The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius

BMC Genomics

Research Article

Eveline Peeters¹  Han Liu¹  Kun Wang²  Ann-Christin Lindås² 

[1] Department of Bio-Engineering Sciences, Research Group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium;Department of Molecular Biosciences, The Wenner-Gren Institute, Stockholm University, Svante Arrhenius v. 20C, SE-10691, Stockholm, Sweden;

关键词: β-alanine;    Sulfolobus;    Leucine-responsive regulatory protein;    Transcription regulation;    ChIP-seq;   

DOI  :  10.1186/s12864-016-2890-0

 received in 2016-03-26, accepted in 2016-07-06,  发布年份 2016

来源: Springer

【 摘 要 】

BackgroundThe Leucine-responsive Regulatory Protein (Lrp) family is a widespread family of regulatory transcription factors in prokaryotes. BarR is an Lrp-like transcription factor in the model archaeon Sulfolobus acidocaldarius that activates the expression of a β-alanine aminotransferase gene, which is involved in β-alanine degradation. In contrast to classical Lrp-like transcription factors, BarR is not responsive to any of the α-amino acids but interacts specifically with β-alanine. Besides the juxtaposed β-alanine aminotransferase gene, other regulatory targets of BarR have not yet been identified although β-alanine is the precursor of coenzyme A and thus an important central metabolite. The aim of this study is to extend the knowledge of the DNA-binding characteristics of BarR and of its corresponding regulon from a local to a genome-wide perspective.ResultsWe characterized the genome-wide binding profile of BarR using chromatin immunoprecipation combined with high-throughput sequencing (ChIP-seq). This revealed 21 genomic binding loci. High-enrichment binding regions were validated to interact with purified BarR protein in vitro using electrophoretic mobility shift assays and almost all targets were also shown to harbour a conserved semi-palindromic binding motif. Only a small subset of enriched genomic sites are located in intergenic regions at a relative short distance to a promoter, and qRT-PCR analysis demonstrated that only one additional operon is under activation of BarR, namely the glutamine synthase operon. The latter is also a target of other Lrp-like transcription factors. Detailed inspection of the BarR ChIP-seq profile at the β-alanine aminotransferase promoter region in combination with binding motif predictions indicate that the operator structure is more complicated than previously anticipated, consisting of multiple (major and auxiliary) operators.ConclusionsBarR has a limited regulon, and includes also glutamine synthase genes besides the previously characterized β-alanine aminotransferase. Regulation of glutamine synthase is suggestive of a link between β-alanine and α-amino acid metabolism in S. acidocaldarius. Furthermore, this work reveals that the BarR regulon overlaps with that of other Lrp-like regulators.

【 授权许可】

CC BY   
© The Author(s). 2016