Expression of a Gene Cluster
            <i>kaiABC</i>
            as a Circadian Feedback Process in Cyanobacteria

Ishiura, Masahiro; Kutsuna, Shinsuke; Aoki, Setsuyuki; Iwasaki, Hideo; Andersson, Carol R.; Tanabe, Akio; Golden, Susan S.; Johnson, Carl Hirschie; Kondo, Takao

doi:10.1126/science.281.5382.1519

Cited by 686 publications

(901 citation statements)

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“…In Neurospora yeast, the FRQ gene product exhibits a qualitatively similar cycle (Merrow et al, 1997;Luo et al, 1998). Even in cyanobacteria, genes that constitute an analogous negative-feedback loop have been found (Ishiura et al, 1998).…”

Section: 2mentioning

confidence: 99%

Modeling Transcriptional Control in Gene Networks—Methods, Recent Results, and Future Directions

Smolen

Baxter

Byrne

2000

Bulletin of Mathematical Biology

280

161

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Mathematical models are useful for providing a framework for integrating data and gaining insights into the static and dynamic behavior of complex biological systems such as networks of interacting genes. We review the dynamic behaviors expected from model gene networks incorporating common biochemical motifs, and we compare current methods for modeling genetic networks. A common modeling technique, based on simply modeling genes as ON-OFF switches, is readily implemented and allows rapid numerical simulations. However, this method may predict dynamic solutions that do not correspond to those seen when systems are modeled with a more detailed method using ordinary differential equations. Until now, the majority of gene network modeling studies have focused on determining the types of dynamics that can be generated by common biochemical motifs such as feedback loops or protein oligomerization. For example, these elements can generate multiple stable states for gene product concentrations, state-dependent responses to stimuli, circadian rhythms and other oscillations, and optimal stimulus frequencies for maximal transcription. In the future, as new experimental techniques increase the ease of characterization of genetic networks, qualitative modeling will need to be supplanted by quantitative models for specific systems.

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Section: 2mentioning

confidence: 99%

Modeling Transcriptional Control in Gene Networks—Methods, Recent Results, and Future Directions

Smolen

Baxter

Byrne

2000

Bulletin of Mathematical Biology

280

161

View full text Add to dashboard Cite

show abstract

“…The cyanobacterial system was the first to use the promoter trap technique (Liu et al, 1995), and the application of this methodology may explain why pervasive clock control over gene expression was found. This profound control of transcriptional activity in the cyanobacterium Synechococcus elongatus PCC 7942 is regulated by a molecular clockwork that is encoded by 3 genes-kaiA, kaiB, and kaiC-that form a cluster on the chromosome; inactivation of any of the kai genes abolishes clock function (Ishiura et al, 1998). The proteins encoded by these genes interact with one another (Iwasaki et al, 1999;Taniguchi et al, 2001;Xu et al, 1999) to form large complexes in vivo with KaiC as the core (Kageyama et al, 2003).…”

Section: The Circadian Clock System In Cyanobacteriamentioning

confidence: 99%

No Promoter Left Behind: Global Circadian Gene Expression in Cyanobacteria

Woelfle

Johnson

2006

J Biol Rhythms

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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 transcriptiontranslation 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. Keywords circadian; biological clock; kai; prokaryote; global gene expression; supercoiling Animals, plants, fungi, and cyanobacteria all display daily or circadian rhythms in their biochemistry, physiology, and/or behavior that are controlled by biological clocks (Dunlap et al., 2004). A variety of biological processes in various organisms are controlled by biological clocks such as gene expression, photosynthesis, sleeping/waking, and development, and this regulation is thought to help organisms adapt to the daily changes in light, temperature, and other factors in their environment. Circadian regulation of gene expression (i.e., the levels of specific proteins in cells) can be accomplished by clock control of transcription, mRNA stability, translation, and protein degradation. A particularly fascinating example of translational control by a circadian clock is that in the dinoflagellate alga, Gonyaulax (Rossini et al., 2003). However, we focus our discussion specifically on clock control of cyanobacterial gene expression at the level of transcription.In general, studies of circadian gene expression in eukaryotes have often used microarray analyses to show that a relatively small proportion of genes (~5%-15%) in eukaryotic genomes display rhythms in mRNA abundance. While microarray technology is well advanced, it should be noted that microarrays are not very sensitive to small changes of mRNA abundance, and moreover, they are not a good measure of rhythmic transcriptional activity for mRNAs that are either very unstable or very stable. Therefore, microarray results might not be reflective of transcriptional control in detail.

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“…KaiC, which has two ATP-binding motifs (Ishiura et al 1998), was expected to display a robust ATPase activity because the hexameric structure of KaiC resembles that of a number of DNA-associated ATPases (Leipe et al 2000). However, so far, KaiC only shows slow kinase and phosphatase activities.…”

Section: The Atpase Activity Of Kaic Serves As the Basic Timing Mechamentioning

confidence: 99%

“…All of the mutations were mapped to the kaiC-coding region and resulted in single-aminoacid substitutions. For the loci and details of the mutant phenotypes, see Ishiura et al (1998). phorylation to be equalized among KaiC hexamers with different configurations.…”

Section: Kai Protein Complex Dynamics In the Kaic Phosphorylation Cycmentioning

confidence: 99%

“…Continuous overexpression of KaiC nullifies circadian rhythms through an amelioration of kaiBC expression, whereas a transient increase in KaiC sets the phase of the rhythm. These observations led to a model of the cyanobacterial transcription-translation-based oscillator (TTO) that explains prokaryotic circadian rhythm generation (Ishiura et al 1998); in this model, KaiC and KaiA negatively and positively regulate kaiBC transcription, respectively. This TTO model, however, did not explain how this loop obtains the characteristics unique to a circadian clock, i.e., circadian periodicity and stability against alterations in temperature and metabolic activity.…”

Section: Introductionmentioning

confidence: 99%

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