Global analysis of circadian expression in the cyanobacterium Synechocystis sp. 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.

FIG. 1.

An overview of Synechocystis cycling genes. (A) Expression profile of cycling genes. Relative expression at each time point was normalized to the mean expression at all time points and represented by color scale. White and gray boxes represent subjective day and night, respectively. Numbers above the boxes indicate the actual time after transfer to continuous light conditions. (B) Peak expression times for all cycling genes. Genes were sorted according to circadian time at which peak expression occurred. Data from two independent experiments are shown (see Fig. S1 in the supplemental material).

FIG. 2.

Expression profiles of kai genes. Red, kaiA (slr0756); black, kaiB3 (sll0486); orange, kaiC1 (slr0758); blue, kaiC3 (slr1942). A representative result from two biological replicates is shown. The vertical axis shows the relative expression at each time point normalized to the mean expression at all time points. The horizontal axis indicates the actual time after transfer to continuous light conditions. These kai genes do not form an operon. White and gray boxes represent subjective day and night, respectively.

FIG. 3.

(A, B, and C) Structure of cycling gene clusters slr0772-slr0773-sll0772 (A), slr0572-sll0543 (B), and sll0062-slr0058 (C). Arrows indicate transcription units and their direction of transcription. Black and gray boxes represent cycling genes that were identified under stringent and relaxed filtering conditions, respectively. (D, E, and F) Expression profiles of genes contained in the clusters slr0772-slr0773-sll0772 (D), slr0572-sll0543 (E), and sll0062-slr0058 (F). The vertical axis shows the relative expression at each time point normalized to the mean expression at all time points. The horizontal axis indicates the actual time after transfer to continuous light conditions. White and gray boxes represent subjective day and night, respectively.

FIG. 4.

Circadian expression of genes associated with respiration. (A) An overview of respiration in cyanobacteria. Boxes and a circle represent protein components of the electron transport chain. Thick gray arrows indicate electron flow. For the pentose phosphate cycle, enzymes that exhibited circadian patterns of expression are shown as pink arrows. Asterisks denote rate-limiting enzymes. NDH, NAD(P)H dehydrogenase; PQ, plastoquinone; Cyt, cytochrome; COX, cytochrome c oxidase; P, phosphate; GA, glyceraldehyde; Zwf, glucose-6-phosphate 1-dehydrogenase; Glc, 6-phosphogluconolactonase; Gnd, 6-phosphogluconate dehydrogenase; TalB, transaldolase. (B to E) Expression profiles of genes associated with respiration. The vertical axes show the expression at each time point normalized to the mean expression at all time points. The horizontal axes indicate actual time after transfer to continuous light conditions. White and gray boxes represent subjective day and night, respectively. (B) Four genes associated with the pentose phosphate cycle. Asterisks denote rate-limiting enzymes. (C) HoxE (sll1220) (blue) and three subunits of the cytochrome c oxidase complex (slr1136, slr1137, and slr1138) (orange). (D) Subunit c of ATP synthase (ssl2615). (E) Seven subunits of the cytochrome b₆f complex (sll1182, sll1316, sll1317, slr0342, slr0343, sml0004, and smr0010).

FIG. 5.

Circadian regulation in the PHA synthesis pathway. (A) PHA biosynthetic pathway. Enzymes showing circadian rhythm are boxed. CoA, coenzyme A. (B) Expression profiles of cycling genes associated with PHA biosynthesis. Open circles and closed squares represent slr1993 and slr1829, respectively. The vertical axis shows the expression at each time point normalized to the mean expression at all time points. The horizontal axis indicates the actual time after transfer to continuous light conditions. White and gray boxes represent subjective day and night, respectively.

FIG. 6.

Expression profiles of genes associated with transcription and translation, including a sigma factor (closed triangle, sll1689), a response regulator with a DNA-binding domain (open circle, sll1330), and prolyl-tRNA synthetase (open square, sll1425). The vertical axis shows the expression at each time point normalized to the mean expression at all time points. The horizontal axis indicates the actual time after transfer to continuous light conditions. White and gray boxes represent subjective day and night, respectively.