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Journal of Bacteriology, November 2007, p. 7690-7696, Vol. 189, No. 21
0021-9193/07/$08.00+0     doi:10.1128/JB.00835-07
Copyright © 2007, American Society for Microbiology. All Rights Reserved.

The Circadian Clock-Related Gene pex Regulates a Negative cis Element in the kaiA Promoter Region

Shinsuke Kutsuna,^1,2* Takao Kondo,² Haruki Ikegami,¹ Tatsuya Uzumaki,^2,3, Mitsunori Katayama,^2,4 and Masahiro Ishiura^2,3*

International Graduate School of Arts and Sciences, Yokohama-City University, 22-2 Seto, Kanazawa-ku, Yokohama 236-0027, Japan,¹ Division of Biological Science, Graduate School of Science, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan,² Center for Gene Research, Group of Plant Genomics, Nagoya University, Furocho, Chikusa, Nagoya 464-8602, Japan,³ Department of Liberal Arts and Basic Sciences, College of Industrial Technology, Nihon University, 2-11-1 Shinei, Narashino, Chiba 275-8576, Japan⁴

Received 29 May 2007/ Accepted 10 August 2007

In the cyanobacterium Synechococcus sp. strain PCC 7942, a circadian clock-related gene, pex, was identified as the gene prolonging the period of the clock. A PadR domain, which is a newly classified transcription factor domain, and the X-ray crystal structure of the Pex protein suggest a role for Pex in transcriptional regulation in the circadian system. However, the regulatory target of the Pex protein is unknown. To determine the role of Pex, we monitored bioluminescence rhythms that reported the expression activity of the kaiA gene or the kaiBC operon in pex deficiency, pex constitutive expression, and the wild-type genotype. The expression of kaiA in the pex-deficient or constitutive expression genotype was 7 or 1/7 times that of the wild type, respectively, suggesting that kaiA is the target of negative regulation by Pex. In contrast, the expression of the kaiBC gene in the two pex-related genotypes was the same as that in the wild type, suggesting that Pex specifically regulates kaiA expression. We used primer extension analysis to map the transcription start site for the kaiA gene 66 bp upstream of the translation start codon. Mapping with deletion and base pair substitution of the kaiA upstream region revealed that a 5-bp sequence in this region was essential for the regulation of kaiA. The repression or constitutive expression of the kaiA transgene caused the prolongation or shortening of the circadian period, respectively, suggesting that the Pex protein changes the period via the negative regulation of kaiA.

Published ahead of print on 17 August 2007.

Present address: Division of Material Science, Graduate School of Science, Nagoya University, Furocho, Chikusaku, Nagoya 464-8602, Japan.

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