optimize photosynthesis reactions during a solar day, most of them are timed to be active during the light phase. This includes the components of the thylakoid membranes in chloroplasts. Prominent representatives are the proteins of the light-harvesting complex (LHC). The synthesis of both the Lhc mRNA and the LHC protein occurs during the day and is regulated by the circadian clock, exhibiting the following pattern: increasing levels after sunrise, reaching a maximum around noon, and decreasing levels in the afternoon. To elucidate the involved control elements and regulatory circuits, the following strategies were applied: (1) analysis of promoters of Lhc genes, (2) analysis of DNA binding proteins, and (3) screening and investigation of mutants. The most promising elements found so far that may be involved in mediating the circadian rhythmicity of Lhc mRNA oscillations are a myb-like transcription factor CCA1 (Wang et al. 1997) and the corresponding DNA binding sequence (Piechulla et al. 1998).

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.