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

The Chlamydomonas reinhardtii plastid chromosome: islands of genes in a sea of repeats

Chlamydomonas reinhardtii is a unicellular eukaryotic alga possessing a single chloroplast that is widely used as a model system for the study of photosynthetic processes. This report analyzes the surprising structural and evolutionary features of the completely sequenced 203,395-bp plastid chromosome. The genome is divided by 21.2-kb inverted repeats into two single-copy regions of approximately 80 kb and contains only 99 genes, including a full complement of tRNAs and atypical genes encoding the RNA polymerase. A remarkable feature is that >20% of the genome is repetitive DNA: the majority of intergenic regions consist of numerous classes of short dispersed repeats (SDRs), which may have structural or evolutionary significance. Among other sequenced chlorophyte plastid genomes, only that of the green alga Chlorella vulgaris appears to share this feature. The program MultiPipMaker was used to compare the genic complement of Chlamydomonas with those of other chloroplast genomes and to scan the genomes for sequence similarities and repetitive DNAs. Among the results was evidence that the SDRs were not derived from extant coding sequences, although some SDRs may have arisen from other genomic fragments. Phylogenetic reconstruction of changes in plastid genome content revealed that an accelerated rate of gene loss also characterized the Chlamydomonas/Chlorella lineage, a phenomenon that might be independent of the proliferation of SDRs. Together, our results reveal a dynamic and unusual plastid genome whose existence in a model organism will allow its features to be tested functionally.

Chlamydomonas reinhardtii as a unicellular model for circadian rhythm analysis

Chlamydomonas reinhardtii has been used as an experimental model organism for circadian rhythm research for more than 30 yr. Some of the physiological rhythms of this alga are well established, and several clock mutants have been isolated. The cloning of clock genes from these mutant strains by positional cloning is under way and should give new insights into the mechanism of the circadian clock. In a spectacular space experiment, the question of the existence of an endogenous clock vs. an exogenous mechanism has been studied in this organism. With the emergence of molecular analysis of circadian rhythms in plants in 1985, a circadian gene expression pattern of several nuclear and chloroplast genes was detected. Evidence is now accumulating that shows circadian control at the translational level. In addition, the gating of the cell cycle by the circadian clock has been analyzed. This review focuses on the different aspects of circadian rhythm research in C. reinhardtii over the past 30 yr. The suitability of Chlamydomonas as a model system in chronobiology research and the adaptive significance of the observed rhythms will be discussed.

Endogenous timekeepers in photosynthetic organisms

Circadian and photoperiodic timing mechanisms were first described in photosynthetic organisms. These organisms depend upon sunlight for their energy, so adaptation to daily and seasonal fluctuations in light must have generated a strong selective pressure. Studies of the endogenous timekeepers of photosynthetic organisms provide evidence for both a fitness advantage and for selective pressures involved in early evolution of circadian clocks. Photoperiodic timing mechanisms in plants appear to use their circadian timers as the ruler by which the day/night length is measured. As in animals, the overall clock system in plants appears to be complex; the system includes multiple oscillators, several input pathways, and a myriad of outputs. Genes have now been isolated from plants that are likely to encode components of the central clockwork or at least that act very close to the central mechanism. Genetic and biochemical analyses of the central clockwork of a photosynthetic organism are most highly advanced in cyanobacteria, where a cluster of clock genes and interacting factors have been characterized.

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).

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.

Circadian expression of the carbonic anhydrase gene, Cah1, in Chlamydomonas reinhardtii

We have investigated whether the expression of carbonic anhydrase genes (Cah1 and Cah2) is regulated by a circadian clock in Chlamydomonas. When cells were grown in ordinary air under 12 h light/12 h dark (LD) cycles, the levels of the Cah2 mRNA hardly altered during the cycles, while the Cah1 mRNA showed a strong diurnal rhythm. The rhythm of about 24 h continued at least 3 days even under continuous light. Temperature compensation of the rhythm was demonstrated, using cultures maintained at 16, 22, and 28 degrees C. These results indicate that the abundance of the Cah1 transcript is controlled by a circadian clock.

Transcription of CABII is regulated by the biological clock in Chlamydomonas reinhardtii

The small gene family encoding the chlorophyll a/b-binding proteins of photosystem II (CABII or lhcb) is known to exhibit circadian rhythms of mRNA abundance in Chlamydomonas reinhardtii. In this study we investigated the role of transcription in the phenomenon. We used as reporters Chlamydomonas genes that encode nitrate reductase (NITI) and arylsulfatase (ARS2) transcriptionally fused to sequences upstream of one of the CABII genes (called CABII-1). We found that both reporters exhibited the same circadian rhythm of mRNA abundance in phase, period, and amplitude as does the endogenous CABII-1 gene. We also evaluated the efficacy of arylsulfatase enzymatic activity as a reporter and found that its half-life is too long to make it a useful reporter of rhythmic transcription during a circadian or diurnal cycle. The amount of mRNA synthesis from the CABII-1 gene was examined by in vivo labeling experiments and a circadian rhythm in transcription rate was demonstrated. In vivo labeling also revealed a circadian rhythm of mRNA synthesis for the CABII gene family as a whole. The results from the transcriptional reporter assays together with the in vivo labeling experiments strongly support the conclusion that the biological clock regulates the transcriptional activity of the CABII-I gene, and moreover that regulation at the transcriptional level is the predominant mode by which the clock regulates this gene.