Circadian rhythms in gene transcription imparted by chromosome compaction in the cyanobacterium Synechococcus elongatus

Abstract

In the cyanobacterium Synechococcus elongatus (PCC 7942) the kai genes A, B, and C and the sasA gene encode the functional protein core of the timing mechanism essential for circadian clock regulation of global gene expression. The Kai proteins comprise the central timing mechanism, and the sensor kinase SasA is a primary transducer of temporal information. We demonstrate that the circadian clock also regulates a chromosome compaction rhythm. This chromosome compaction rhythm is both circadian clockcontrolled and kai-dependent. Although sasA is required for global gene expression rhythmicity, it is not required for these chromosome compaction rhythms. We also demonstrate direct control by the Kai proteins on the rate at which the SasA protein autophosphorylates. Thus, to generate and maintain circadian rhythms in gene expression, the Kai proteins keep relative time, communicate temporal information to SasA, and may control access to promoter elements by imparting rhythmic chromosome compaction.cyanobacteria ͉ regulation C ircadian clocks have evolved within the cyanobacteria (an extremely diverse group of oxygenic photosynthesizing bacteria) and many, if not all, eukaryotes. These clocks effectively tune gene expression patterns, and thus metabolic activity and behavior, to distinct daily frequencies (1-3). In each of several well studied model systems, circadian gene expression patterns are generated and maintained by the combined functions of fairly small sets of proteins (1-3). Amazingly, in vitro combination of only three proteins, KaiA, KaiB, and KaiC, from the cyanobacterium Synechococcus elongatus results in a functional circadian timing mechanism (4). This phenomenon underscores recent data demonstrating that a transcription and translation feedback loop, once considered essential for circadian timing, is not required for rhythmic activity in this cyanobacterium (5). Interestingly, demonstration of this simple proteinaceous clock, and presumption of its straightforward transfer to newly formed daughter cells, explains the enigma of how a circadian (24-h) timing mechanism can function in cyanobacteria that have generation times of 8 h or less.Despite those compelling data, questions concerning how this timing mechanism connects circadian clock function to global regulation of gene expression still loom (6). Existent data show functional interactions among the three Kai proteins and the SasA sensor kinase protein as essential for this global regulation (7). For example, the KaiC protein forms a homohexamer upon binding ATP and is an autokinase. It also interacts with double-stranded DNA molecules (8, 9). Overproduction of KaiC represses gene expression on a global scale (8, 9). In an sasA-null strain, except for kai gene expression patterns, all other tested genes are arrhythmically expressed (7). SasA protein thus appears to act as temporal output regulator from the clock. In addition, clock-regulated gene expression rhythms consist of at least two temporal classes (10-12). The major class includes kaiB g...

No Promoter Left Behind: Global Circadian Gene Expression in Cyanobacteria

“…Assuming that plasmids in S. elongatus accurately reflect a phenomenon that also occurs in the chromosome, these results suggest that changes in DNA topology are regulated by the circadian clock of cyanobacteria and that these changes in DNA topology affect promoter activity. Interestingly, the kai-dependent rhythms of chromosomal compaction (Smith and Williams, 2006) are in more or less the same phase as the rhythms of plasmid supercoiling that we have observed. In general, as the cyanobacterial chromosome compacts during the course of the day, the endogenous plasmid displays increased supercoiling, and as the chromosome decompacts during the night, supercoiling in the endogenous plasmid is reduced.…”

“…The observation that circadian clock function in cyanobacteria does not require negative feedback of clock proteins on DNA sequences in specific clock promoters and that overexpression of KaiC represses the activity of all promoters (Xu et al, 2003;Nakahira et al, 2004) is also consistent with this hypothesis. Furthermore, Smith and Williams (2006) have recently provided direct evidence to support this hypothesis. DAPI staining of chromosomes in S. elongatus cells has shown that the cyanobacterial circadian clock regulates a daily rhythm of chromosome compaction (Smith and Williams, 2006); this rhythm of chromosome compaction is kai dependent but not dependent on SasA.…”

“…Furthermore, Smith and Williams (2006) have recently provided direct evidence to support this hypothesis. DAPI staining of chromosomes in S. elongatus cells has shown that the cyanobacterial circadian clock regulates a daily rhythm of chromosome compaction (Smith and Williams, 2006); this rhythm of chromosome compaction is kai dependent but not dependent on SasA.…”

“…When phosphorylated, the response regulator undergoes a conformational change to affect changes in cellular processes such as gene expression or locomotion. In S. elongatus, the core clock protein KaiC interacts with SasA , and even though KaiC does not have an identifiable kinase domain, it stimulates the autophosphorylation of SasA (Smith and Williams, 2006;Takai et al, 2006). SasA, however, does not alter the phosphorylation status of KaiC, implying that information from the clock is being transmitted to SasA and not vice versa (Smith and Williams, 2006).…”

“…In S. elongatus, the core clock protein KaiC interacts with SasA , and even though KaiC does not have an identifiable kinase domain, it stimulates the autophosphorylation of SasA (Smith and Williams, 2006;Takai et al, 2006). SasA, however, does not alter the phosphorylation status of KaiC, implying that information from the clock is being transmitted to SasA and not vice versa (Smith and Williams, 2006). It is possible that SasA transduces information from the KaiABC oscillator by interacting with its putative response regulator to globally control transcription of cyanobacterial genes or by controlling the expression of a subset of genes, the products of which cascade to regulate the expression of downstream genes in a circadian manner (Tomita et al, 2005;Takai et al, 2006).…”