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Diversity of cyanobacterial circadian clocks
Cyanobacteria use a circadian clock to control cellular processes in daily cycles. The underlying mechanism is intensively investigated in the model organism Synechococcus elongatus PCC 7942. In contrast to eukaryotes the core clock is a posttranslational oscillator composed of the 3 proteins KaiA, KaiB and KaiC (Ishiura et al. 1998 , Nakajima et al. 2005). A complex protein network reads out cyclic activities of KaiC and regulates circadian outputs like rhythmic gene expression, chromosome compaction and metabolic processes (see e.g. Snijder and Axmann 2019 for a review on the circadian clock of Synechococcus). Homologs of the Kai proteins are found in other cyanobacteria and other (non-cyanobacterial) prokaryotes (reviewed in Schmelling, Scheurer et al. 2021). Based on their sequence identity they can be separated in diverged groups. Some cyanobacteria express homologs from multiple Kai protein groups, which implies that circadian regulation might be more complex in those organisms.
The circadian clock of Synechocystis sp. PCC 6803
In our group we aim at understanding the role and complexity of clock proteins beyond the model organism Synechococcus elongatus PCC7942. We characterized selected proteins from different organisms in vitro and in silico.
Currently our work focuses mainly on Synechocystis sp. PCC 6803, which is an important cyanobacterial model organism in general. It harbors three KaiB and KaiC proteins and serves as a good representative to study the function and interplay of diverged clock proteins (Wiegard, Dörrich et al. 2013, Wiegard, Kobler et al. 2020). Together with our collaborators we discovered that further a second KaiA protein (KaiA3) is present in Synechocystis. In vitro and in vivo studies indicate that two interconnected Kai protein oscillators might run together in one cell (Köbler, Schmelling et al. 2023). We are currently investigating the interplay of these two oscillators.
To simplify analysis of circadian oscillations and further establish Synechocystis as a model for cyanobacterial circadian research, we developed a method that allows detection of circadian rhythms without insertion of any reporter. Circadian rhythms can simply be read out via online monitoring of the backscatter properties of cells (Berwanger, Thumm et al. 2023).
Overall, our circadian projects combine in vitro, in vivo and in silico analysis. As methods we use for example:
- molecular cloning
- heterologous protein expression and purification
- in vitro activity assays
- protein-protein interaction studies (e.g. native PAGE, yeast two hybrid)
- protein-DNA interaction studies (e.g. ChIP)
- cyanobacterial cultivation and phenotypic analysis
- online monitoring of backscatter oscillation
- BLAST analysis
Collaborators:
- Annegret Wilde, Albert Ludwigs University Freiburg, Germany
- Markus Kollmann, HeinrichHeine University, Düsseldorf, Germany
- Joost Snijder and Albert Heck, Utrecht University, The Netherlands
- Kazuki Terauchi, Ritsumeikan University, Japan
- Michael J. Rust, The University of Chicago, USA
Practical Bachelor and Master thesis
We regularly offer Bachelor and Master projects. If you are interested, please send us an email with your CV and motivation letter.
Key Publications
Berwanger, L. C., N. Thumm, R. Gholamipoor, A. Wiegard, J. Schlebusch, M. Kollmann and I. M. Axmann (2023). "Self-sustained rhythmic behavior of Synechocystis PCC 6803 under continuous light conditions in the absence of light-dark entrainment." bioRxiv: 2023.2009.2026.559469.
Köbler, C., N. M. Schmelling, A. Pawlowski, P. Spät, N. M. Scheurer, K. Sebastian, L. C. Berwanger, B. Maček, A. Wiegard, I. M. Axmann and A. Wilde (2023). "Two circadian oscillators in one cyanobacterium." bioRxiv: 2021.2007.2020.453058.
Schmelling, N. M., N. Scheurer, C. Köbler, A. Wilde and I. M. Axmann (2021). Diversity of Timing Systems in Cyanobacteria and Beyond. Circadian Rhythms in Bacteria and Microbiomes. C. H. Johnson and M. J. Rust. Cham, Springer International Publishing: 179-202.
Snijder, J. and I. M. Axmann (2019). The Kai-Protein Clock-Keeping Track of Cyanobacteria's Daily Life. Macromolecular Protein Complexes II: Structure and Function. J. R. Harris and J. Marles-Wright. 93: 359-391.
Wiegard, A., A. K. Dörrich, H. T. Deinzer, C. Beck, A. Wilde, J. Holtzendorff and I. M. Axmann (2013). "Biochemical analysis of three putative KaiC clock proteins from Synechocystis sp. PCC 6803 suggests their functional divergence." Microbiology 159: 948-958.
Wiegard, A., C. Kobler, K. Oyama, A. K. Dorrich, C. Azai, K. Terauchi, A. Wilde and I. M. Axmann (2020). "Synechocystis KaiC3 Displays Temperature- and KaiB-Dependent ATPase Activity and Is Important for Growth in Darkness." J Bacteriol 202(4).
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