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Terrell JR, Taylor SJ, Schneider AL, Lu Y, Vernon TN, Xhani S, Gumpper RH, Luo M, Wilson WD, Steidl U, Poon GMK. DNA selection by the master transcription factor PU.1. Cell Rep 2023; 42:112671. [PMID: 37352101 PMCID: PMC10479921 DOI: 10.1016/j.celrep.2023.112671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2022] [Revised: 04/07/2023] [Accepted: 06/02/2023] [Indexed: 06/25/2023] Open
Abstract
The master transcriptional regulator PU.1/Spi-1 engages DNA sites with affinities spanning multiple orders of magnitude. To elucidate this remarkable plasticity, we have characterized 22 high-resolution co-crystallographic PU.1/DNA complexes across the addressable affinity range in myeloid gene transactivation. Over a purine-rich core (such as 5'-GGAA-3') flanked by variable sequences, affinity is negotiated by direct readout on the 5' flank via a critical glutamine (Q226) sidechain and by indirect readout on the 3' flank by sequence-dependent helical flexibility. Direct readout by Q226 dynamically specifies PU.1's characteristic preference for purines and explains the pathogenic mutation Q226E in Waldenström macroglobulinemia. The structures also reveal how disruption of Q226 mediates strand-specific inhibition by DNA methylation and the recognition of non-canonical sites, including the authentic binding sequence at the CD11b promoter. A re-synthesis of phylogenetic and structural data on the ETS family, considering the centrality of Q226 in PU.1, unifies the model of DNA selection by ETS proteins.
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Affiliation(s)
- J Ross Terrell
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Samuel J Taylor
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA
| | - Amelia L Schneider
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Yue Lu
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Tyler N Vernon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Suela Xhani
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ryan H Gumpper
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA
| | - Ming Luo
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - W David Wilson
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA
| | - Ulrich Steidl
- Departments of Cell Biology, Oncology, and Medicine, Ruth L. and David S. Gottesman Institute for Stem Cell Research and Regenerative Medicine, Blood Cancer Institute, and the Montefiore Einstein Cancer Center, Albert Einstein College of Medicine, Bronx, NY 10461, USA.
| | - Gregory M K Poon
- Department of Chemistry, Georgia State University, Atlanta, GA 30303, USA; Center for Diagnostics and Therapeutics, Georgia State University, Atlanta, GA 30303, USA.
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Hadži S, Lah J. Analysis of Protein-DNA Interactions Using Isothermal Titration Calorimetry: Successes and Failures. Methods Mol Biol 2022; 2516:239-257. [PMID: 35922630 DOI: 10.1007/978-1-0716-2413-5_13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Isothermal titration calorimetry (ITC) is a golden standard for the characterization of protein-DNA binding affinities and allows direct assessment of the accompanying thermodynamic driving forces. Their interpretation can give insight into role of electrostatics, specificity of the DNA recognition, contribution of protein folding upon DNA binding and help to distinguish between minor and major groove binders. The main advantages of ITC are that the binding is measured in solution, and it requires no labeling of the samples, however, the method is not well suited for high-performance studies. Here we describe the sample preparation, a procedure to perform a typical ITC experiment, data analysis, and lastly discuss how to interpret the obtained thermodynamic parameters. In conclusion, we show examples of several unsuccessful ITC experiments and identify the underlying reasons for failed experiments. In most cases with a proper adjustment of the experimental setup, it was possible to obtain data appropriate for further analysis.
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Affiliation(s)
- San Hadži
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia.
| | - Jurij Lah
- Department of Physical Chemistry, Faculty of Chemistry and Chemical Technology, University of Ljubljana, Ljubljana, Slovenia
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Aditham AK, Markin CJ, Mokhtari DA, DelRosso N, Fordyce PM. High-Throughput Affinity Measurements of Transcription Factor and DNA Mutations Reveal Affinity and Specificity Determinants. Cell Syst 2020; 12:112-127.e11. [PMID: 33340452 DOI: 10.1016/j.cels.2020.11.012] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2020] [Revised: 08/08/2020] [Accepted: 11/24/2020] [Indexed: 01/28/2023]
Abstract
Transcription factors (TFs) bind regulatory DNA to control gene expression, and mutations to either TFs or DNA can alter binding affinities to rewire regulatory networks and drive phenotypic variation. While studies have profiled energetic effects of DNA mutations extensively, we lack similar information for TF variants. Here, we present STAMMP (simultaneous transcription factor affinity measurements via microfluidic protein arrays), a high-throughput microfluidic platform enabling quantitative characterization of hundreds of TF variants simultaneously. Measured affinities for ∼210 mutants of a model yeast TF (Pho4) interacting with 9 oligonucleotides (>1,800 Kds) reveal that many combinations of mutations to poorly conserved TF residues and nucleotides flanking the core binding site alter but preserve physiological binding, providing a mechanism by which combinations of mutations in cis and trans could modulate TF binding to tune occupancies during evolution. Moreover, biochemical double-mutant cycles across the TF-DNA interface reveal molecular mechanisms driving recognition, linking sequence to function. A record of this paper's Transparent Peer Review process is included in the Supplemental Information.
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Affiliation(s)
- Arjun K Aditham
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA
| | - Craig J Markin
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Daniel A Mokhtari
- Department of Biochemistry, Stanford University, Stanford, CA 94305, USA
| | - Nicole DelRosso
- Graduate Program in Biophysics, Stanford University, Stanford, CA 94305, USA
| | - Polly M Fordyce
- Department of Bioengineering, Stanford University, Stanford, CA 94305, USA; Stanford ChEM-H, Stanford University, Stanford, CA 94305, USA; Department of Genetics, Stanford University, Stanford, CA 94305, USA; Chan Zuckerberg Biohub, San Francisco, CA 94110, USA.
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