ArticleNucleic acids research2007
Analysis of the DNA-binding sequence specificity of the archaeal transcriptional regulator Ss-LrpB from Sulfolobus solfataricus by systematic mutagenesis and high resolution contact probing.
Article in Nucleic acids research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Article
- YtrAFrontiers in microbiology · 2019Article
- Two membrane-bound transcription factors regulate expression of various type-IV-pili surface structures inPeerJ · 2019Article
- The genome-scale DNA-binding profile of BarR, a β-alanine responsive transcription factor in the archaeon Sulfolobus acidocaldarius.BMC genomics · 2016Article
- Evolution of context dependent regulation by expansion of feast/famine regulatory proteins.BMC systems biology · 2014Article
- Article
- Article
- The genome-wide binding profile of the Sulfolobus solfataricus transcription factor Ss-LrpB shows binding events beyond direct transcription regulation.BMC genomics · 2013Article
- Expanded target and cofactor repertoire for the transcriptional activator LysM from Sulfolobus.Nucleic acids research · 2013Article
- Nanobody(R)-based chromatin immunoprecipitation/micro-array analysis for genome-wide identification of transcription factor DNA binding sites.Nucleic acids research · 2013Article
- The Lrp family of transcription regulators in archaea.Archaea (Vancouver, B.C.) · 2010Article
- The protein-DNA contacts in RutR•carAB operator complexes.Nucleic acids research · 2010Article
- Transcriptional control by two leucine-responsive regulatory proteins in Halobacterium salinarum R1.BMC molecular biology · 2010Article
- The DNA-recognition mode shared by archaeal feast/famine-regulatory proteins revealed by the DNA-binding specificities of TvFL3, FL10, FL11 and Ss-LrpB.Nucleic acids research · 2009Article
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4 authors.
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Abstract
To determine the sequence specificity of dimeric Ss-LrpB, a high resolution contact map was constructed and a saturation mutagenesis conducted on one half of the palindromic consensus box. Premodification binding interference indicates that Ss-LrpB establishes most of its tightest contacts with a single strand of two major groove segments and interacts with the minor groove at the center of the box. The requirement for bending is reflected in the preference for an A+T rich center and confirmed with C.G and C.I substitutions. The saturation mutagenesis indicates that major groove contacts with C.G at position 5 and its symmetrical counterpart are most critical for the specificity and strength of the interaction. Conservation at the remaining positions improved the binding. Hydrogen bonding to the O6 and N7 acceptor atoms of the G5' residue play a major role in complex formation. Unlike many other DNA-binding proteins Ss-LrpB does not establish hydrophobic interactions with the methyls of thymine residues. The binding energies determined from the saturation mutagenesis were used to construct a sequence logo, which pin-points the overwhelming importance of C.G at position 5. The knowledge of the DNA-binding specificity will constitute a precious tool for the search of new physiologically relevant binding sites for Ss-LrpB in the genome.
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