title: Operator recognition by the ROK transcription factor family members, NagC and Mlc.
abstract: NagC and Mlc, paralogous members of the ROK family of proteins with almost identical helix-turn-helix DNA binding motifs, specifically regulate genes for transport and utilization of N-acetylglucosamine and glucose. We previously showed that two amino acids in a linker region outside the canonical helix-turn-helix motif are responsible for Mlc site specificity. In this work we identify four amino acids in the linker, which are required for recognition of NagC targets. These amino acids allow Mlc and NagC to distinguish between a C/G and an A/T bp at positions ±11 of the operators. One linker position, glycine in NagC and arginine in Mlc, corresponds to the major specificity determinant for the two proteins. In certain contexts it is possible to switch repression from Mlc-style to NagC-style, by interchanging this glycine and arginine. Secondary determinants are supplied by other linker positions or the helix-turn-helix motif. A wide genomic survey of unique ROK proteins shows that glycine- and arginine-rich sequences are present in the linkers of nearly all ROK family repressors. Conserved short sequence motifs, within the branches of the ROK evolutionary tree, suggest that these sequences could also be involved in operator recognition in other ROK family members.
authors.affiliation: CNRS-FRE3630 (ex UPR9073), Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France.
authors.forename: Dominique
authors.initials: D
authors.lastname: Bréchemier-Baey
authors.affiliation: Division de Ciencias Biologicas y la Salud, Universidad Autonoma Metropolitana, Lerma, Lerma de Villada, Mexico.
authors.forename: Lenin
authors.initials: L
authors.lastname: Domínguez-Ramírez
authors.affiliation: UMR8621-CNRS Institut de Génétique et Microbiologie, Université Paris XI, 91405 Orsay, France.
authors.forename: Jacques
authors.initials: J
authors.lastname: Oberto
authors.affiliation: CNRS-FRE3630 (ex UPR9073), Université Paris Diderot, Sorbonne Paris Cité, Institut de Biologie Physico-Chimique, 13 rue P. et M. Curie, 75005 Paris, France jackie.plumbridge@ibpc.fr.
authors.forename: Jacqueline
authors.initials: J
authors.lastname: Plumbridge
mesh_terms: D020816:Amino Acid Motifs; D001665:Binding Sites; D029968:Escherichia coli Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism; D015964:Gene Expression Regulation, Bacterial; D009154:Mutation; D009875:Operator Regions, Genetic; D011485:Protein Binding; D012097:Repressor Proteins / Q000737:chemistry* / Q000235:genetics / Q000378:metabolism
chemical_list: D029968:Escherichia coli Proteins; C111065:Mlc protein, E coli; D012097:Repressor Proteins; C067862:nagC protein, E coli