Functional divergence of the circadian clock proteins in prokaryotes |
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Authors: | Volodymyr Dvornyk Bjarne Knudsen |
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Institution: | (1) Osteoporosis Research Center and Department of Biomedical Sciences, Creighton University, 601 N. 30th St., Ste. 6767, Omaha, NE 68131, USA;(2) Department of Zoology, University of Florida, Box 118525, Gainesville, FL 32611--8525, USA |
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Abstract: | 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 (~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. |
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Keywords: | circadian genes cyanobacteria functional divergence rate shift |
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