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Staller MV, Holehouse AS, Swain-Lenz D, Das RK, Pappu RV, Cohen BA. A High-Throughput Mutational Scan of an Intrinsically Disordered Acidic Transcriptional Activation Domain. Cell Syst 2018; 6:444-455.e6. [PMID: 29525204 PMCID: PMC5920710 DOI: 10.1016/j.cels.2018.01.015] [Citation(s) in RCA: 90] [Impact Index Per Article: 15.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2017] [Revised: 11/14/2017] [Accepted: 01/25/2018] [Indexed: 01/11/2023]
Abstract
Transcriptional activation domains are essential for gene regulation, but their intrinsic disorder and low primary sequence conservation have made it difficult to identify the amino acid composition features that underlie their activity. Here, we describe a rational mutagenesis scheme that deconvolves the function of four activation domain sequence features-acidity, hydrophobicity, intrinsic disorder, and short linear motifs-by quantifying the activity of thousands of variants in vivo and simulating their conformational ensembles using an all-atom Monte Carlo approach. Our results with a canonical activation domain from the Saccharomyces cerevisiae transcription factor Gcn4 reconcile existing observations into a unified model of its function: the intrinsic disorder and acidic residues keep two hydrophobic motifs from driving collapse. Instead, the most-active variants keep their aromatic residues exposed to the solvent. Our results illustrate how the function of intrinsically disordered proteins can be revealed by high-throughput rational mutagenesis.
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Affiliation(s)
- Max V Staller
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Alex S Holehouse
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; Center for Biological Systems Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Devjanee Swain-Lenz
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA
| | - Rahul K Das
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; Center for Biological Systems Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA; Center for Biological Systems Engineering, Washington University in St. Louis, Saint Louis, MO 63130, USA
| | - Barak A Cohen
- The Edison Family Center for Genome Sciences and Systems Biology, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA; Department of Genetics, Washington University in St. Louis School of Medicine, Saint Louis, MO 63110, USA.
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Sun F, Zhou L, Zhao BC, Deng X, Cho H, Yi C, Jian X, Song CX, Luan CH, Bae T, Li Z, He C. Targeting MgrA-mediated virulence regulation in Staphylococcus aureus. ACTA ACUST UNITED AC 2011; 18:1032-41. [PMID: 21867918 DOI: 10.1016/j.chembiol.2011.05.014] [Citation(s) in RCA: 51] [Impact Index Per Article: 3.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2011] [Revised: 05/02/2011] [Accepted: 05/26/2011] [Indexed: 12/17/2022]
Abstract
Increasing antibiotic resistance in human pathogens necessitates the development of new approaches against infections. Targeting virulence regulation at the transcriptional level represents a promising strategy yet to be explored. A global transcriptional regulator, MgrA in Staphylococcus aureus, was identified previously as a key virulence determinant. We have performed a fluorescence anisotropy (FA)-based high-throughput screen that identified 5, 5-methylenedisalicylic acid (MDSA), which blocks the DNA binding of MgrA. MDSA represses the expression of α-toxin that is up-regulated by MgrA and activates the transcription of protein A, a gene down-regulated by MgrA. MDSA alters bacterial antibiotic susceptibilities via an MgrA-dependent pathway. A mouse model of infection indicated that MDSA could attenuate S. aureus virulence. This work is a rare demonstration of utilizing small molecules to block protein-DNA interaction, thus tuning important biological regulation at the transcriptional level.
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Affiliation(s)
- Fei Sun
- Department of Chemistry and Institute for Biophysical Dynamics, The University of Chicago, Chicago, IL 60637, USA
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Rodríguez-Martínez JA, Peterson-Kaufman KJ, Ansari AZ. Small-molecule regulators that mimic transcription factors. BIOCHIMICA ET BIOPHYSICA ACTA-GENE REGULATORY MECHANISMS 2010; 1799:768-74. [PMID: 20804876 DOI: 10.1016/j.bbagrm.2010.08.010] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/25/2010] [Revised: 08/17/2010] [Accepted: 08/22/2010] [Indexed: 02/06/2023]
Abstract
Transcription factors (TFs) are responsible for decoding and expressing the information stored in the genome, which dictates cellular function. Creating artificial transcription factors (ATFs) that mimic endogenous TFs is a major goal at the interface of biology, chemistry, and molecular medicine. Such molecular tools will be essential for deciphering and manipulating transcriptional networks that lead to particular cellular states. In this minireview, the framework for the design of functional ATFs is presented and current challenges in the successful implementation of ATFs are discussed.
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Majmudar CY, Labut AE, Mapp AK. Tra1 as a screening target for transcriptional activation domain discovery. Bioorg Med Chem Lett 2009; 19:3733-5. [PMID: 19497740 PMCID: PMC4322765 DOI: 10.1016/j.bmcl.2009.05.045] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/19/2009] [Revised: 05/09/2009] [Accepted: 05/12/2009] [Indexed: 01/20/2023]
Abstract
There is tremendous interest in developing activator artificial transcription factors that functionally mimic endogenous transcriptional activators for use as mechanistic probes, as components of synthetic cell circuitry, and in transcription-targeted therapies. Here, we demonstrate that a phage display selection against the transcriptional activation domain binding motif of the coactivator Tra1(TRRAP) produces distinct sequences that function with similar binding modes and potency as natural activators. These findings set the stage for binding screens with small molecule libraries against TAD binding motifs to yield next-generation small molecule TADs.
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Affiliation(s)
- Chinmay Y. Majmudar
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
| | - Anne E. Labut
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
| | - Anna K. Mapp
- Department of Chemistry, University of Michigan, 930 N. University, Ann Arbor, MI 48109, USA
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Abstract
The paradigm of gene regulation was forever changed by the discovery that short RNA duplexes could directly regulate gene expression. Most regulatory roles attributed to noncoding RNA were often repressive. Recent observations are beginning to reveal that duplex RNA molecules can stimulate gene transcription. These RNA activators employ a wide array of mechanisms to up-regulate transcription of target genes, including functioning as DNA-tethered activation domains, as coactivators and modulators of general transcriptional machinery, and as regulators of other noncoding transcripts. The discoveries over the past few years defy "Moore's law" in the breath-taking rapidity with which new roles for noncoding RNA in gene expression are being revealed. As gene regulatory networks are reconstructed to accommodate the influence of noncoding RNAs, their importance in maintenance of cellular health will become increasingly apparent. In fact, a new generation of therapeutic agents will focus on modulating the function of noncoding RNA.
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Affiliation(s)
- Aseem Z Ansari
- Department of Biochemistry & The Genome Center of Wisconsin, University of Wisconsin-Madison, 53706, USA.
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Casey RJ, Desaulniers JP, Hojfeldt JW, Mapp AK. Expanding the repertoire of small molecule transcriptional activation domains. Bioorg Med Chem 2009; 17:1034-43. [DOI: 10.1016/j.bmc.2008.02.045] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2007] [Revised: 02/08/2008] [Accepted: 02/13/2008] [Indexed: 10/22/2022]
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Abstract
Designer molecules that can be used to impose exogenous control on gene transcription, artificial transcription factors (ATFs), are highly desirable as mechanistic probes of gene regulation, as potential therapeutic agents, and as components of cell-based devices. Recently, several advances have been made in the design of ATFs that activate gene transcription (activator ATFs), including reports of small-molecule-based systems and ATFs that exhibit potent activity. However, the many open mechanistic questions about transcriptional activators, in particular, the structure and function of the transcriptional activation domain (TAD), have hindered rapid development of synthetic ATFs. A compelling need thus exists for chemical tools and insights toward a more detailed portrait of the dynamic process of gene activation.
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Affiliation(s)
- Anna K Mapp
- Department of Chemistry, University of Michigan, 930 N. University Ave., Ann Arbor, Michigan 48109, USA.
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Lum JK, Majmudar CY, Ansari AZ, Mapp AK. Converting inactive peptides into potent transcriptional activators. ACS Chem Biol 2006; 1:639-43. [PMID: 17175579 DOI: 10.1021/cb600363n] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Significant efforts have been devoted to the development of artificial transcriptional activators for use as mechanistic tools, as therapeutic agents, and for biomanufacturing applications. One of the primary challenges has been the development of artificial activators that exhibit potency in cells comparable to that of endogenous activators; the vast majority function only moderately in the cellular context. Here we demonstrate that the superimposition of two distinct binding modes, a masking interaction and an interaction with the transcriptional machinery, has a profoundly positive effect on the cellular activity of artificial activators, with up to 600-fold enhancement observed. Incorporation of this feature into future generations of small molecule transcriptional activators should increase their nuclear uptake and facilitate their accessibility to their target proteins, thus significantly augmenting both their activity and utility.
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