title: Dual function of Ixr1 in transcriptional regulation and recognition of cisplatin-DNA adducts is caused by differential binding through its two HMG-boxes.
abstract: Ixr1 is a transcriptional factor involved in the response to hypoxia, which is also related to DNA repair. It binds to DNA through its two in-tandem high mobility group box (HMG-box) domains. Each function depends on recognition of different DNA structures, B-form DNA at specific consensus sequences for transcriptional regulation, or distorted DNA, like cisplatin-DNA adducts, for DNA repair. However, the contribution of the HMG-box domains in the Ixr1 protein to the formation of different protein-DNA complexes is poorly understood. We have biophysically and biochemically characterized these interactions with specific DNA sequences from the promoters regulated by Ixr1, or with cisplatin-DNA adducts. Both HMG-boxes are necessary for transcriptional regulation, and they are not functionally interchangeable. The in-tandem arrangement of their HMG-boxes is necessary for functional folding and causes sequential cooperative binding to specific DNA sequences, with HMG-box A showing a higher contribution to DNA binding and bending than the HMG-box B. Binding of Ixr1 HMG boxes to specific DNA sequences is entropy driven, whereas binding to platinated DNA is enthalpy driven for HMG-box A and entropy driven for HMG-box B. This is the first proof that HMG-box binding to different DNA structures is associated with predictable thermodynamic differences. Based on our study, we present a model to explain the dual function of Ixr1 in the regulation of gene expression and recognition of distorted DNA structures caused by cisplatin treatment.
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Vizoso-Vázquez
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Lamas-Maceiras
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
authors.forename: R
authors.initials: R
authors.lastname: Fernández-Leiro
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
authors.forename: A
authors.initials: A
authors.lastname: Rico-Díaz
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain.
authors.forename: M
authors.initials: M
authors.lastname: Becerra
authors.affiliation: Universidade da Coruña, Grupo EXPRELA, Centro de Investigacións Científicas Avanzadas (CICA), Departamento de Bioloxía Celular e Molecular, Facultade de Ciencias, A Coruña, Spain. Electronic address: esper.cerdan@udc.es.
authors.forename: M E
authors.initials: ME
authors.lastname: Cerdán
mesh_terms: D000595:Amino Acid Sequence; D002945:Cisplatin / Q000378:metabolism*; D004247:DNA / Q000378:metabolism; D018736:DNA Adducts / Q000378:metabolism*; D004260:DNA Repair / Q000235:genetics; D004268:DNA-Binding Proteins / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal / Q000235:genetics*; D024742:HMG-Box Domains / Q000235:genetics*; D006609:High Mobility Group Proteins / Q000378:metabolism*; D009690:Nucleic Acid Conformation; D011401:Promoter Regions, Genetic / Q000235:genetics; D011485:Protein Binding / Q000235:genetics; D017510:Protein Folding; D012441:Saccharomyces cerevisiae / Q000378:metabolism; D029701:Saccharomyces cerevisiae Proteins / Q000378:metabolism*; D016415:Sequence Alignment; D013816:Thermodynamics; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D018736:DNA Adducts; D004268:DNA-Binding Proteins; D006609:High Mobility Group Proteins; C082364:IXR1 protein, S cerevisiae; D029701:Saccharomyces cerevisiae Proteins; C057270:cisplatin-DNA adduct; D004247:DNA; D002945:Cisplatin
keywords: DNA repair; HMGB proteins; Protein-DNA interactions; SOX transcriptional factors; Saccharomyces cerevisiae; Thermodynamics