Two KaiA-binding domains of cyanobacterial circadian clock protein KaiC

The Kai-Protein Clock-Keeping Track of Cyanobacteria's Daily Life

Life has adapted to Earth's day-night cycle with the evolution of endogenous biological clocks. Whereas these circadian rhythms typically involve extensive transcription-translation feedback in higher organisms, cyanobacteria have a circadian clock, which functions primarily as a protein-based post-translational oscillator. Known as the Kai system, it consists of three proteins KaiA, KaiB, and KaiC. In this chapter, we provide a detailed structural overview of the Kai components and how they interact to produce circadian rhythms of global gene expression in cyanobacterial cells. We discuss how the circadian oscillation is coupled to gene expression, intertwined with transcription-translation feedback mechanisms, and entrained by input from the environment. We discuss the use of mathematical models and summarize insights into the cyanobacterial circadian clock from theoretical studies. The molecular details of the Kai system are well documented for the model cyanobacterium Synechococcus elongatus, but many less understood varieties of the Kai system exist across the highly diverse phylum of Cyanobacteria. Several species contain multiple kai-gene copies, while others like marine Prochlorococcus strains have a reduced kaiBC-only system, lacking kaiA. We highlight recent findings on the genomic distribution of kai genes in Bacteria and Archaea and finally discuss hypotheses on the evolution of the Kai system.

Clock Gene Evolution and Functional Divergence

In considering the impact of the earth’s changing geophysical conditions during the history of life, it is surprising to learn that the earth’s rotational period may have been as short as 4 h, as recently as 1900 million years ago (or 1.9 billion years ago). The implications of such figures for the origin and evolution of clocks are considerable, and the authors speculate on how this short rotational period might have influenced the development of the “protoclock” in early microorganisms, such as the Cyanobacteria, during the geological periodsin which they arose and flourished. They then discuss the subsequent duplication of clock genes that took place around and after the Cambrian period, 543 million years ago, and its consequences. They compare the relative divergences of the canonical clock genes, which reveal the Per family to be the most rapidly evolving. In addition, the authors use a statistical test to predict which residues within the PER and CRY families may have undergone functional specialization.

An arginine tetrad as mediator of input-dependent and input-independent ATPases in the clock protein KaiC

A post-translational oscillator (PTO) composed of the proteins KaiA, KaiB and KaiC is at the heart of the cyanobacterial circadian clock. KaiC interacts with KaiA and KaiB over the daily cycle, and CII domains undergo rhythmic phosphorylation/dephosphorylation with a 24 h period. Both the N-terminal (CI) and C-terminal (CII) rings of KaiC exhibit ATPase activity. The CI ATPase proceeds in an input-independent fashion, but the CII ATPase is subject to metabolic input signals. The crystal structure of KaiC from Thermosynechococcus elongatus allows insight into the different anatomies of the CI and CII ATPases. Four consecutive arginines in CI (Arg linker) that connect the P-loop, CI subunits and CI and CII at the ring interface are primary candidates for the coordination of the CI and CII activities. The mutation of linker residues alters the period or triggers arhythmic behavior. Comparison between the CI and CII structures also reveals differences in loop regions that are key to KaiA and KaiB binding and activation of CII ATPase and kinase. Common packing features in KaiC crystals shed light on the KaiB-KaiC interaction.

Loop-loop interactions regulate KaiA-stimulated KaiC phosphorylation in the cyanobacterial KaiABC circadian clock

The Synechococcus elongatus KaiA, KaiB, and KaiC proteins in the presence of ATP generate a post-translational oscillator that runs in a temperature-compensated manner with a period of 24 h. KaiA dimer stimulates phosphorylation of KaiC hexamer at two sites per subunit, T432 and S431, and KaiB dimers antagonize KaiA action and induce KaiC subunit exchange. Neither the mechanism of KaiA-stimulated KaiC phosphorylation nor that of KaiB-mediated KaiC dephosphorylation is understood in detail at present. We demonstrate here that the A422V KaiC mutant sheds light on the former mechanism. It was previously reported that A422V is less sensitive to dark pulse-induced phase resetting and has a reduced amplitude of the KaiC phosphorylation rhythm in vivo. A422 maps to a loop (422-loop) that continues toward the phosphorylation sites. By pulling on the C-terminal peptide of KaiC (A-loop), KaiA removes restraints from the adjacent 422-loop whose increased flexibility indirectly promotes kinase activity. We found in the crystal structure that A422V KaiC lacks phosphorylation at S431 and exhibits a subtle, local conformational change relative to wild-type KaiC. Molecular dynamics simulations indicate higher mobility of the 422-loop in the absence of the A-loop and mobility differences in other areas associated with phosphorylation activity between wild-type and mutant KaiCs. The A-loop-422-loop relay that informs KaiC phosphorylation sites of KaiA dimer binding propagates to loops from neighboring KaiC subunits, thus providing support for a concerted allosteric mechanism of phosphorylation.

Dephosphorylation of the core clock protein KaiC in the cyanobacterial KaiABC circadian oscillator proceeds via an ATP synthase mechanism

The circadian clock of the cyanobacterium Synechococcus elongatus can be reconstituted in vitro from three proteins, KaiA, KaiB, and KaiC in the presence of ATP, to tick in a temperature-compensated manner. KaiC, the central cog of this oscillator, forms a homohexamer with 12 ATP molecules bound between its N- and C-terminal domains and exhibits unusual properties. Both the N-terminal (CI) and C-terminal (CII) domains harbor ATPase activity, and the subunit interfaces between CII domains are the sites of autokinase and autophosphatase activities. Hydrolysis of ATP correlates with phosphorylation at threonine and serine sites across subunits in an orchestrated manner, such that first T432 and then S431 are phosphorylated, followed by dephosphorylation of these residues in the same order. Although structural work has provided insight into the mechanisms of ATPase and kinase, the location and mechanism of the phosphatase have remained enigmatic. From the available experimental data based on a range of approaches, including KaiC crystal structures and small-angle X-ray scattering models, metal ion dependence, site-directed mutagenesis (i.e., E318, the general base), and measurements of the associated clock periods, phosphorylation patterns, and dephosphorylation courses as well as a lack of sequence motifs in KaiC that are typically associated with known phosphatases, we hypothesized that KaiCII makes use of the same active site for phosphorylation and dephosphorlyation. We observed that wild-type KaiC (wt-KaiC) exhibits an ATP synthase activity that is significantly reduced in the T432A/S431A mutant. We interpret the first observation as evidence that KaiCII is a phosphotransferase instead of a phosphatase and the second that the enzyme is capable of generating ATP, both from ADP and P(i) (in a reversal of the ATPase reaction) and from ADP and P-T432/P-S431 (dephosphorylation). This new concept regarding the mechanism of dephosphorylation is also supported by the strikingly similar makeups of the active sites at the interfaces between α/β heterodimers of F1-ATPase and between monomeric subunits in the KaiCII hexamer. Several KaiCII residues play a critical role in the relative activities of kinase and ATP synthase, among them R385, which stabilizes the compact form and helps kinase action reach a plateau, and T426, a short-lived phosphorylation site that promotes and affects the order of dephosphorylation.

The itty-bitty time machine genetics of the cyanobacterial circadian clock

The cyanobacterium Synechococcus elongatus PCC 7942 has been used as the prokaryotic model system for the study of circadian rhythms for the past two decades. Its genetic malleability has been instrumental in the discovery of key input, oscillator, and output components and has also provided monumental insights into the mechanism by which proteins function to maintain and dictate 24-h time. In addition, basic research into the prokaryotic system has led to interesting advances in eukaryotic circadian mechanisms. Undoubtedly, continued genetic and mutational analyses of this single-celled cyanobacterium will aid in teasing out the intricacies of the Kai-based circadian clock to advance our understanding of this system as well as other more "complex" systems.

Intermolecular associations determine the dynamics of the circadian KaiABC oscillator

Three proteins from cyanobacteria (KaiA, KaiB, and KaiC) can reconstitute circadian oscillations in vitro. At least three molecular properties oscillate during this reaction, namely rhythmic phosphorylation of KaiC, ATP hydrolytic activity of KaiC, and assembly/disassembly of intermolecular complexes among KaiA, KaiB, and KaiC. We found that the intermolecular associations determine key dynamic properties of this in vitro oscillator. For example, mutations within KaiB that alter the rates of binding of KaiB to KaiC also predictably modulate the period of the oscillator. Moreover, we show that KaiA can bind stably to complexes of KaiB and hyperphosphorylated KaiC. Modeling simulations indicate that the function of this binding of KaiA to the KaiB*KaiC complex is to inactivate KaiA's activity, thereby promoting the dephosphorylation phase of the reaction. Therefore, we report here dynamics of interaction of KaiA and KaiB with KaiC that determine the period and amplitude of this in vitro oscillator.

Intramolecular regulation of phosphorylation status of the circadian clock protein KaiC

Background

KaiC, a central clock protein in cyanobacteria, undergoes circadian oscillations between hypophosphorylated and hyperphosphorylated forms in vivo and in vitro. Structural analyses of KaiC crystals have identified threonine and serine residues in KaiC at three residues (T426, S431, and T432) as potential sites at which KaiC is phosphorylated; mutation of any of these three sites to alanine abolishes rhythmicity, revealing an essential clock role for each residue separately and for KaiC phosphorylation in general. Mass spectrometry studies confirmed that the S431 and T432 residues are key phosphorylation sites, however, the role of the threonine residue at position 426 was not clear from the mass spectrometry measurements.

Methodology and Principal Findings

Mutational approaches and biochemical analyses of KaiC support a key role for T426 in control of the KaiC phosphorylation status in vivo and in vitro and demonstrates that alternative amino acids at residue 426 dramatically affect KaiC's properties in vivo and in vitro, especially genetic dominance/recessive relationships, KaiC dephosphorylation, and the formation of complexes of KaiC with KaiA and KaiB. These mutations alter key circadian properties, including period, amplitude, robustness, and temperature compensation. Crystallographic analyses indicate that the T426 site is phosphorylatible under some conditions, and in vitro phosphorylation assays of KaiC demonstrate labile phosphorylation of KaiC when the primary S431 and T432 sites are blocked.

Conclusions and Significance

T426 is a crucial site that regulates KaiC phosphorylation status in vivo and in vitro and these studies underscore the importance of KaiC phosphorylation status in the essential cyanobacterial circadian functions. The regulatory roles of these phosphorylation sites–including T426–within KaiC enhance our understanding of the molecular mechanism underlying circadian rhythm generation in cyanobacteria.

A novel allele of kaiA shortens the circadian period and strengthens interaction of oscillator components in the cyanobacterium Synechococcus elongatus PCC 7942

The basic circadian oscillator of the unicellular fresh water cyanobacterium Synechococcus elongatus PCC 7942, the model organism for cyanobacterial circadian clocks, consists of only three protein components: KaiA, KaiB, and KaiC. These proteins, all of which are homomultimers, periodically interact to form large protein complexes with stoichiometries that depend on the phosphorylation state of KaiC. KaiA stimulates KaiC autophosphorylation through direct physical interactions. Screening a library of S. elongatus transposon mutants for circadian clock phenotypes uncovered an atypical short-period mutant that carries a kaiA insertion. Genetic and biochemical analyses showed that the short-period phenotype is caused by the truncation of KaiA by three amino acid residues at its C terminus. The disruption of a negative element upstream of the kaiBC promoter was another consequence of the insertion of the transposon; when not associated with a truncated kaiA allele, this mutation extended the circadian period. The circadian rhythm of KaiC phosphorylation was conserved in these mutants, but with some modifications in the rhythmic pattern of KaiC phosphorylation, such as the ratio of phosphorylated to unphosphorylated KaiC and the relative phase of the circadian phosphorylation peak. The results showed that there is no correlation between the phasing of the KaiC phosphorylation pattern and the rhythm of gene expression, measured as bioluminescence from luciferase reporter genes. The interaction between KaiC and the truncated KaiA was stronger than normal, as shown by fluorescence anisotropy analysis. Our data suggest that the KaiA-KaiC interaction and the circadian pattern of KaiC autophosphorylation are both important for determining the period, but not the relative phasing, of circadian rhythms in S. elongatus.

Circadian rhythms of superhelical status of DNA in cyanobacteria

The cyanobacterium Synechococcus elongatus expresses robust circadian (daily) rhythms under the control of the KaiABC-based core clockwork. Unlike eukaryotic circadian systems characterized thus far, the cyanobacterial clockwork modulates gene expression patterns globally and specific clock gene promoters are not necessary in mediating the circadian feedback loop. The oscilloid model postulates that global rhythms of transcription are based on rhythmic changes in the status of the cyanobacterial chromosome that are ultimately controlled by the KaiABC oscillator. By using a nonessential, cryptic plasmid (pANS) as a reporter of the superhelical state of DNA in cyanobacteria, we show that the supercoiling status of this plasmid changes in a circadian manner in vivo. The rhythm of topological change in the plasmid is conditional; this change is rhythmic in constant light and in light/dark cycles, but not in constant darkness. In further support of the oscilloid model, cyanobacterial promoters that are removed from their native chromosomal locations and placed on a plasmid preserve their circadian expression patterns.

Elucidating the ticking of an in vitro circadian clockwork

A biochemical oscillator can be reconstituted in vitro with three purified proteins, that displays the salient properties of circadian (daily) rhythms, including self-sustained 24-h periodicity that is temperature compensated. We analyze the biochemical basis of this oscillator by quantifying the time-dependent interactions of the three proteins (KaiA, KaiB, and KaiC) by electron microscopy and native gel electrophoresis to elucidate the timing of the formation of complexes among the Kai proteins. The data are used to derive a dynamic model for the in vitro oscillator that accurately reproduces the rhythms of KaiABC complexes and of KaiC phosphorylation, and is consistent with biophysical observations of individual Kai protein interactions. We use fluorescence resonance energy transfer (FRET) to confirm that monomer exchange among KaiC hexamers occurs. The model demonstrates that the function of this monomer exchange may be to maintain synchrony among the KaiC hexamers in the reaction, thereby sustaining a high-amplitude oscillation. Finally, we apply the first perturbation analyses of an in vitro oscillator by using temperature pulses to reset the phase of the KaiABC oscillator, thereby testing the resetting characteristics of this unique circadian oscillator. This study analyzes a circadian clockwork to an unprecedented level of molecular detail.

Circadian biological clocks are present in a diverse range of organisms, from bacteria to humans. A central function of circadian clocks is controlling the adaptive response to the daily cycle of light and darkness. As such, altering the clock (e.g., by jet lag or shiftwork) affects mental and physical health in humans. It has generally been thought that the underlying molecular mechanism of circadian oscillations is an autoregulatory transcriptional/translational feedback loop. However, in cyanobacteria, only three purified clock proteins can reconstitute a circadian rhythm of protein phosphorylation in a test tube (in vitro). Using this in vitro system we found that the three proteins interact to form complexes of different compositions throughout the cycle. We derived a dynamic model for the in vitro oscillator that accurately reproduces the rhythms of complexes and of protein phosphorylation. One of the proteins undergoes phase-dependent exchange of its monomers, and the model demonstrates that this monomer exchange allows the maintenance of robust oscillations. Finally, we perturbed the in vitro oscillator with temperature pulses to demonstrate the resetting characteristics of this unique circadian oscillator. Our study analyzes a circadian clockwork to an unprecedented level of molecular detail.

The interaction dynamics of the three-Kai-protein in vitro oscillator derived from the cyanobacterial circadian clock were determined to an unprecedented level of molecular detail.

No promoter left behind: global circadian gene expression in cyanobacteria

Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a clock system that appears to be similar to those of eukaryotes in many ways. On the other hand, the KaiABC-based core cyanobacterial clockwork is clearly different from the transcription-translation feedback loop model of eukaryotic clocks in that the cyanobacterial clock system regulates gene expression patterns globally, and specific clock gene promoters are not essential in mediating the circadian feedback loop. A novel model, the oscilloid model, proposes that the KaiABC oscillator ultimately mediates rhythmic changes in the status of the cyanobacterial chromosome, and these topological changes underlie the global rhythms of transcription. The authors suggest that this model represents one of several possible modes of regulating gene expression by circadian clocks, even those of eukaryotes.

labA: a novel gene required for negative feedback regulation of the cyanobacterial circadian clock protein KaiC

In the cyanobacterium Synechococcus elongatus PCC 7942, circadian timing is transmitted from the KaiABC-based central oscillator to the transcription factor RpaA via the KaiC-interacting histidine kinase SasA to activate transcription, thereby generating rhythmic circadian gene expression. However, KaiC can also repress circadian gene expression, including its own. The mechanism and significance of this negative feedback regulation have been unclear. Here, we report a novel gene, labA (low-amplitude and bright), that is required for negative feedback regulation of KaiC. Disruption of labA abolished transcriptional repression caused by overexpression of KaiC and elevated the trough levels of circadian gene expression, resulting in a low-amplitude phenotype. In contrast, overexpression of labA significantly lowered circadian gene expression. Furthermore, genetic analysis indicated that labA and sasA function in parallel pathways to regulate kaiBC expression, whereas rpaA functions downstream from labA for kaiBC expression. These results suggest that temporal information from the KaiABC-based oscillator diverges into a LabA-dependent negative pathway and a SasA-dependent positive pathway, and then converges onto RpaA to generate robust circadian gene expression. It is likely that quantitative information of KaiC is transmitted to RpaA through LabA, whereas SasA mediates the state of the KaiABC-based oscillator.

Analysis of KaiA-KaiC protein interactions in the cyano-bacterial circadian clock using hybrid structural methods

The cyanobacterial circadian clock can be reconstituted in vitro by mixing recombinant KaiA, KaiB and KaiC proteins with ATP, producing KaiC phosphorylation and dephosphorylation cycles that have a regular rhythm with a ca. 24-h period and are temperature-compensated. KaiA and KaiB are modulators of KaiC phosphorylation, whereby KaiB antagonizes KaiA's action. Here, we present a complete crystallographic model of the Synechococcus elongatus KaiC hexamer that includes previously unresolved portions of the C-terminal regions, and a negative-stain electron microscopy study of S. elongatus and Thermosynechococcus elongatus BP-1 KaiA-KaiC complexes. Site-directed mutagenesis in combination with EM reveals that KaiA binds exclusively to the CII half of the KaiC hexamer. The EM-based model of the KaiA-KaiC complex reveals protein-protein interactions at two sites: the known interaction of the flexible C-terminal KaiC peptide with KaiA, and a second postulated interaction between the apical region of KaiA and the ATP binding cleft on KaiC. This model brings KaiA mutation sites that alter clock period or abolish rhythmicity into contact with KaiC and suggests how KaiA might regulate KaiC phosphorylation.

Evolution of the Circadian Clock Mechanism in Prokaryotes

The circadian system of prokaryotes is probably the oldest among the circadian systems of living organisms. The genes comprising the system are very different in their evolutionary histories. The reconstruction of macroevolution of the circadian genes in cyanobacteria suggests that there are probably at least two types of circadian systems, based either on the threekaigenes (kaiA, kaiB, andkaiC) or onkaiBandkaiC.When referred to the recently published results about a genomic timescale of prokaryote evolution, the origin ofkaiBandsasAcorresponds to the appearance of anoxygenic photosynthesis, while the origin of thekaiBCoperon corresponds to the time when oxygenic photosynthesis evolved.

The results of the studies performed so far suggest that major steps in macroevolution of the circadian system in cyanobacteria have been related to global changes in the environment and to keystone advances in biological evolution. This macroevolution has involved selection, multiple lateral transfers, gene duplications, and fusions as its primary driving forces. The proposed scenario of the circadian system's macroevolution is far from complete and will be updated as new genomic and sequence data are accumulated.

A Circadian Timing Mechanism in the Cyanobacteria

Cyanobacteria such as Synechococcus elongatus PCC 7942, Thermosynechococcus elongatus BP-1, and Synechocystis species strain PCC 6803 have an endogenous timing mechanism that can generate and maintain a 24 h (circadian) periodicity to global (whole genome) gene expression patterns. This rhythmicity extends to many other physiological functions, including chromosome compaction. These rhythmic patterns seem to reflect the periodicity of availability of the primary energy source for these photoautotrophic organisms, the Sun. Presumably, eons of environmentally derived rhythmicity--light/dark cycles--have simply been mechanistically incorporated into the regulatory networks of these cyanobacteria. Genetic and biochemical experimentation over the last 15 years has identified many key components of the primary timing mechanism that generates rhythmicity, the input pathways that synchronize endogenous rhythms to exogenous rhythms, and the output pathways that transduce temporal information from the timekeeper to the regulators of gene expression and function. Amazingly, the primary timing mechanism has evidently been extracted from S. elongatus PCC 7942 and can also keep time in vitro. Mixing the circadian clock proteins KaiA, KaiB, and KaiC from S. elongatus PCC 7942 in vitro and adding ATP results in a circadian rhythm in the KaiC protein phosphorylation state. Nonetheless, many questions still loom regarding how this circadian clock mechanism works, how it communicates with the environment and how it regulates temporal patterns of gene expression. Many details regarding structure and function of the individual clock-related proteins are provided here as a basis to discuss these questions. A strong, data-intensive foundation has been developed to support the working model for the cyanobacterial circadian regulatory system. The eventual addition to that model of the metabolic parameters participating in the command and control of this circadian global regulatory system will ultimately allow a fascinating look into whole-cell physiology and metabolism and the consequential organization of global gene expression patterns.

Functional divergence of the circadian clock proteins in prokaryotes

Cyanobacteria are only prokaryotes known so far to have a circadian system. It may be based either on two (kaiB and kaiC) or three (kaiA, kaiB and kaiC) circadian genes. The homologs of two circadian proteins, KaiB and KaiC, form four major subfamilies (K1-K4) and also occur in some other prokaryotes. Using the likelihood-ratio tests, we studied a rate shift at the functional divergence of the proteins from the different subfamilies. It appears that only two of the subfamilies (K1 and K2) perform circadian functions. We identified in total 92 sites that have significantly different rates of evolution between the clades K1/K2 and K3/K4; 67 sites (15 in KaiB and 52 in KaiC) been evolving significantly slower in K1/K2 than the overall average for the entire sequence. Many critical sites are located in the identified functionally important motifs and regions, e.g. one of the Walker's motif As, DXXG motif, and two KaiA-binding domains of KaiC. There are also 36 sites (approximately 5%) with rate shift between K1 and K2. The rate shift at these sites may be related to the interaction with KaiA. Rate shift analyses have identified residues whose manipulation in the Kai proteins may lead to better understanding of their functions in the two different types of the cyanobacterial circadian system.

Functionally important substructures of circadian clock protein KaiB in a unique tetramer complex

KaiB is a component of the circadian clock molecular machinery in cyanobacteria, which are the simplest organisms that exhibit circadian rhythms. Here we report the x-ray crystal structure of KaiB from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. The KaiB crystal diffracts at a resolution of 2.6 A and includes four subunits organized as a dimer of dimers, each composed of two non-equivalent subunits. The overall shape of the tetramer is an elongated hexagonal plate, with a single positively charged cleft flanked by two negatively charged ridges whose surfaces includes several terminal chains. Site-directed mutagenesis of Synechococcus KaiB confirmed that alanine substitution of residues Lys-11 or Lys-43 in the cleft, or deletion of C-terminal residues 95-108, which forms part of the ridges, strongly weakens in vivo circadian rhythms. Characteristics of KaiB deduced from the x-ray crystal structure were also confirmed by physicochemical measurements of KaiB in solution. These data suggest that the positively charged cleft and flanking negatively charged ridges in KaiB are essential for the biological function of KaiB in the circadian molecular machinery in cyanobacteria.

Recent cyanobacterial Kai protein structures suggest a rotary clock

The cyanobacterial circadian oscillator consists of three Kai proteins, KaiA, KaiB, and KaiC, in its oscillation feedback loop. Structural comparison reveals that the Kai system resembles the F1-ATPase system in which KaiC is equivalent to alpha(3)beta(3), KaiA to gammadelta, and KaiB to its inhibitory factor. It also suggests that there exists a possible haemagglutinin-like spring-loaded mechanism for the activation of KaiA during the formation of Kai complexes.

A novel mutation in kaiC affects resetting of the cyanobacterial circadian clock

Light is the most important factor controlling circadian systems in response to day-night cycles. In order to better understand the regulation of circadian rhythms by light in Synechococcus elongatus PCC 7942, we screened for mutants with defective phase shifting in response to dark pulses. Using a 5-h dark-pulse protocol, we identified a mutation in kaiC that we termed pr1, for phase response 1. In the pr1 mutant, a 5-h dark pulse failed to shift the phase of the circadian rhythm, while the same pulse caused a 10-h phase shift in wild-type cells. The rhythm in accumulation of KaiC was abolished in the pr1 mutant, and the rhythmicity of KaiC phosphorylation was reduced. Additionally, the pr1 mutant was defective in mediating the feedback inhibition of kaiBC. Finally, overexpression of mutant KaiC led to a reduced phase shift compared to that for wild-type KaiC. Thus, KaiC appears to play a role in resetting the cellular clock in addition to its documented role in the feedback regulation of circadian rhythms.

Nucleotide-dependent domain motions within rings of the RecA/AAA(+) superfamily

The oligomeric rings formed by RecA-fold proteins are mechanochemical motors that perform many important biological functions. Their RecA-fold domains convert the chemical energy of ATP into mechanical work through large nucleotide-dependent conformational changes. This review summarizes recent structural and mechanistic works on the F1-ATPase and HslU regarding to the force generation by individual RecA folds in the context of ring structures. The F1-ATPase ring for example generates the force perpendicular to the ring axis, while the HslU ring generates forces presumably parallel to it. There exists a strong correlation between the directions of forces generated and the orientation of the RecA folds, not only in these two proteins but also in T7 DNA helicase, suggesting that it should be possible to predict the direction of forces generated by other members of this family on the basis of the orientation of their RecA folds.

Identification of key phosphorylation sites in the circadian clock protein KaiC by crystallographic and mutagenetic analyses

In cyanobacteria, KaiC is an essential hexameric clock protein that forms the core of a circadian protein complex. KaiC can be phosphorylated, and the ratio of phospho-KaiC to non-phospho-KaiC is correlated with circadian period. Structural analyses of KaiC crystals identify three potential phosphorylation sites within a 10-A radius of the ATP binding regions that are at the T432, S431, and T426 residues in the KaiCII domains. When these residues are mutated by alanine substitution singly or in combination, KaiC phosphorylation is altered, and circadian rhythmicity is abolished. These alanine substitutions do not prevent KaiC from hexamerizing. Intriguingly, the ability of KaiC overexpression to repress its own promoter is also not prevented by alanine substitutions at these sites, implying that the capability of KaiC to repress its promoter is not sufficient to allow the clockwork to oscillate. The KaiC structure and the mutational analysis suggest that S431 and T426 may share a phosphate that can shuttle between these two residues. Because the phosphorylation status of KaiC oscillates over the daily cycle, and KaiC phosphorylation is essential for clock function as shown here, daily modulations of KaiC activity by phosphorylation at T432 and S431/T426 seem to be key components of the circadian clockwork in cyanobacteria.

Visualizing a circadian clock protein: crystal structure of KaiC and functional insights

Circadian (daily) biological clocks express characteristics that are difficult to explain by known biochemical mechanisms, and will ultimately require characterizing the structures, functions, and interactions of their molecular components. KaiC is an essential circadian protein in cyanobacteria that forms the core of the KaiABC clock protein complex. We report the crystal structure of the KaiC homohexameric complex at 2.8 A resolution. The structure resembles a double doughnut with a central pore that is partially sealed at one end. The crystal structure reveals ATP binding, inter-subunit organization, a scaffold for Kai-protein complex formation, the location of critical KaiC mutations, and evolutionary relationships to other proteins. A key auto-phosphorylation site on KaiC (T432) is identified from the crystal structure, and mutation of this residue abolishes circadian rhythmicity. The crystal structure of KaiC will be essential for understanding this circadian clockwork and for establishing its links to global gene expression.

Role of KaiC phosphorylation in the circadian clock system of Synechococcus elongatus PCC 7942

In the cyanobacterium Synechococcus elongatus PCC 7942, KaiA, KaiB, and KaiC are essential proteins for the generation of a circadian rhythm. KaiC is proposed as a negative regulator of the circadian expression of all genes in the genome, and its phosphorylation is regulated positively by KaiA and negatively by KaiB and shows a circadian rhythm in vivo. To study the functions of KaiC phosphorylation in the circadian clock system, we identified two autophosphorylation sites, Ser-431 and Thr-432, by using mass spectrometry (MS). We generated Synechococcus mutants in which these residues were substituted for alanine by using site-directed mutagenesis. Phosphorylation of KaiC was reduced in the single mutants and was completely abolished in the double mutant, indicating that KaiC is also phosphorylated at these sites in vivo. These mutants lost circadian rhythm, indicating that phosphorylation at each of the two sites is essential for the control of the circadian oscillation. Although the nonphosphorylatable mutant KaiC was able to form a hexamer in vitro, it failed to form a clock protein complex with KaiA, KaiB, and SasA in the Synechococcus cells. When nonphosphorylatable KaiC was overexpressed, the kaiBC promoter activity was only transiently repressed. These results suggest that KaiC phosphorylation regulates its transcriptional repression activity by controlling its binding affinity for other clock proteins.

Structure of the C-terminal domain of the clock protein KaiA in complex with a KaiC-derived peptide: implications for KaiC regulation

Circadian clocks are widespread endogenous mechanisms that control the temporal pattern of diverse biological processes, including gene transcription. KaiA is the positive element of the cyanobacterial clock because KaiA overexpression elevates transcription levels of clock components. Recently, we showed that the structure of KaiA is that of a domain-swapped homodimer. The N-terminal domain is a pseudo-receiver; thus, it is likely to be involved in signal transduction in the clock-resetting pathway. The C-terminal domain of KaiA is structurally novel and enhances the KaiC autokinase activity directly. Here, we report the NMR structure of the C-terminal domain of KaiA (ThKaiA180C) in complex with a KaiC-derived peptide from the cyanobacterium Thermosynechococcus elongatus BP-1. The protein-peptide interface is revealed to be different from a model that was proposed earlier, is stabilized by a combination of hydrophobic and electrostatic interactions, and includes many residues known to produce a circadian-period phenotype upon substitution. Although the structure of the monomeric subunit of ThKaiA180C is largely unchanged upon peptide binding, the intersubunit dimerization angle changes. It is proposed that modulation of the C-terminal KaiA domain dimerization angle regulates KaiA-KaiC interactions.

Crystal structure of the C-terminal clock-oscillator domain of the cyanobacterial KaiA protein

KaiA, KaiB and KaiC constitute the circadian clock machinery in cyanobacteria, and KaiA activates kaiBC expression whereas KaiC represses it. Here we show that KaiA is composed of three functional domains, the N-terminal amplitude-amplifier domain, the central period-adjuster domain and the C-terminal clock-oscillator domain. The C-terminal domain is responsible for dimer formation, binding to KaiC, enhancing KaiC phosphorylation and generating the circadian oscillations. The X-ray crystal structure at a resolution of 1.8 A of the C-terminal clock-oscillator domain of KaiA from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1 shows that residue His270, located at the center of a KaiA dimer concavity, is essential to KaiA function. KaiA binding to KaiC probably occurs via the concave surface. On the basis of the structure, we predict the structural roles of the residues that affect circadian oscillations.

Crystal Structure of Circadian Clock Protein KaiA from Synechococcus elongatus

The circadian clock found in Synechococcus elongatus, the most ancient circadian clock, is regulated by the interaction of three proteins, KaiA, KaiB, and KaiC. While the precise function of these proteins remains unclear, KaiA has been shown to be a positive regulator of the expression of KaiB and KaiC. The 2.0-A structure of KaiA of S. elongatus reported here shows that the protein is composed of two independently folded domains connected by a linker. The NH(2)-terminal pseudo-receiver domain has a similar fold with that of bacterial response regulators, whereas the COOH-terminal four-helix bundle domain is novel and forms the interface of the 2-fold-related homodimer. The COOH-terminal four-helix bundle domain has been shown to contain the KaiC binding site. The structure suggests that the KaiB binding site is covered in the dimer interface of the KaiA "closed" conformation, observed in the crystal structure, which suggests an allosteric regulation mechanism.

Global orchestration of gene expression by the biological clock of cyanobacteria

Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks.

Prokaryotic cyanobacteria express robust circadian (daily) rhythms under the control of a central clock. Recent studies shed light on the mechanisms governing circadian rhythms in cyanobacteria and highlight key differences between prokaryotic and eukaryotic clocks.

NMR structure of the KaiC-interacting C-terminal domain of KaiA, a circadian clock protein: implications for KaiA-KaiC interaction

KaiA is a two-domain circadian clock protein in cyanobacteria, acting as the positive element in a feedback loop that sustains the oscillation. The structure of the N-terminal domain of KaiA is that of a pseudo-receiver, similar to those of bacterial response regulators, which likely interacts with components of the clock-resetting pathway. The C-terminal domain of KaiA is highly conserved among cyanobacteria and enhances the autokinase activity of KaiC. Here we present the NMR structure of the C-terminal domain of KaiA from the thermophilic cyanobacterium Thermosynechococcus elongatus BP-1. This domain adopts a novel all alpha-helical homodimeric structure. Several mutations known to affect the period of the circadian oscillator are shown to be located at an exposed groove near the dimer interface. This NMR structure and a 21-A-resolution electron microscopy structure of the hexameric KaiC particle allow us to postulate a mode of KaiA-KaiC interaction, in which KaiA binds a linker region connecting two globular KaiC domains.

Cyanobacterial circadian clocks — timing is everything

For more than three billion years, the organisms on this planet have known, like Little Orphan Annie, that "The sun'll come out tomorrow", and many have honed their biochemistry to exploit this knowledge. The cyanobacteria have had ample time to fashion a suitable timepiece, as they are among the oldest inhabitants of the earth. For these organisms, light is food, and it is a nutrient that shows up at the same time every day. Not surprisingly, cyanobacteria have learned to arrange their days around dinnertime.

A Cyanobacterial Circadian Timing Mechanism

Cyanobacteria such as Synechococcus elongatus PCC 7942 exhibit 24-h rhythms of gene expression that are controlled by an endogenous circadian clock that is mechanistically distinct from those described for diverse eukaryotes. Genetic and biochemical experiments over the past decade have identified key components of the circadian oscillator, input pathways that synchronize the clock with the daily environment, and output pathways that relay temporal information to downstream genes. The mechanism of the cyanobacterial circadian clock that is emerging is based principally on the assembly and disassembly of a large complex at whose heart are the proteins KaiA, KaiB, and KaiC. Signal transduction pathways that feed into and out of the clock employ protein domains that are similar to those in two-component regulatory systems of bacteria.

Timekeeping in bacteria: the cyanobacterial circadian clock

The prokaryotes known as cyanobacteria possess an endogenous 24h biological (circadian) clock that provides temporal coordination for physiological processes. Although the cyanobacterial clock has the same fundamental properties as circadian clocks in eukaryotes, its components are non-homologous to those of animals, plants or fungi. Moreover, its mechanism is likely to be very different from that depicted in eukaryotic clock models. The picture that is emerging for the timing mechanism in cyanobacteria is of a multiprotein, multimeric, molecular machine composed of proteins whose domains exhibit twists on common themes. Signal transduction into and out of the clock core appears to occur via histidine protein kinase-based phosphorylation relays.

Origin and evolution of circadian clock genes in prokaryotes

Regulation of physiological functions with approximate daily periodicity, or circadian rhythms, is a characteristic feature of eukaryotes. Until recently, cyanobacteria were the only prokaryotes reported to possess circadian rhythmicity. It is controlled by a cluster of three genes: kaiA, kaiB, and kaiC. Using sequence data of approximately 70 complete prokaryotic genomes from the various public depositories, we show here that the kai genes and their homologs have quite a different evolutionary history and occur in Archaea and Proteobacteria as well. Among the three genes, kaiC is evolutionarily the oldest, and kaiA is the youngest and likely evolved only in cyanobacteria. Our data suggest that the prokaryotic circadian pacemakers have evolved in parallel with the geological history of the earth, and that natural selection, multiple lateral transfers, and gene duplications and losses have been the major factors shaping their evolution.

KaiA-stimulated KaiC phosphorylation in circadian timing loops in cyanobacteria

Cyanobacterial clock proteins KaiA and KaiC are proposed as positive and negative regulators in the autoregulatory circadian kaiBC expression, respectively. Here, we show that activation of kaiBC expression by kaiA requires KaiC, suggesting a positive feedback control in the cyanobacterial clockwork. We found that robust circadian phosphorylation of KaiC. KaiA was essential for in vivo KaiC phosphorylation and activated in vitro KaiC autophosphorylation. These effects of KaiA were attenuated by the kaiA2 long period mutation. Both the long period phenotype and the abnormal KaiC phosphorylation in this mutant were suppressed by a previously undocumented kaiC mutation. We propose that KaiA-stimulated circadian KaiC phosphorylation is important for circadian timing.

Mutations in KaiA, a clock protein, extend the period of circadian rhythm in the cyanobacterium Synechococcus elongatus PCC 7942

KaiA KaiB and KaiC are essential circadian clock proteins in the unicellular cyanobacterium Synechococcus elongatus PCC 7942. KaiA protein activates transcription of the kaiBC operon, which is believed to be a crucial step in the oscillating feedback loop of cyanobacteria. In this study, approximately approximately 400 mutations were introduced into kaiA by PCR-based mutagenesis, and rhythmic phenotypes of these mutants were studied by a bioluminescence reporter. In contrast to mutations in KaiB or KaiC, the vast majority of KaiA mutations extended the period and only rarely shortened it. The period could be extended to 35 h without lowering the mean or peak levels of kaiBC expression. However, several mutations resulted in low-amplitude oscillations or arrhythmia, which were accompanied by lowered kaiBC transcription. These results imply that the KaiA protein can change the period length of the circadian rhythm directly (through an unknown biochemical mechanism) or indirectly (by lowering kaiBC expression). Specific mutations of KaiA were identified in 34 mutants. While mutations mapped to various locations of the KaiA sequence, two clusters of period-altering mutations were found. This suggested that these regions are important domains of the KaiA protein for defining the period length. On the other hand, different sequences within KaiA to which arrhythmic mutations were mapped are important to enhance kaiBC expression.

Long-term microclimatic stress causes rapid adaptive radiation of kaiABC clock gene family in a cyanobacterium, Nostoc linckia, from "Evolution Canyons" I and II, Israel

Cyanobacteria are the only prokaryotes known thus far possessing regulation of physiological functions with approximate daily periodicity, or circadian rhythms, that are controlled by a cluster of three genes, kaiA, kaiB, and kaiC. Here we demonstrate considerably higher genetic polymorphism and extremely rapid evolution of the kaiABC gene family in a filamentous cyanobacterium, Nostoc linckia, permanently exposed to the acute natural environmental stress in the two microsite evolutionary models known as "Evolution Canyons," I (Mount Carmel) and II (Upper Galilee) in Israel. The family consists of five distinct subfamilies (kaiI-kaiV) comprising at least 20 functional genes and pseudogenes. The obtained data suggest that the duplications of kai genes have adaptive significance, and some of them are evolutionarily quite recent (approximately 80,000 years ago). The observed patterns of within- and between-subfamily polymorphisms indicate that positive diversifying, balancing, and purifying selections are the principal driving forces of the kai gene family's evolution.