Genome-Wide and Heterocyst-Specific Circadian Gene Expression in the Filamentous Cyanobacterium Anabaena sp. Strain PCC 7120

Kushige, Hiroko; Kugenuma, Hideyuki; Matsuoka, Masaki; Ehira, Shigeki; Ohmori, Masayuki; Iwasaki, Hideo

doi:10.1128/jb.02067-12

Cited by 18 publications

(38 citation statements)

References 49 publications

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“…Here, peak expression of these genes occurred prior to dawn (Fig. 3d), mirroring the pattern that is observed in other heterocystous cyanobacteria [41] and the pattern observed for the Richelia nif genes (Fig. 3a, b).…”

Section: Patterns Of Diel Gene Expression In Richelia From the Npsgsupporting

confidence: 81%

Periodic and coordinated gene expression between a diazotroph and its diatom host

et al. 2018

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In the surface ocean, light fuels photosynthetic carbon fixation of phytoplankton, playing a critical role in ecosystem processes including carbon export to the deep sea. In oligotrophic oceans, diatom-diazotroph associations (DDAs) play a keystone role in ecosystem function because diazotrophs can provide otherwise scarce biologically available nitrogen to the diatom host, fueling growth and subsequent carbon sequestration. Despite their importance, relatively little is known about the nature of these associations in situ. Here we used metatranscriptomic sequencing of surface samples from the North Pacific Subtropical Gyre (NPSG) to reconstruct patterns of gene expression for the diazotrophic symbiont Richelia and we examined how these patterns were integrated with those of the diatom host over day-night transitions. Richelia exhibited significant diel signals for genes related to photosynthesis, N fixation, and resource acquisition, among other processes. N fixation genes were significantly co-expressed with host nitrogen uptake and metabolism, as well as potential genes involved in carbon transport, which may underpin the exchange of nitrogen and carbon within this association. Patterns of expression suggested cell division was integrated between the host and symbiont across the diel cycle. Collectively these data suggest that symbiont-host physiological ecology is strongly interconnected in the NPSG.

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Section: Patterns Of Diel Gene Expression In Richelia From the Npsgsupporting

confidence: 81%

Periodic and coordinated gene expression between a diazotroph and its diatom host

et al. 2018

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“…The two biological replicates of the Anabaena sp. PCC 7120 dataset were concatenated for the following analyses [ 80 ], similar to the Synechocystis 6803 dataset [ 81 ]. Expression profiles were smoothed using a Savitzky-Golay lowpass filter, as proposed by Yang and colleagues [ 82 ], in order to remove pseudo peaks prior to the detection of periodic genes.…”

Section: Methodsmentioning

confidence: 99%

Minimal tool set for a prokaryotic circadian clock

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Lehmann

Chaudhury³

et al. 2017

BMC Evol Biol

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BackgroundCircadian clocks are found in organisms of almost all domains including photosynthetic Cyanobacteria, whereby large diversity exists within the protein components involved. In the model cyanobacterium Synechococcus elongatus PCC 7942 circadian rhythms are driven by a unique KaiABC protein clock, which is embedded in a network of input and output factors. Homologous proteins to the KaiABC clock have been observed in Bacteria and Archaea, where evidence for circadian behavior in these domains is accumulating. However, interaction and function of non-cyanobacterial Kai-proteins as well as homologous input and output components remain mainly unclear.ResultsUsing a universal BLAST analyses, we identified putative KaiC-based timing systems in organisms outside as well as variations within Cyanobacteria. A systematic analyses of publicly available microarray data elucidated interesting variations in circadian gene expression between different cyanobacterial strains, which might be correlated to the diversity of genome encoded clock components. Based on statistical analyses of co-occurrences of the clock components homologous to Synechococcus elongatus PCC 7942, we propose putative networks of reduced and fully functional clock systems. Further, we studied KaiC sequence conservation to determine functionally important regions of diverged KaiC homologs. Biochemical characterization of exemplary cyanobacterial KaiC proteins as well as homologs from two thermophilic Archaea demonstrated that kinase activity is always present. However, a KaiA-mediated phosphorylation is only detectable in KaiC1 orthologs.ConclusionOur analysis of 11,264 genomes clearly demonstrates that components of the Synechococcus elongatus PCC 7942 circadian clock are present in Bacteria and Archaea. However, all components are less abundant in other organisms than Cyanobacteria and KaiA, Pex, LdpA, and CdpA are only present in the latter. Thus, only reduced KaiBC-based or even simpler, solely KaiC-based timing systems might exist outside of the cyanobacterial phylum, which might be capable of driving diurnal oscillations.Electronic supplementary materialThe online version of this article (doi:10.1186/s12862-017-0999-7) contains supplementary material, which is available to authorized users.

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“…To address these questions, we turned to the cyanobacterial circadian clock. Cyanobacteria are a diverse clade of photosynthetic prokaryotes that carry kai clock genes that generate daily oscillations in physiology 9 – 11 . The core mechanism of oscillation in the cyanobacterial clock is post-translational and can be reconstituted using purified proteins 12 .…”

Section: Introductionmentioning

confidence: 99%

High protein copy number is required to suppress stochasticity in the cyanobacterial circadian clock

et al. 2018

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Circadian clocks generate reliable ~24-h rhythms despite being based on stochastic biochemical reactions. The circadian clock in Synechococcus elongatus uses a post-translational oscillator that cycles deterministically in a test tube. Because the volume of a single bacterial cell is much smaller than a macroscopic reaction, we asked how clocks in single cells function reliably. Here, we show that S. elongatus cells must express many thousands of copies of Kai proteins to effectively suppress timing errors. Stochastic modeling shows that this requirement stems from noise amplification in the post-translational feedback loop that sustains oscillations. The much smaller cyanobacterium Prochlorococcus expresses only hundreds of Kai protein copies and has a simpler, hourglass-like Kai system. We show that this timer strategy can outperform a free-running clock if internal noise is significant. This conclusion has implications for clock evolution and synthetic oscillator design, and it suggests hourglass-like behavior may be widespread in microbes.

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Genome-Wide and Heterocyst-Specific Circadian Gene Expression in the Filamentous Cyanobacterium Anabaena sp. Strain PCC 7120

Cited by 18 publications

References 49 publications

Periodic and coordinated gene expression between a diazotroph and its diatom host

Periodic and coordinated gene expression between a diazotroph and its diatom host

Minimal tool set for a prokaryotic circadian clock

High protein copy number is required to suppress stochasticity in the cyanobacterial circadian clock

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