title: Binding of transcription factor GabR to DNA requires recognition of DNA shape at a location distinct from its cognate binding site.
abstract: Mechanisms for transcription factor recognition of specific DNA base sequences are well characterized and recent studies demonstrate that the shape of these cognate binding sites is also important. Here, we uncover a new mechanism where the transcription factor GabR simultaneously recognizes two cognate binding sites and the shape of a 29 bp DNA sequence that bridges these sites. Small-angle X-ray scattering and multi-angle laser light scattering are consistent with a model where the DNA undergoes a conformational change to bend around GabR during binding. In silico predictions suggest that the bridging DNA sequence is likely to be bendable in one direction and kinetic analysis of mutant DNA sequences with biolayer interferometry, allowed the independent quantification of the relative contribution of DNA base and shape recognition in the GabR-DNA interaction. These indicate that the two cognate binding sites as well as the bendability of the DNA sequence in between these sites are required to form a stable complex. The mechanism of GabR-DNA interaction provides an example where the correct shape of DNA, at a clearly distinct location from the cognate binding site, is required for transcription factor binding and has implications for bioinformatics searches for novel binding sites.
authors.affiliation: School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Walid A
authors.initials: WA
authors.lastname: Al-Zyoud
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Robert M G
authors.initials: RM
authors.lastname: Hynson
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Lorraine A
authors.initials: LA
authors.lastname: Ganuelas
authors.affiliation: School of Mathematics and Statistics, University of New South Wales, Sydney, NSW 2052, Australia.
authors.forename: Adelle C F
authors.initials: AC
authors.lastname: Coster
authors.affiliation: Australian Nuclear Science and Technology Organisation, Lucas Heights, NSW 2234, Australia.
authors.forename: Anthony P
authors.initials: AP
authors.lastname: Duff
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Matthew A B
authors.initials: MA
authors.lastname: Baker
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Alastair G
authors.initials: AG
authors.lastname: Stewart
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Eleni
authors.initials: E
authors.lastname: Giannoulatou
authors.affiliation: The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia.
authors.forename: Joshua W K
authors.initials: JW
authors.lastname: Ho
authors.affiliation: School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia.
authors.forename: Katharina
authors.initials: K
authors.lastname: Gaus
authors.affiliation: Department of Chemistry and Biochemistry, Loyola University, Chicago, IL 60660, USA.
authors.forename: Dali
authors.initials: D
authors.lastname: Liu
authors.affiliation: School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia The Victor Chang Cardiac Research Institute, 405 Liverpool St Darlinghurst, Darlinghurst, NSW 2010, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia lawrence.lee@unsw.edu.au.
authors.forename: Lawrence K
authors.initials: LK
authors.lastname: Lee
authors.affiliation: School of Medical Sciences, The University of New South Wales, Sydney, NSW 2052, Australia EMBL Australia Node for Single Molecule Science, The University of New South Wales, Corner Botany and High Street, Kensington Campus 2052, NSW 2052, Australia till.boecking@unsw.edu.au.
authors.forename: Till
authors.initials: T
authors.lastname: Böcking
mesh_terms: D001412:Bacillus subtilis / Q000235:genetics / Q000378:metabolism; D001426:Bacterial Proteins / Q000737:chemistry* / Q000378:metabolism; D001483:Base Sequence; D001665:Binding Sites / Q000235:genetics; D002850:Chromatography, Gel; D004269:DNA, Bacterial / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009690:Nucleic Acid Conformation; D009876:Operon / Q000235:genetics; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding; D055503:Protein Multimerization; D017434:Protein Structure, Tertiary; D053838:Scattering, Small Angle; D012689:Sequence Homology, Nucleic Acid; D014157:Transcription Factors / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D014961:X-Ray Diffraction
chemical_list: D001426:Bacterial Proteins; D004269:DNA, Bacterial; D014157:Transcription Factors