1
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Pattelli ON, Valdivia EM, Beyersdorf MS, Regan CS, Rivas M, Hebert KA, Merajver SD, Cierpicki T, Mapp AK. A Lipopeptidomimetic of Transcriptional Activation Domains Selectively Disrupts the Coactivator Med25 Protein-Protein Interactions. Angew Chem Int Ed Engl 2024; 63:e202400781. [PMID: 38527936 PMCID: PMC11134611 DOI: 10.1002/anie.202400781] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2024] [Revised: 03/18/2024] [Accepted: 03/25/2024] [Indexed: 03/27/2024]
Abstract
Short amphipathic peptides are capable of binding to transcriptional coactivators, often targeting the same binding surfaces as native transcriptional activation domains. However, they do so with modest affinity and generally poor selectivity, limiting their utility as synthetic modulators. Here we show that incorporation of a medium-chain, branched fatty acid to the N-terminus of one such heptameric lipopeptidomimetic (LPPM-8) increases the affinity for the coactivator Med25 >20-fold (Ki >100 μM to 4 μM), rendering it an effective inhibitor of Med25 protein-protein interactions (PPIs). The lipid structure, the peptide sequence, and the C-terminal functionalization of the lipopeptidomimetic each influence the structural propensity of LPPM-8 and its effectiveness as an inhibitor. LPPM-8 engages Med25 through interaction with the H2 face of its activator interaction domain and in doing so stabilizes full-length protein in the cellular proteome. Further, genes regulated by Med25-activator PPIs are inhibited in a cell model of triple-negative breast cancer. Thus, LPPM-8 is a useful tool for studying Med25 and mediator complex biology and the results indicate that lipopeptidomimetics may be a robust source of inhibitors for activator-coactivator complexes.
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Affiliation(s)
- Olivia N. Pattelli
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Estefanía Martínez Valdivia
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Matthew S. Beyersdorf
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
| | - Clint S. Regan
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | - Mónica Rivas
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
| | | | - Sofia D. Merajver
- Department of Internal Medicine, Hematology/Oncology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Tomasz Cierpicki
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Pathology, University of Michigan Medical School, Ann Arbor, MI 48109 USA
| | - Anna K. Mapp
- Life Sciences Institute, University of Michigan, Ann Arbor, MI 48109 USA
- Program in Chemical Biology, University of Michigan, Ann Arbor, MI 48109 USA
- Department of Chemistry, University of Michigan, Ann Arbor, MI 48109 USA
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2
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Mahata B, Cabrera A, Brenner DA, Guerra-Resendez RS, Li J, Goell J, Wang K, Guo Y, Escobar M, Parthasarathy AK, Szadowski H, Bedford G, Reed DR, Kim S, Hilton IB. Compact engineered human mechanosensitive transactivation modules enable potent and versatile synthetic transcriptional control. Nat Methods 2023; 20:1716-1728. [PMID: 37813990 PMCID: PMC10630135 DOI: 10.1038/s41592-023-02036-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Accepted: 09/05/2023] [Indexed: 10/11/2023]
Abstract
Engineered transactivation domains (TADs) combined with programmable DNA binding platforms have revolutionized synthetic transcriptional control. Despite recent progress in programmable CRISPR-Cas-based transactivation (CRISPRa) technologies, the TADs used in these systems often contain poorly tolerated elements and/or are prohibitively large for many applications. Here, we defined and optimized minimal TADs built from human mechanosensitive transcription factors. We used these components to construct potent and compact multipartite transactivation modules (MSN, NMS and eN3x9) and to build the CRISPR-dCas9 recruited enhanced activation module (CRISPR-DREAM) platform. We found that CRISPR-DREAM was specific and robust across mammalian cell types, and efficiently stimulated transcription from diverse regulatory loci. We also showed that MSN and NMS were portable across Type I, II and V CRISPR systems, transcription activator-like effectors and zinc finger proteins. Further, as proofs of concept, we used dCas9-NMS to efficiently reprogram human fibroblasts into induced pluripotent stem cells and demonstrated that mechanosensitive transcription factor TADs are efficacious and well tolerated in therapeutically important primary human cell types. Finally, we leveraged the compact and potent features of these engineered TADs to build dual and all-in-one CRISPRa AAV systems. Altogether, these compact human TADs, fusion modules and delivery architectures should be valuable for synthetic transcriptional control in biomedical applications.
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Affiliation(s)
- Barun Mahata
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Alan Cabrera
- Department of Bioengineering, Rice University, Houston, TX, USA
| | | | | | - Jing Li
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Jacob Goell
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Kaiyuan Wang
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Yannie Guo
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Mario Escobar
- Department of BioSciences, Rice University, Houston, TX, USA
| | | | - Hailey Szadowski
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA
| | - Guy Bedford
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Daniel R Reed
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Sunghwan Kim
- Department of Bioengineering, Rice University, Houston, TX, USA
| | - Isaac B Hilton
- Department of Bioengineering, Rice University, Houston, TX, USA.
- Systems, Synthetic, and Physical Biology Graduate Program, Rice University, Houston, TX, USA.
- Department of BioSciences, Rice University, Houston, TX, USA.
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3
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Houser J, Jendruchova K, Knight A, Piskacek M. The NFkB activation domain is 14-amino-acid-long variant of the 9aaTAD. Biochem J 2023; 480:297-306. [PMID: 36825663 DOI: 10.1042/bcj20220605] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2022] [Revised: 02/22/2023] [Accepted: 02/23/2023] [Indexed: 02/25/2023]
Abstract
The nine-amino-acid transactivation domains (9aaTAD) was identified in numerous transcription factors including Gal4, p53, E2A, MLL, c-Myc, N-Myc, and also in SP, KLF, and SOX families. Most of the 9aaTAD domains interact with the KIX domain of transcription mediators MED15 and CBP to activate transcription. The NFkB activation domain occupied the same position on the KIX domain as the 9aaTADs of MLL, E2A, and p53. Binding of the KIX domain is established by the two-point interaction involving 9aaTAD positions p3-4 and p6-7. The NFkB primary binding region (positions p3-4) is almost identical with MLL and E2A, but secondary NFkB binding region differs by the position and engages the distal NFkB region p10-11. Thus, the NFkB activation domain is five amino acids longer than the other 9aaTADs. The NFkB activation domain includes an additional region, which we called the Omichinski Insert extending activation domain length to 14 amino acids. By deletion, we demonstrated that Omichinski Insert is an entirely non-essential part of NFkB activation domain. In summary, we recognized the NFkB activation domain as prolonged 9aaTAD conserved in evolution from humans to amphibians.
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Affiliation(s)
- Josef Houser
- Central European Institute of Technology (CEITEC), Masaryk University Brno, Brno, Czech Republic
- National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University Brno, Brno, Czech Republic
- Core Facility Biomolecular Interactions and Crystallization (CF BIC), Masaryk University Brno, Brno, Czech Republic
| | - Kristina Jendruchova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
- Department of Neurosurgery, University Hospital Brno, Brno, Czech Republic
- Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00 Brno, Czech Republic
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4
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Knight A, Piskacek M. Cryptic inhibitory regions nearby activation domains. Biochimie 2022; 200:19-26. [PMID: 35561946 DOI: 10.1016/j.biochi.2022.05.004] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/12/2022] [Revised: 04/23/2022] [Accepted: 05/05/2022] [Indexed: 11/27/2022]
Abstract
Previously, the Nine amino acid TransActivation Domain (9aaTAD) was identified in the Gal4 region 862-870 (DDVYNYLFD). Here, we identified 9aaTADs in the distal Gal4 orthologs by our prediction algorithm and found their conservation in the family. The 9aaTAD function as strong activators was demonstrated. We identified adjacent Gal4 region 871-811 (DEDTPPNPKKE) as a natural 9aaTAD inhibitory domain located at the extreme Gal4 terminus. Moreover, we identified conserved Gal4 region 172-185 (FDWSEEDDMSDGLP), which was capable to reverse the 9aaTAD inhibition. In conclusion, our results uncover the existence of the cryptic inhibitory domains, which need to be carefully implemented in all functional studies with transcription factors to avoid incorrect conclusions.
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Affiliation(s)
- Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.
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5
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Piskacek M, Otasevic T, Repko M, Knight A. The 9aaTAD Activation Domains in the Yamanaka Transcription Factors Oct4, Sox2, Myc, and Klf4. Stem Cell Rev Rep 2021; 17:1934-1936. [PMID: 34342803 DOI: 10.1007/s12015-021-10225-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/20/2021] [Indexed: 10/20/2022]
Affiliation(s)
- Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.
| | - Tomas Otasevic
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.,Joint Repair and Regeneration, Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno, Brno, Czech Republic
| | - Martin Repko
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.,Joint Repair and Regeneration, Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno, Brno, Czech Republic
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic.
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6
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Liang JJ, Peng H, Wang JJ, Liu XH, Ma L, Ni YR, Yang HJ, Zhang YQ, Ai WB, Wu JF. Relationship between the structure and function of the transcriptional regulator E2A. ACTA ACUST UNITED AC 2021; 28:15. [PMID: 34271975 PMCID: PMC8283981 DOI: 10.1186/s40709-021-00146-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 06/30/2021] [Indexed: 11/10/2022]
Abstract
E proteins are transcriptional regulators that regulate many developmental processes in animals and lymphocytosis and leukemia in Homo sapiens. In particular, E2A, a member of the E protein family, plays a major role in the transcriptional regulatory network that promotes the differentiation and development of B and T lymphocytes. E2A-mediated transcriptional regulation usually requires the formation of E2A dimers, which then bind to coregulators. In this review, we summarize the mechanisms by which E2A participates in transcriptional regulation from a structural perspective. More specifically, the C-terminal helix-loop-helix (HLH) region of the basic HLH (bHLH) domain first dimerizes, and then the activation domains of E2A bind to different coactivators or corepressors in different cell contexts, resulting in histone acetylation or deacetylation, respectively. Then, the N-terminal basic region (b) of the bHLH domain binds to or dissociates from a specific DNA motif (E-box sequence). Last, trans-activation or trans-repression occurs. We also summarize the properties of these E2A domains and their interactions with the domains of other proteins. The feasibility of developing drugs based on these domains is discussed.
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Affiliation(s)
- Jia-Jie Liang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Hu Peng
- Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China
| | - Jiao-Jiao Wang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Xiao-Hui Liu
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Lan Ma
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Yi-Ran Ni
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Huai-Jie Yang
- The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000, Hubei, China
| | - Yan-Qiong Zhang
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China.,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China
| | - Wen-Bing Ai
- The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China.
| | - Jiang-Feng Wu
- Medical College, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,Institute of Organ Fibrosis and Targeted Drug Delivery, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,Hubei Key Laboratory of Tumor Microenvironment and Immunotherapy, China Three Gorges University, 8 Daxue Road, Xiling District, Yichang, 443002, China. .,The People's Hospital of China Three Gorges University, 31 Huti Subdistrict, Xi Ling District, Yichang, 443000, Hubei, China. .,The Yiling Hospital of Yichang, 32 Donghu Road, Yi Ling District, Yichang, 443100, Hubei, China.
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7
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Hofrova A, Lousa P, Kubickova M, Hritz J, Otasevic T, Repko M, Knight A, Piskacek M. Universal two-point interaction of mediator KIX with 9aaTAD activation domains. J Cell Biochem 2021; 122:1544-1555. [PMID: 34224597 DOI: 10.1002/jcb.30075] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2021] [Revised: 06/14/2021] [Accepted: 06/18/2021] [Indexed: 01/05/2023]
Abstract
The nine-amino-acid activation domain (9aaTAD) is defined by a short amino acid pattern including two hydrophobic regions (positions p3-4 and p6-7). The KIX domain of mediator transcription CBP interacts with the 9aaTAD domains of transcription factors MLL, E2A, NF-kB, and p53. In this study, we analyzed the 9aaTADs-KIX interactions by nuclear magnetic resonance. The positions of three KIX helixes α1-α2-α3 are influenced by sterically-associated hydrophobic I611, L628, and I660 residues that are exposed to solvent. The positions of two rigid KIX helixes α1 and α2 generate conditions for structural folding in the flexible KIX-L12-G2 regions localized between them. The three KIX I611, L628, and I660 residues interact with two 9aaTAD hydrophobic residues in positions p3 and p4 and together build a hydrophobic core of five residues (5R). Numerous residues in 9aaTAD position p3 and p4 could provide this interaction. Following binding of the 9aaTAD to KIX, the hydrophobic I611, L628, and I660 residues are no longer exposed to solvent and their position changes inside the hydrophobic core together with position of KIX α1-α2-α3 helixes. The new positions of the KIX helixes α1 and α2 allow the KIX-L12-G2 enhanced formation. The second hydrophobic region of the 9aaTAD (positions p6 and p7) provides strong binding with the KIX-L12-G2 region. Similarly, multiple residues in 9aaTAD position p6 and p7 could provide this interaction. In conclusion, both 9aaTAD regions p3, p4 and p6, p7 provide co-operative and highly universal binding to mediator KIX. The hydrophobic core 5R formation allows new positions of the rigid KIX α-helixes and enables the enhanced formation of the KIX-L12-G2 region. This contributes to free energy and is the key for the KIX-9aaTAD binding. Therefore, the 9aaTAD-KIX interactions do not operate under the rigid key-and-lock mechanism what explains the 9aaTAD natural variability.
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Affiliation(s)
- Alena Hofrova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,National Centre for Biomolecular Research (NCBR), Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Petr Lousa
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic
| | - Monika Kubickova
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Core Facility Biomolecular Interactions and Crystallization (CF BIC), Masaryk University, Brno, Czech Republic
| | - Jozef Hritz
- Central European Institute of Technology (CEITEC), Masaryk University, Brno, Czech Republic.,Department of Chemistry, Faculty of Science, Masaryk University, Brno, Czech Republic
| | - Tomas Otasevic
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Martin Repko
- Orthopaedic Clinic, University Hospital Brno and Faculty of Medicine Masaryk University Brno
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
| | - Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University, Brno, Czech Republic
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Piskacek M, Havelka M, Jendruchova K, Knight A, Keegan LP. The evolution of the 9aaTAD domain in Sp2 proteins: inactivation with valines and intron reservoirs. Cell Mol Life Sci 2020; 77:1793-1810. [PMID: 31375868 PMCID: PMC11105055 DOI: 10.1007/s00018-019-03251-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2019] [Revised: 07/10/2019] [Accepted: 07/24/2019] [Indexed: 12/28/2022]
Abstract
The universal nine-amino-acid transactivation domains (9aaTADs) have been identified in numerous transcription activators. Here, we identified the conserved 9aaTAD motif in all nine members of the specificity protein (SP) family. Previously, the Sp1 transcription factor has been defined as a glutamine-rich activator. We showed by amino acid substitutions that the glutamine residues are completely dispensable for 9aaTAD function and are not conserved in the SP family. We described the origin and evolutionary history of 9aaTADs. The 9aaTADs of the ancestral Sp2 gene became inactivated in early chordates. We next discovered that an accumulation of valines in 9aaTADs inactivated their transactivation function and enabled their strict conservation during evolution. Subsequently, in chordates, Sp2 has duplicated and created new paralogs, Sp1, Sp3, and Sp4 (the SP1-4 clade). During chordate evolution, the dormancy of the Sp2 activation domain lasted over 100 million years. The dormant but still intact ancestral Sp2 activation domains allowed diversification of the SP1-4 clade into activators and repressors. By valine substitution in the 9aaTADs, Sp1 and Sp3 regained their original activator function found in ancestral lower metazoan sea sponges. Therefore, the vertebrate SP1-4 clade could include both repressors and activators. Furthermore, we identified secondary 9aaTADs in Sp2 introns present from fish to primates, including humans. In the gibbon genome, introns containing 9aaTADs were used as exons, which turned the Sp2 gene into an activator. Similarly, we identified introns containing 9aaTADs used conditionally as exons in the (SP family-unrelated) transcription factor SREBP1, suggesting that the intron-9aaTAD reservoir is a general phenomenon.
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Affiliation(s)
- Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Laboratory of Cancer Biology and Genetics, Masaryk University Brno, Kamenice 5, Brno, 625 00, Czech Republic.
| | - Marek Havelka
- Department of Pathological Physiology, Faculty of Medicine, Laboratory of Cancer Biology and Genetics, Masaryk University Brno, Kamenice 5, Brno, 625 00, Czech Republic
| | - Kristina Jendruchova
- Department of Pathological Physiology, Faculty of Medicine, Laboratory of Cancer Biology and Genetics, Masaryk University Brno, Kamenice 5, Brno, 625 00, Czech Republic
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Gamma Delta T Cell Laboratory, Masaryk University Brno, Kamenice 5, Brno, 625 00, Czech Republic.
| | - Liam P Keegan
- CEITEC, Masaryk University, Kamenice 753/5, Pavilion A35, Brno, 62 500, Czech Republic.
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9
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Haseeb A, Lefebvre V. The SOXE transcription factors-SOX8, SOX9 and SOX10-share a bi-partite transactivation mechanism. Nucleic Acids Res 2019; 47:6917-6931. [PMID: 31194875 PMCID: PMC6649842 DOI: 10.1093/nar/gkz523] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2019] [Revised: 05/23/2019] [Accepted: 06/03/2019] [Indexed: 12/20/2022] Open
Abstract
SOX8, SOX9 and SOX10 compose the SOXE transcription factor group. They govern cell fate and differentiation in many lineages, and mutations impairing their activity cause severe diseases, including campomelic dysplasia (SOX9), sex determination disorders (SOX8 and SOX9) and Waardenburg-Shah syndrome (SOX10). However, incomplete knowledge of their modes of action limits disease understanding. We here uncover that the proteins share a bipartite transactivation mechanism, whereby a transactivation domain in the middle of the proteins (TAM) synergizes with a C-terminal one (TAC). TAM comprises amphipathic α-helices predicted to form a protein-binding pocket and overlapping with minimal transactivation motifs (9-aa-TAD) described in many transcription factors. One 9-aa-TAD sequence includes an evolutionarily conserved and functionally required EΦ[D/E]QYΦ motif. SOXF proteins (SOX7, SOX17 and SOX18) contain an identical motif, suggesting evolution from a common ancestor already harboring this motif, whereas TAC and other transactivating SOX proteins feature only remotely related motifs. Missense variants in this SOXE/SOXF-specific motif are rare in control individuals, but have been detected in cancers, supporting its importance in development and physiology. By deepening understanding of mechanisms underlying the central transactivation function of SOXE proteins, these findings should help further decipher molecular networks essential for development and health and dysregulated in diseases.
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Affiliation(s)
- Abdul Haseeb
- Department of Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
| | - Véronique Lefebvre
- Department of Surgery/Division of Orthopaedic Surgery, The Children's Hospital of Philadelphia, Philadelphia, PA 19104, USA
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10
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Piskacek M, Havelka M, Jendruchova K, Knight A. Nuclear hormone receptors: Ancient 9aaTAD and evolutionally gained NCoA activation pathways. J Steroid Biochem Mol Biol 2019; 187:118-123. [PMID: 30468856 DOI: 10.1016/j.jsbmb.2018.11.008] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/06/2018] [Revised: 11/18/2018] [Accepted: 11/18/2018] [Indexed: 12/12/2022]
Abstract
In higher metazoans, the nuclear hormone receptors activate transcription trough their specific adaptors, nuclear hormone receptor adaptors NCoA, which are absent in lower metazoans. The Nine amino acid TransActivation Domain, 9aaTAD, was reported for a large number of the transcription activators that recruit general mediators of transcription. In this study, we demonstrated that the 9aaTAD from NHR-49 receptor of nematode C.elegans activates transcription as a small peptide. We showed that the ancient 9aaTAD domains are conserved in the nuclear hormone receptors including human HNF4, RARa, VDR and PPARg. Also their small 9aaTAD peptides effectively activated transcription in absence of the NCoA adaptors. We also showed that adjacent H11 domains in ancient and modern hormone receptors have an inhibitory effect on their 9aaTAD function.
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Affiliation(s)
- Martin Piskacek
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic.
| | - Marek Havelka
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
| | - Kristina Jendruchova
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
| | - Andrea Knight
- Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Czech Republic; Laboratory of Cancer Biology and Genetics, Czech Republic; Gamma Delta T Cell Laboratory, Czech Republic
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Ramaswamy K, Forbes L, Minuesa G, Gindin T, Brown F, Kharas MG, Krivtsov AV, Armstrong SA, Still E, de Stanchina E, Knoechel B, Koche R, Kentsis A. Peptidomimetic blockade of MYB in acute myeloid leukemia. Nat Commun 2018; 9:110. [PMID: 29317678 PMCID: PMC5760651 DOI: 10.1038/s41467-017-02618-6] [Citation(s) in RCA: 60] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 12/13/2017] [Indexed: 02/08/2023] Open
Abstract
Aberrant gene expression is a hallmark of acute leukemias. MYB-driven transcriptional coactivation with CREB-binding protein (CBP)/P300 is required for acute lymphoblastic and myeloid leukemias, including refractory MLL-rearranged leukemias. Using structure-guided molecular design, we developed a peptidomimetic inhibitor MYBMIM that interferes with the assembly of the molecular MYB:CBP/P300 complex and rapidly accumulates in the nuclei of AML cells. Treatment of AML cells with MYBMIM led to the dissociation of the MYB:CBP/P300 complex in cells, its displacement from oncogenic enhancers enriched for MYB binding sites, and downregulation of MYB-dependent gene expression, including of MYC and BCL2 oncogenes. AML cells underwent mitochondrial apoptosis in response to MYBMIM, which was partially rescued by ectopic expression of BCL2. MYBMIM impeded leukemia growth and extended survival of immunodeficient mice engrafted with primary patient-derived MLL-rearranged leukemia cells. These findings elucidate the dependence of human AML on aberrant transcriptional coactivation, and establish a pharmacologic approach for its therapeutic blockade.
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Affiliation(s)
- Kavitha Ramaswamy
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
| | - Lauren Forbes
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA
| | - Gerard Minuesa
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Tatyana Gindin
- Department of Pathology and Cell Biology, Columbia University Medical Center and New York Presbyterian Hospital, New York, NY, 10065, USA
| | - Fiona Brown
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Michael G Kharas
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Andrei V Krivtsov
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Scott A Armstrong
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Eric Still
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Elisa de Stanchina
- Antitumor Assessment Core Facility, Memorial Sloan Kettering Cancer Center, New York, NY, 10065, USA
| | - Birgit Knoechel
- Department of Pediatric Oncology, Dana-Farber Cancer Institute, Boston, MA, 02215, USA
| | - Richard Koche
- Center for Epigenetics Research, Sloan Kettering Institute, New York, NY, 10065, USA
| | - Alex Kentsis
- Molecular Pharmacology Program, Sloan Kettering Institute, New York, NY, 10065, USA.
- Department of Pediatrics, Memorial Sloan Kettering Cancer Center, New York, 10065, NY, USA.
- Departments of Pediatrics, Pharmacology, and Physiology & Biophysics, Weill Cornell Medical College, Cornell University, New York, NY, 10065, USA.
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Abstract
The Gal4 protein is a well-known prototypic acidic activator that has multiple activation domains. We have previously identified a new activation domain called the nine amino acid transactivation domain (9aaTAD) in Gal4 protein. The family of the 9aaTAD activators currently comprises over 40 members including p53, MLL, E2A and other members of the Gal4 family; Oaf1, Pip2, Pdr1 and Pdr3. In this study, we revised function of all reported Gal4 activation domains. Surprisingly, we found that beside of the activation domain 9aaTAD none of the previously reported activation domains had considerable transactivation potential and were not involved in the activation of transcription. Our results demonstrated that the 9aaTAD domain is the only decisive activation domain in the Gal4 protein. We found that the artificial peptides included in the original Gal4 constructs were results of an unintended consequence of cloning that were responsible for the artificial transcriptional activity. Importantly, the activation domain 9aaTAD, which is the exclusive activation domain in Gal4, is also the central part of a conserved sequence recognized by the inhibitory protein Gal80. We propose a revision of the Gal4 regulation, in which the activation domain 9aaTAD is directly linked to both activation function and Gal80 mediated inhibition.
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13
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Lee K, Goh GYS, Wong MA, Klassen TL, Taubert S. Gain-of-Function Alleles in Caenorhabditis elegans Nuclear Hormone Receptor nhr-49 Are Functionally Distinct. PLoS One 2016; 11:e0162708. [PMID: 27618178 PMCID: PMC5019492 DOI: 10.1371/journal.pone.0162708] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2016] [Accepted: 08/27/2016] [Indexed: 02/07/2023] Open
Abstract
Nuclear hormone receptors (NHRs) are transcription factors that regulate numerous physiological and developmental processes and represent important drug targets. NHR-49, an ortholog of Hepatocyte Nuclear Factor 4 (HNF4), has emerged as a key regulator of lipid metabolism and life span in the nematode worm Caenorhabditis elegans. However, many aspects of NHR-49 function remain poorly understood, including whether and how it regulates individual sets of target genes and whether its activity is modulated by a ligand. A recent study identified three gain-of-function (gof) missense mutations in nhr-49 (nhr-49(et7), nhr-49(et8), and nhr-49(et13), respectively). These substitutions all affect the ligand-binding domain (LBD), which is critical for ligand binding and protein interactions. Thus, these alleles provide an opportunity to test how three specific residues contribute to NHR-49 dependent gene regulation. We used computational and molecular methods to delineate how these mutations alter NHR-49 activity. We find that despite originating from a screen favoring the activation of specific NHR-49 targets, all three gof alleles cause broad upregulation of NHR-49 regulated genes. Interestingly, nhr-49(et7) and nhr-49(et8) exclusively affect nhr-49 dependent activation, whereas the nhr-49(et13) surprisingly affects both nhr-49 mediated activation and repression, implicating the affected residue as dually important. We also observed phenotypic non-equivalence of these alleles, as they unexpectedly caused a long, short, and normal life span, respectively. Mechanistically, the gof substitutions altered neither protein interactions with the repressive partner NHR-66 and the coactivator MDT-15 nor the subcellular localization or expression of NHR-49. However, in silico structural modeling revealed that NHR-49 likely interacts with small molecule ligands and that the missense mutations might alter ligand binding, providing a possible explanation for increased NHR-49 activity. In sum, our findings indicate that the three nhr-49 gof alleles are non-equivalent, and highlight the conserved V411 residue affected by et13 as critical for gene activation and repression alike.
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Affiliation(s)
- Kayoung Lee
- Graduate Program in Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics and Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Grace Ying Shyen Goh
- Centre for Molecular Medicine and Therapeutics and Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC, Canada
| | - Marcus Andrew Wong
- Centre for Molecular Medicine and Therapeutics and Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
| | - Tara Leah Klassen
- Faculty of Pharmaceutical Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Stefan Taubert
- Graduate Program in Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- Centre for Molecular Medicine and Therapeutics and Child & Family Research Institute, University of British Columbia, Vancouver, BC, Canada
- Graduate Program in Cell and Developmental Biology, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Genetics, University of British Columbia, Vancouver, BC, Canada
- * E-mail:
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Piskacek M, Havelka M, Rezacova M, Knight A. The 9aaTAD Transactivation Domains: From Gal4 to p53. PLoS One 2016; 11:e0162842. [PMID: 27618436 PMCID: PMC5019370 DOI: 10.1371/journal.pone.0162842] [Citation(s) in RCA: 38] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2016] [Accepted: 08/29/2016] [Indexed: 12/30/2022] Open
Abstract
The family of the Nine amino acid Transactivation Domain, 9aaTAD family, comprises currently over 40 members. The 9aaTAD domains are universally recognized by the transcriptional machinery from yeast to man. We had identified the 9aaTAD domains in the p53, Msn2, Pdr1 and B42 activators by our prediction algorithm. In this study, their competence to activate transcription as small peptides was proven. Not surprisingly, we elicited immense 9aaTAD divergence in hundreds of identified orthologs and numerous examples of the 9aaTAD species' convergence. We found unforeseen similarity of the mammalian p53 with yeast Gal4 9aaTAD domains. Furthermore, we identified artificial 9aaTAD domains generated accidentally by others. From an evolutionary perspective, the observed easiness to generate 9aaTAD transactivation domains indicates the natural advantage for spontaneous generation of transcription factors from DNA binding precursors.
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Affiliation(s)
- Martin Piskacek
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Marek Havelka
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Martina Rezacova
- Laboratory of Cancer Biology and Genetics, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
| | - Andrea Knight
- Gamma Delta T Cell Laboratory, Department of Pathological Physiology, Faculty of Medicine, Masaryk University Brno, Kamenice 5, 625 00, Brno, Czech Republic
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Ehrlichia chaffeensis TRP32 is a Nucleomodulin that Directly Regulates Expression of Host Genes Governing Differentiation and Proliferation. Infect Immun 2016; 84:3182-3194. [PMID: 27572329 DOI: 10.1128/iai.00657-16] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Ehrlichia chaffeensis is an obligately intracellular bacterium that reprograms the mononuclear phagocyte through diverse effector-host interactions to modulate numerous host cell processes, including transcription. In a previous study, we reported that E. chaffeensis TRP32, a type 1 secreted effector, interacts with multiple host nucleus-associated proteins and also auto-activates reporter gene expression in yeast. In this study, we demonstrate that TRP32 is a nucleomodulin that binds host DNA and alters host gene transcription. TRP32 enters the host cell nucleus via a noncanonical translocation mechanism that involves phosphorylation of Y179 located in a C-terminal tri-tyrosine motif. Both genistein and mutation of Y179 inhibited TRP32 nuclear entry. An electromobility shift assay (EMSA) demonstrated TRP32 host DNA binding via its tandem repeat domain. TRP32 DNA binding and motif preference were further confirmed by supershift assays, as well as competition and mutant probe analyses. Using ChIP-Seq, we determined that TRP32 binds a G-rich motif primarily within ±500 bp of the gene transcription start site. An ontology analysis identified genes involved in processes such as immune cell differentiation, chromatin remodeling, and RNA transcription and processing, as primary TRP32 targets. TRP32 bound genes (n=1223) were distributed on all chromosomes and included several global regulators of proliferation and inflammation such as FOS and JUN, AKT3 and NRAS, and non-coding RNA genes, miRNA 21 and miRNA 142. TRP32 target genes were differentially regulated during infection, the majority of which were repressed, and direct repression/activation of these genes by TRP32 was confirmed in vitro with a cellular luciferase reporter assay.
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