Nucleic Acids Research, 2000, Vol. 28, No. 5 1206-1210
© 2000 Oxford University Press
Evaluation and characterization of catabolite-responsive elements (cre) of Bacillus subtilis
Faculty of Engineering, Fukuyama University, Fukuyama 729-0292, Japan and 1Computer Laboratory, National Institute for Basic Biology, Okazaki 444-8585, Japan
A global mechanism of catabolite repression of the genus Bacillus comprises negative regulation exerted through the binding of the CcpA protein to the catabolite-responsive elements (cres) of the target genes. We searched for cre sequences in the Bacillus subtilis genome using a query sequence, WTGNAANCGNWNNCW (N and W stand for any base and A or T, respectively), picking out 126 putative and known cre sequences. To examine their cre function, we integrated spac promoter (Pspac)-cre-lacZ fusions into the amyE locus. Examination of catabolite repression of ß-galactosidase synthesis in the integrants led us to the following conclusions: (i) lower mismatching of cre sequences to the query sequence is required for their function; (ii) although cre sequences are partially palindromic, low mismatching in the same direction as that of transcription of the target genes is more critical for their function than that in the inverse direction; and (iii) yet, a more palindromic nature of cre sequences is desirable for a better function. Furthermore, the alignment of 22 cres that function in vivo implicated a consensus sequence, WWTGNAARCGNWWWCAWW (R stands for G or A). Interestingly, in the case where cre sequences are located in the protein-coding regions of the target genes, their conserved bases are preferentially the third bases of codons where base degeneracy is allowed.
* To whom correspondence should be addressed at: Department of Biotechnology, Faculty of Engineering, Fukuyama University, 985 Sanzo, Higashimura-cho, Fukuyama-shi, Hiroshima 729-0292, Japan. Tel: +81 849 36 2111; Fax: +81 849 36 2459; Email: yfujita@bt.fubt.fukuyama-u.ac.jp Present address: Atsushi Ogiwara, Tsukuba Research Laboratories, Glaxo Wellcome K.K., Tsukuba 300-4247, Japan
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