Global Analysis of Circadian Expression in the CyanobacteriumSynechocystissp. Strain PCC 6803

Abstract

Cyanobacteria are the only bacterial species found to have a circadian clock. We used DNA microarrays to examine circadian expression patterns in the cyanobacterium Synechocystis sp. strain PCC 6803. Our analysis identified 54 (2%) and 237 (9%) genes that exhibited circadian rhythms under stringent and relaxed filtering conditions, respectively. The expression of most cycling genes peaked around the time of transition from subjective day to night, suggesting that the main role of the circadian clock in Synechocystis is to adjust the physiological state of the cell to the upcoming night environment. There were several chromosomal regions where neighboring genes were expressed with similar circadian patterns. The physiological functions of the cycling genes were diverse and included a wide variety of metabolic pathways, membrane transport, and signal transduction. Genes involved in respiration and poly(3-hydroxyalkanoate) synthesis showed coordinated circadian expression, suggesting that the regulation is important for the supply of energy and carbon source in the night. Genes involved in transcription and translation also followed circadian cycling patterns. These genes may be important for output of the rhythmic information generated by the circadian clock. Our findings provided critical insights into the importance of the circadian clock on cellular physiology and the mechanism of clock-controlled gene regulation.Circadian rhythm is a self-sustaining oscillation whose period length coincides with the 24-h day-night cycle. Many biological activities show circadian patterns, allowing organisms to adapt to daily fluctuations in the environment. Circadian rhythms are widespread and involve functions as diverse as human sleep-wake cycles and cyanobacterial nitrogen fixation. The molecular basis of circadian rhythms involves negative and positive feedback regulation of clock genes (16).Cyanobacteria are the only bacterial species found to have a circadian clock. Three clock genes, kaiA, kaiB, and kaiC, have been identified in Synechococcus sp. strain PCC 7942 (25). kaiB and kaiC form an operon and are coordinately transcribed, while kaiA is transcribed independently. All of the kai genes show circadian rhythms of expression. Continuous overexpression of kaiC represses expression of kaiBC, but overexpression of kaiA enhances expression of kaiBC. This suggests that kaiC is regulated by a negative feedback autoregulatory loop and that KaiA activates kaiBC expression, thus sustaining the cyclical expression of kaiBC (25).In cyanobacteria, activities as diverse as cell division, amino acid uptake, nitrogen fixation, respiration, and carbohydrate synthesis are under circadian control (18), but a clear mechanistic link between physiological rhythms and the regulation of output genes is still lacking. Promoter trap analyses were performed with two cyanobacterial species, Synechococcus sp. strain PCC 7942 (33) and Synechocystis sp. strain PCC 6803 (4). The percentage of rhythmic clones was lower in Synechocystis organisms (77...

Genome-wide analysis of diel gene expression in the unicellular N2-fixing cyanobacterium Crocosphaera watsonii WH 8501

“…The transcriptional regulation of cyanobacterial metabolism and cellular processes over light-dark cycles has been described in details previously (Kucho et al, 2005;Labiosa et al, 2006;Stö ckel et al, 2008;Zinser et al, 2009), and similar coregulation of major processes in C. watsonii was not unexpected. The genes from the DEP pool can be divided into four categories based on the timing of maximal expression (Figure 2).…”

“…Moreover, differential diel expression was reported for one primary and four alternative sigma factors in Prochlorococcus (Zinser et al, 2009) and two sigma factors in Synechocystis sp. PCC 6803 (Kucho et al, 2005). Alternative sigma factors activate transcription of many genes in response to various stresses (Los et al, 2008) and are also involved in maintaining the circadian rhythm (Nair et al, 2002).…”

“…A majority of the unicellular cyanobacteria fix N 2 at night, when O 2 is not being produced by photosynthesis. Cyanobacteria control metabolism during light-dark cycles through complex gene expression patterns that include circadian rhythms (Chen et al, 1996;Kucho et al, 2005;Toepel et al, 2009;Zinser et al, 2009). The expression of nitrogenase genes in Trichodesmium and in the intertidal or coastal marine unicellular cyanobacterium Cyanothece sp.…”

No Promoter Left Behind: Global Circadian Gene Expression in Cyanobacteria

“…One possible explanation for the discrepancies between the results obtained with microarrays and those of promoter trap assays is the different sampling intervals that can lead to differences in sensitivity to changes of gene expression (Kucho et al, 2005). For example, in the promoter trap analyses, luminescence (as a gauge of promoter activity) was monitored every 30 min to 1 h, but in the microarray experiments, the time between measurements of mRNA abundances was 4 h (in Synechocystis) and 12 h (in Thermosynechococcus).…”

“…For example, a promoter trap experiment using a promoterless luxAB reporter in Synechocystis sp. strain PCC 6803 showed that 80% of the 72 bioluminescent colonies isolated showed circadian rhythms of luxAB expression (Aoki et al, 1995), but in a genomewide screen using microarrays, the mRNA abundances of onlỹ 9% of genes displayed circadian rhythms (Kucho et al, 2005). In the thermophilic cyanobacterium, T. elongatus BP-1, microarrays revealed that the mRNA abundance of ~6% of genes was rhythmic (Kucho et al, 2004).…”