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.2021 May 11;11(1):9995.
doi: 10.1038/s41598-021-89345-7.

Evolution of kaiA, a key circadian gene of cyanobacteria

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Evolution of kaiA, a key circadian gene of cyanobacteria

Volodymyr Dvornyk et al. Sci Rep..

Abstract

The circadian system of cyanobacteria is built upon a central oscillator consisting of three genes, kaiA, kaiB, and kaiC. The KaiA protein plays a key role in phosphorylation/dephosphorylation cycles of KaiC, which occur over the 24-h period. We conducted a comprehensive evolutionary analysis of the kaiA genes across cyanobacteria. The results show that, in contrast to the previous reports, kaiA has an ancient origin and is as old as cyanobacteria. The kaiA homologs are present in nearly all analyzed cyanobacteria, except Gloeobacter, and have varying domain architecture. Some Prochlorococcales, which were previously reported to lack the kaiA gene, possess a drastically truncated homolog. The existence of the diverse kaiA homologs suggests significant variation of the circadian mechanism, which was described for the model cyanobacterium, Synechococcus elongatus PCC7942. The major structural modifications in the kaiA genes (duplications, acquisition and loss of domains) have apparently been induced by global environmental changes in the different geological periods.

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Conflict of interest statement

The authors declare no competing interests.

Figures

Figure 1
Figure 1
The domain architecture of KaiA proteins. (a)Synechococcus (ABB57248); (b)Trichodesmium (WP_044137784); (c)Phormidium (WP_087707133); (d)Prochlorothrix (KKJ01719); (e)Nostoc (WP_015140002); (f)Nostoc (WP_010997035); (g)Prochlorococcus (WP_036914277). Homology to the OmpR domain is weak and denoted by dashed box.
Figure 2
Figure 2
Group-conserved residues identified by ConSurf. Degrees of conservation in subfamilies were visualized by Chimera v.1.10.2. (a) Conserved sites of the KaiA protein. Number the residues is accordant with theSynechococcus KaiA (ABB57248). The black bars above sequence indicate the level of conservation (1–9). (b) Conserved sites labeled (red) in the 3D structure of theSynechococcus elongatus KaiA protein (PDB: 1R8J_A) (left: N-terminal region; right: KaiA domain).
Figure 3
Figure 3
The maximum-likelihood phylogenetic trees of: (a) the 16S and 23S rRNA genes (species tree) and (b) KaiA homologs (gene tree). The node support values are ultrafast bootstrap/SH-aLRT branch test/approximate Bayes test.
Figure 3
Figure 3
The maximum-likelihood phylogenetic trees of: (a) the 16S and 23S rRNA genes (species tree) and (b) KaiA homologs (gene tree). The node support values are ultrafast bootstrap/SH-aLRT branch test/approximate Bayes test.
Figure 4
Figure 4
Models of the 3D structure of the KaiA homologs from different cyanobacteria. (a)Synechococcus (ABB57248, PDB: 1R8J); (b)Trichodesmium (WP_044137784); (c)Phormidium (WP_087707133); (d)Prochlorothrix (KKJ01719); (e)Nostoc (WP_015140002); (f)Nostoc (WP_010997035, PDB: 1R5Q); (g)Prochlorococcus (WP_036914277). The KaiA domain is boxed. Models (a) and (f) are experimental, the others are computer generated.
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