title: Examination of the transcription factor NtcA-binding motif by in vitro selection of DNA sequences from a random library.
abstract: A recursive in vitro selection among random DNA sequences was used for analysis of the cyanobacterial transcription factor NtcA-binding motifs. An eight-base palindromic sequence, TGTA-(N(8))-TACA, was found to be the optimal NtcA-binding sequence. The more divergent the binding sequences, compared to this consensus sequence, the lower the NtcA affinity. The second and third bases in each four-nucleotide half of the consensus sequence were crucial for NtcA binding, and they were in general highly conserved. The most frequently occurring sequence in the middle weakly conserved region was similar to that of the NtcA-binding motif of the Anabaena sp. strain PCC 7120 glnA gene, previously known to have high affinity for NtcA. This indicates that the middle sequences were selected for high NtcA affinity. Analysis of natural NtcA-binding motifs showed that these could be classified into two groups based on differences in recognition consensus sequences. It is suggested that NtcA naturally recognizes different DNA-binding motifs, or has differential affinities to these sequences under different physiological conditions.
authors.affiliation: Department of Biochemistry, Uppsala University, Biomedical Center, Uppsala, S-751 23, Sweden.
authors.forename: F
authors.initials: F
authors.lastname: Jiang
authors.forename: S
authors.initials: S
authors.lastname: Wisén
authors.forename: M
authors.initials: M
authors.lastname: Widersten
authors.forename: B
authors.initials: B
authors.lastname: Bergman
authors.forename: B
authors.initials: B
authors.lastname: Mannervik
mesh_terms: D001426:Bacterial Proteins; D001482:Base Composition; D001483:Base Sequence; D001665:Binding Sites; D003001:Cloning, Molecular / Q000379:methods; D016384:Consensus Sequence / Q000235:genetics*; D017124:Conserved Sequence / Q000235:genetics; D000458:Cyanobacteria / Q000235:genetics*; D004247:DNA / Q000235:genetics / Q000378:metabolism*; D004269:DNA, Bacterial / Q000235:genetics / Q000378:metabolism; D004268:DNA-Binding Proteins / Q000378:metabolism*; D015964:Gene Expression Regulation, Bacterial; D015723:Gene Library; D008957:Models, Genetic; D009154:Mutation / Q000235:genetics; D020218:Response Elements / Q000235:genetics*; D017422:Sequence Analysis, DNA; D013816:Thermodynamics; D014157:Transcription Factors / Q000378:metabolism*
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D004268:DNA-Binding Proteins; D014157:Transcription Factors; C075617:ntcA protein, Synechococcus; D004247:DNA