Examination of the transcription factor NtcA-binding motif by in vitro selection of DNA sequences from a random library

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...

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Bibliographic Details
Published in:Journal of molecular biology 2000-08, Vol.301 (4), p.783-793
Main Authors: Jiang, F, Wisén, S, Widersten, M, Bergman, B, Mannervik, B
Format: Article
Language:English
Subjects:
Anabaena
Bacterial Proteins
Base Composition
Base Sequence
Binding Sites
Biochemistry
Biokemi
Chemistry
Cloning, Molecular - methods
Consensus Sequence - genetics
Conserved Sequence - genetics
Cyanobacteria - genetics
DNA - genetics
DNA - metabolism
DNA, Bacterial - genetics
DNA, Bacterial - metabolism
DNA-Binding Proteins - metabolism
Gene Expression Regulation, Bacterial
Gene Library
glnA gene
Kemi
Models, Genetic
Mutation - genetics
NATURAL SCIENCES
NATURVETENSKAP
NtcA protein
Response Elements - genetics
Sequence Analysis, DNA
Thermodynamics
Transcription Factors - metabolism
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Summary: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.
ISSN:0022-2836
1089-8638
DOI:10.1006/jmbi.2000.4000