The genome-wide binding profile of the Sulfolobus solfataricustranscription factor Ss-LrpB shows binding events beyond direct transcription regulation

BMC Genomics

Research Article

Serge Muyldermans¹  Gholamreza Hassanzadeh-Ghassabeh¹  Trong Nguyen-Duc²  Eveline Peeters³  Daniel Charlier³  Ningning Song³  Liesbeth van Oeffelen⁴ 

[1] Research group of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium;Department of Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium;Research group of Cellular and Molecular Immunology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium;Department of Structural Biology, VIB, Pleinlaan 2, B-1050, Brussels, Belgium;Department of Microbiology and Immunology, State University of New York at Buffalo, 321 Cary Hall, 3435 Main Street, 14214, Buffalo, NY, United States;Research group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium;Research group of Microbiology, Vrije Universiteit Brussel, Pleinlaan 2, B-1050, Brussels, Belgium;IMEC, Kapeldreef 75, B-3001, Leuven, Belgium;

关键词: Archaea;    Sulfolobus;    Leucine-responsive regulatory protein;    CRISPR;    ChIP-chip;   

DOI  :  10.1186/1471-2164-14-828

 received in 2013-06-13, accepted in 2013-11-15,  发布年份 2013

来源: Springer

【 摘 要 】

BackgroundGene regulatory processes are largely resulting from binding of transcription factors to specific genomic targets. Leucine-responsive Regulatory Protein (Lrp) is a prevalent transcription factor family in prokaryotes, however, little information is available on biological functions of these proteins in archaea. Here, we study genome-wide binding of the Lrp-like transcription factor Ss-LrpB from Sulfolobus solfataricus.ResultsChromatin immunoprecipitation in combination with DNA microarray analysis (ChIP-chip) has revealed that Ss-LrpB interacts with 36 additional loci besides the four previously identified local targets. Only a subset of the newly identified binding targets, concentrated in a highly variable IS-dense genomic region, is also bound in vitro by pure Ss-LrpB. There is no clear relationship between the in vitro measured DNA-binding specificity of Ss-LrpB and the in vivo association suggesting a limited permissivity of the crenarchaeal chromatin for transcription factor binding. Of 37 identified binding regions, 29 are co-bound by LysM, another Lrp-like transcription factor in S. solfataricus. Comparative gene expression analysis in an Ss-lrpB mutant strain shows no significant Ss-LrpB-mediated regulation for most targeted genes, with exception of the CRISPR B cluster, which is activated by Ss-LrpB through binding to a specific motif in the leader region.ConclusionsThe genome-wide binding profile presented here implies that Ss-LrpB is associated at additional genomic binding sites besides the local gene targets, but acts as a specific transcription regulator in the tested growth conditions. Moreover, we have provided evidence that two Lrp-like transcription factors in S. solfataricus, Ss-LrpB and LysM, interact in vivo.

【 授权许可】

Unknown   
© Nguyen-Duc et al.; licensee BioMed Central Ltd. 2013. This article is published under license to BioMed Central Ltd. This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.