Mechanism of cognate sequence discrimination by the ETS-family transcription factor ETS-1

• Published in: The Journal of biological chemistry Vol. 294; no. 25; pp. 9666 - 9678
• Main Authors: Huang, Kenneth, Xhani, Suela, Albrecht, Amanda V., Ha, Van L.T., Esaki, Shingo, Poon, Gregory M.K.
• Format: Journal Article
• Language: English
• Published: United States Elsevier Inc 21.06.2019; American Society for Biochemistry and Molecular Biology
• Subjects: allosteric regulation; Animals; Base Sequence; Binding Sites; developmental factor; DNA - chemistry; DNA - metabolism; DNA binding protein; DNA sequence motif; DNA-binding domain; ETS proto-oncogene 1 transcription factor (ETS1); ETS transcription factor family; low-affinity DNA binding; Mice; Models, Molecular; Molecular Biophysics; molecular dynamics; Molecular Dynamics Simulation; Protein Binding; Protein Conformation; Proto-Oncogene Protein c-ets-1 - chemistry; Proto-Oncogene Protein c-ets-1 - metabolism; suboptimization; transcription enhancer; transcription factor; transcription factor; DNA-binding domain; suboptimization; developmental factor; low-affinity DNA binding; DNA binding protein; transcription enhancer; allosteric regulation; molecular dynamics; DNA sequence motif; ETS transcription factor family; ETS proto-oncogene 1 transcription factor (ETS1)
• ISSN: 0021-9258; 1083-351X
• DOI: 10.1074/jbc.RA119.007866

Functional evidence increasingly implicates low-affinity DNA recognition by transcription factors as a general mechanism for the spatiotemporal control of developmental genes. Although the DNA sequence requirements for affinity are well-defined, the dynamic mechanisms that execute cognate recognition are much less resolved. To address this gap, here we examined ETS1, a paradigm developmental transcription factor, as a model for which cognate discrimination remains enigmatic. Using molecular dynamics simulations, we interrogated the DNA-binding domain of murine ETS1 alone and when bound to high-and low-affinity cognate sites or to nonspecific DNA. The results of our analyses revealed collective backbone and side-chain motions that distinguished cognate versus nonspecific as well as high- versus low-affinity cognate DNA binding. Combined with binding experiments with site-directed ETS1 mutants, the molecular dynamics data disclosed a triad of residues that respond specifically to low-affinity cognate DNA. We found that a DNA-contacting residue (Gln-336) specifically recognizes low-affinity DNA and triggers the loss of a distal salt bridge (Glu-343/Arg-378) via a large side-chain motion that compromises the hydrophobic packing of two core helices. As an intact Glu-343/Arg-378 bridge is the default state in unbound ETS1 and maintained in high-affinity and nonspecific complexes, the low-affinity complex represents a unique conformational adaptation to the suboptimization of developmental enhancers.