51
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Ibrahim Z, Wang T, Destaing O, Salvi N, Hoghoughi N, Chabert C, Rusu A, Gao J, Feletto L, Reynoird N, Schalch T, Zhao Y, Blackledge M, Khochbin S, Panne D. Structural insights into p300 regulation and acetylation-dependent genome organisation. Nat Commun 2022; 13:7759. [PMID: 36522330 PMCID: PMC9755262 DOI: 10.1038/s41467-022-35375-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2022] [Accepted: 11/29/2022] [Indexed: 12/23/2022] Open
Abstract
Histone modifications are deposited by chromatin modifying enzymes and read out by proteins that recognize the modified state. BRD4-NUT is an oncogenic fusion protein of the acetyl lysine reader BRD4 that binds to the acetylase p300 and enables formation of long-range intra- and interchromosomal interactions. We here examine how acetylation reading and writing enable formation of such interactions. We show that NUT contains an acidic transcriptional activation domain that binds to the TAZ2 domain of p300. We use NMR to investigate the structure of the complex and found that the TAZ2 domain has an autoinhibitory role for p300. NUT-TAZ2 interaction or mutations found in cancer that interfere with autoinhibition by TAZ2 allosterically activate p300. p300 activation results in a self-organizing, acetylation-dependent feed-forward reaction that enables long-range interactions by bromodomain multivalent acetyl-lysine binding. We discuss the implications for chromatin organisation, gene regulation and dysregulation in disease.
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Affiliation(s)
- Ziad Ibrahim
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
- Department of Structural Biology, St. Jude Children's Research Hospital, Memphis, United States
| | - Tao Wang
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Olivier Destaing
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Nicola Salvi
- Institut de Biologie Structurale, CNRS, CEA, UGA, Grenoble, France
| | - Naghmeh Hoghoughi
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Clovis Chabert
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Alexandra Rusu
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Jinjun Gao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | - Leonardo Feletto
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Nicolas Reynoird
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Thomas Schalch
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK
| | - Yingming Zhao
- Ben May Department of Cancer Research, The University of Chicago, Chicago, IL, 60637, USA
| | | | - Saadi Khochbin
- CNRS UMR 5309, INSERM U1209, Université Grenoble Alpes, Institute for Advanced Biosciences, Grenoble, France
| | - Daniel Panne
- Leicester Institute of Structural and Chemical Biology, Department of Molecular and Cell Biology, University of Leicester, Leicester, UK.
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52
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Tesarik J, Mendoza-Tesarik R. Cyclic Adenosine Monophosphate: A Central Player in Gamete Development and Fertilization, and Possible Target for Infertility Therapies. Int J Mol Sci 2022; 23:ijms232315068. [PMID: 36499392 PMCID: PMC9736025 DOI: 10.3390/ijms232315068] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2022] [Revised: 11/27/2022] [Accepted: 11/29/2022] [Indexed: 12/04/2022] Open
Abstract
Human infertility, of both male and female origin, is often caused by the deficient response of the testis and the ovary to hormonal stimuli that govern sperm and oocyte development and fertilization. The effects of hormones and other extracellular ligands involved in these events are often mediated by G-protein-coupled receptors that employ cyclic adenosine monophosphate (cAMP) as the principal second messenger transducing the receptor-generated signal to downstream elements. This opinion article summarizes the actions of cAMP in sperm and oocyte development and fertilization, leading to therapeutic actions targeting cAMP metabolism to alleviate human male and female infertility.
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53
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Hricovíni M, Owens RJ, Bak A, Kozik V, Musiał W, Pierattelli R, Májeková M, Rodríguez Y, Musioł R, Slodek A, Štarha P, Piętak K, Słota D, Florkiewicz W, Sobczak-Kupiec A, Jampílek J. Chemistry towards Biology-Instruct: Snapshot. Int J Mol Sci 2022; 23:14815. [PMID: 36499140 PMCID: PMC9739621 DOI: 10.3390/ijms232314815] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2022] [Revised: 11/15/2022] [Accepted: 11/23/2022] [Indexed: 12/05/2022] Open
Abstract
The knowledge of interactions between different molecules is undoubtedly the driving force of all contemporary biomedical and biological sciences. Chemical biology/biological chemistry has become an important multidisciplinary bridge connecting the perspectives of chemistry and biology to the study of small molecules/peptidomimetics and their interactions in biological systems. Advances in structural biology research, in particular linking atomic structure to molecular properties and cellular context, are essential for the sophisticated design of new medicines that exhibit a high degree of druggability and very importantly, druglikeness. The authors of this contribution are outstanding scientists in the field who provided a brief overview of their work, which is arranged from in silico investigation through the characterization of interactions of compounds with biomolecules to bioactive materials.
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Affiliation(s)
- Miloš Hricovíni
- Institute of Chemistry, Slovak Academy of Sciences, Dúbravská cesta 9, 845 38 Bratislava, Slovakia
| | - Raymond J. Owens
- Structural Biology, The Rosalind Franklin Institute, Harwell Science Campus, UK, University of Oxford, Oxford OX11 0QS, UK
- Division of Structural Biology, The Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Andrzej Bak
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Violetta Kozik
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Witold Musiał
- Department of Physical Chemistry and Biophysics, Pharmaceutical Faculty, Wroclaw Medical University, Borowska 211A, 50 556 Wrocław, Poland
| | - Roberta Pierattelli
- Magnetic Resonance Center and Department of Chemistry “Ugo Schiff”, University of Florence, 50019 Sesto Fiorentino, Italy
| | - Magdaléna Májeková
- Center of Experimental Medicine SAS and Department of Biochemical Pharmacology, Institute of Experimental Pharmacology and Toxicology, Slovak Academy of Sciences, Dubravska cesta 9, 841 04 Bratislava, Slovakia
| | - Yoel Rodríguez
- Department of Natural Sciences, Eugenio María de Hostos Community College, City University of New York, 500 Grand Concourse, Bronx, NY 10451, USA
- Department of Pharmacological Sciences, Icahn School of Medicine at Mount Sinai, 1425 Madison Avenue, New York, NY 10029, USA
| | - Robert Musioł
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Aneta Slodek
- Institute of Chemistry, University of Silesia, Szkolna 9, 40 007 Katowice, Poland
| | - Pavel Štarha
- Department of Inorganic Chemistry, Faculty of Science, Palacký University Olomouc, 17. listopadu 1192/12, 771 46 Olomouc, Czech Republic
| | - Karina Piętak
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Dagmara Słota
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Wioletta Florkiewicz
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Agnieszka Sobczak-Kupiec
- Department of Materials Science, Faculty of Materials Engineering and Physics, Cracow University of Technology, 37 Jana Pawła II Av., 31 864 Krakow, Poland
| | - Josef Jampílek
- Department of Analytical Chemistry, Faculty of Natural Sciences, Comenius University, Ilkovičova 6, 842 15 Bratislava, Slovakia
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54
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Usher ET, Showalter SA. Biophysical insights into glucose-dependent transcriptional regulation by PDX1. J Biol Chem 2022; 298:102623. [PMID: 36272648 PMCID: PMC9691942 DOI: 10.1016/j.jbc.2022.102623] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/06/2022] [Revised: 10/13/2022] [Accepted: 10/14/2022] [Indexed: 11/22/2022] Open
Abstract
The pancreatic and duodenal homeobox 1 (PDX1) is a central regulator of glucose-dependent transcription of insulin in pancreatic β cells. PDX1 transcription factor activity is integral to the development and sustained health of the pancreas; accordingly, deciphering the complex network of cellular cues that lead to PDX1 activation or inactivation is an important step toward understanding the etiopathologies of pancreatic diseases and the development of novel therapeutics. Despite nearly 3 decades of research into PDX1 control of Insulin expression, the molecular mechanisms that dictate the function of PDX1 in response to glucose are still elusive. The transcriptional activation functions of PDX1 are regulated, in part, by its two intrinsically disordered regions, which pose a barrier to its structural and biophysical characterization. Indeed, many studies of PDX1 interactions, clinical mutations, and posttranslational modifications lack molecular level detail. Emerging methods for the quantitative study of intrinsically disordered regions and refined models for transactivation now enable us to validate and interrogate the biochemical and biophysical features of PDX1 that dictate its function. The goal of this review is to summarize existing PDX1 studies and, further, to generate a comprehensive resource for future studies of transcriptional control via PDX1.
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Affiliation(s)
- Emery T Usher
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA
| | - Scott A Showalter
- Center for Eukaryotic Gene Regulation, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania, USA; Department of Chemistry, The Pennsylvania State University, University Park, Pennsylvania, USA.
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55
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Zukin SA, Marunde MR, Popova IK, Soczek KM, Nogales E, Patel AB. Structure and flexibility of the yeast NuA4 histone acetyltransferase complex. eLife 2022; 11:e81400. [PMID: 36263929 PMCID: PMC9643008 DOI: 10.7554/elife.81400] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2022] [Accepted: 10/17/2022] [Indexed: 11/13/2022] Open
Abstract
The NuA4 protein complex acetylates histones H4 and H2A to activate both transcription and DNA repair. We report the 3.1-Å resolution cryo-electron microscopy structure of the central hub of NuA4, which flexibly tethers the histone acetyltransferase (HAT) and Trimer Independent of NuA4 involved in Transcription Interactions with Nucleosomes (TINTIN) modules. The hub contains the large Tra1 subunit and a core that includes Swc4, Arp4, Act1, Eaf1, and the C-terminal region of Epl1. Eaf1 stands out as the primary scaffolding factor that interacts with the Tra1, Swc4, and Epl1 subunits and contributes the conserved HSA helix to the Arp module. Using nucleosome-binding assays, we find that the HAT module, which is anchored to the core through Epl1, recognizes H3K4me3 nucleosomes with hyperacetylated H3 tails, while the TINTIN module, anchored to the core via Eaf1, recognizes nucleosomes that have hyperacetylated H2A and H4 tails. Together with the known interaction of Tra1 with site-specific transcription factors, our data suggest a model in which Tra1 recruits NuA4 to specific genomic sites then allowing the flexible HAT and TINTIN modules to select nearby nucleosomes for acetylation.
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Affiliation(s)
- Stefan A Zukin
- College of Chemistry, University of California, BerkeleyBerkeleyUnited States
| | | | - Irina K Popova
- EpiCypher, Inc, Research Triangle ParkDurhamUnited States
| | - Katarzyna M Soczek
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Innovative Genomics Institute, University of California, BerkeleyBerkeleyUnited States
| | - Eva Nogales
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Department of Molecular and Cellular Biology, University of CaliforniaBerkeleyUnited States
- Molecular Biophysics and Integrative Bio-Imaging Division, Lawrence Berkeley National LaboratoryBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
| | - Avinash B Patel
- California Institute for Quantitative Biology, University of California, BerkeleyBerkeleyUnited States
- Howard Hughes Medical Institute, University of California, BerkeleyBerkeleyUnited States
- Biophysics Graduate Group, University of California, BerkeleyBerkeleyUnited States
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56
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Staller MV. Transcription factors perform a 2-step search of the nucleus. Genetics 2022; 222:iyac111. [PMID: 35939561 PMCID: PMC9526044 DOI: 10.1093/genetics/iyac111] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2022] [Accepted: 07/14/2022] [Indexed: 01/02/2023] Open
Abstract
Transcription factors regulate gene expression by binding to regulatory DNA and recruiting regulatory protein complexes. The DNA-binding and protein-binding functions of transcription factors are traditionally described as independent functions performed by modular protein domains. Here, I argue that genome binding can be a 2-part process with both DNA-binding and protein-binding steps, enabling transcription factors to perform a 2-step search of the nucleus to find their appropriate binding sites in a eukaryotic genome. I support this hypothesis with new and old results in the literature, discuss how this hypothesis parsimoniously resolves outstanding problems, and present testable predictions.
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Affiliation(s)
- Max Valentín Staller
- Corresponding author: Center for Computational Biology, University of California, Berkeley, Berkeley, CA 94720, USA.
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57
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Enhancing glycosylase base-editor activity by fusion to transactivation modules. Cell Rep 2022; 40:111090. [PMID: 35858572 DOI: 10.1016/j.celrep.2022.111090] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2020] [Revised: 05/09/2022] [Accepted: 06/22/2022] [Indexed: 11/21/2022] Open
Abstract
Base editors (BEs) are a group of genetic tools with potential in both scientific and medical research. Recently, a glycosylase BE (GBE), which converts C to G, has been constructed. However, the editing efficiency and targeting scope remains to be further exploited. Here, we renovate the GBE by first fusing it to various transactivation modules including Vp64, leading to a higher conversion of C to G relative to GBE in HEK293T cells. Further, higher editing efficiency, enhanced editing purity, and an enlarged editing window are acquired by the combination of SunTag system, GBE, and VP64. Finally, a SpRY-Cas9 variant is used to expand the targeting scope for Vp64-GBE. Vp64-SpRY-GBE and SpRY-GBE target genomic sites with non-NGG PAM, and Vp64-SpRY-GBE demonstrates better performance compared with SpRY-GBE. The construction of GBE variants with superior performance and versatile editing scope broadens the toolbox of BEs and may contribute to genetic therapies with C-to-G mutation.
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58
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Huang Z, Liu H, Nix J, Xu R, Knoverek CR, Bowman GR, Amarasinghe GK, Sibley LD. The intrinsically disordered protein TgIST from Toxoplasma gondii inhibits STAT1 signaling by blocking cofactor recruitment. Nat Commun 2022; 13:4047. [PMID: 35831295 PMCID: PMC9279507 DOI: 10.1038/s41467-022-31720-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2021] [Accepted: 06/28/2022] [Indexed: 12/31/2022] Open
Abstract
Signal transducer and activator of transcription (STAT) proteins communicate from cell-surface receptors to drive transcription of immune response genes. The parasite Toxoplasma gondii blocks STAT1-mediated gene expression by secreting the intrinsically disordered protein TgIST that traffics to the host nucleus, binds phosphorylated STAT1 dimers, and occupies nascent transcription sites that unexpectedly remain silenced. Here we define a core region within internal repeats of TgIST that is necessary and sufficient to block STAT1-mediated gene expression. Cellular, biochemical, mutational, and structural data demonstrate that the repeat region of TgIST adopts a helical conformation upon binding to STAT1 dimers. The binding interface is defined by a groove formed from two loops in the STAT1 SH2 domains that reorient during dimerization. TgIST binding to this newly exposed site at the STAT1 dimer interface alters its conformation and prevents the recruitment of co-transcriptional activators, thus defining the mechanism of blocked transcription.
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Affiliation(s)
- Zhou Huang
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Hejun Liu
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, 92037, USA
| | - Jay Nix
- Molecular Biology Consortium, Advanced Light Source, Lawrence Berkeley National Laboratory, Berkeley, CA, 94720, USA
| | - Rui Xu
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Catherine R Knoverek
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gregory R Bowman
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - Gaya K Amarasinghe
- Department of Pathology and Immunology, Washington University School of Medicine, St. Louis, MO, 63110, USA
| | - L David Sibley
- Department of Molecular Microbiology, Washington University School of Medicine, St. Louis, MO, 63110, USA.
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59
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Hayek I, Szperlinski M, Lührmann A. Coxiella burnetii Affects HIF1α Accumulation and HIF1α Target Gene Expression. Front Cell Infect Microbiol 2022; 12:867689. [PMID: 35755850 PMCID: PMC9218251 DOI: 10.3389/fcimb.2022.867689] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Accepted: 04/21/2022] [Indexed: 11/23/2022] Open
Abstract
HIF1α is an important transcription factor regulating not only cellular responses to hypoxia, but also anti-infective defense responses. We recently showed that HIF1α hampers replication of the obligate intracellular pathogen Coxiella burnetii which causes the zoonotic disease Q fever. Prior to development of chronic Q fever, it is assumed that the bacteria enter a persistent state. As HIF1α and/or hypoxia might be involved in the induction of C. burnetii persistence, we analyzed the role of HIF1α and hypoxia in the interaction of macrophages with C. burnetii to understand how the bacteria manipulate HIF1α stability and activity. We demonstrate that a C. burnetii-infection initially induces HIF1α stabilization, which decreases then over the course of an infection. This reduction depends on bacterial viability and a functional type IV secretion system (T4SS). While neither the responsible T4SS effector protein(s) nor the molecular mechanism leading to this partial HIF1α destabilization have been identified, our results demonstrate that C. burnetii influences the expression of HIF1α target genes in multiple ways. Therefore, a C. burnetii infection promotes HIF1α-mediated upregulation of several metabolic target genes; affects apoptosis-regulators towards a more pro-apoptotic signature; and under hypoxic conditions, shifts the ratio of the inflammatory genes analyzed towards a pro-inflammatory profile. Taken together, C. burnetii modulates HIF1α in a still elusive manner and alters the expression of multiple HIF1α target genes.
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Affiliation(s)
- Inaya Hayek
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Manuela Szperlinski
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
| | - Anja Lührmann
- Mikrobiologisches Institut - Klinische Mikrobiologie, Immunologie and Hygiene, Universitätsklinikum Erlangen, Friedrich-Alexander-Universität (FAU) Erlangen-Nürnberg, Erlangen, Germany
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60
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Friis Theisen F, Salladini E, Davidsen R, Jo Rasmussen C, Staby L, Kragelund BB, Skriver K. αα-hub coregulator structure and flexibility determine transcription factor binding and selection in regulatory interactomes. J Biol Chem 2022; 298:101963. [PMID: 35452682 PMCID: PMC9127584 DOI: 10.1016/j.jbc.2022.101963] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2022] [Revised: 04/13/2022] [Accepted: 04/15/2022] [Indexed: 11/23/2022] Open
Abstract
Formation of transcription factor (TF)-coregulator complexes is a key step in transcriptional regulation, with coregulators having essential functions as hub nodes in molecular networks. How specificity and selectivity are maintained in these nodes remain open questions. In this work, we addressed specificity in transcriptional networks using complexes formed between TFs and αα-hubs, which are defined by a common αα-hairpin secondary structure motif, as a model. Using NMR spectroscopy and binding thermodynamics, we analyzed the structure, dynamics, stability, and ligand-binding properties of the Arabidopsis thaliana RST domains from TAF4 and known binding partner RCD1, and the TAFH domain from human TAF4, allowing comparison across species, functions, and architectural contexts. While these αα-hubs shared the αα-hairpin motif, they differed in length and orientation of accessory helices as well as in their thermodynamic profiles of ligand binding. Whereas biologically relevant RCD1-ligand pairs displayed high affinity driven by enthalpy, TAF4-ligand interactions were entropy driven and exhibited less binding-induced structuring. We in addition identified a thermal unfolding state with a structured core for all three domains, although the temperature sensitivity differed. Thermal stability studies suggested that initial unfolding of the RCD1-RST domain localized around helix 1, lending this region structural malleability, while effects in TAF4-RST were more stochastic, suggesting variability in structural adaptability upon binding. Collectively, our results support a model in which hub structure, flexibility, and binding thermodynamics contribute to αα-hub-TF binding specificity, a finding of general relevance to the understanding of coregulator-ligand interactions and interactome sizes.
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Affiliation(s)
- Frederik Friis Theisen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Edoardo Salladini
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Rikke Davidsen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Christina Jo Rasmussen
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Lasse Staby
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark
| | - Birthe B Kragelund
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark; Structural Biology and NMR Laboratory, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
| | - Karen Skriver
- REPIN and the Linderstrøm-Lang Centre for Protein Science, Department of Biology, University of Copenhagen, Copenhagen, Denmark.
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61
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Karlsson E, Sorgenfrei FA, Andersson E, Dogan J, Jemth P, Chi CN. The dynamic properties of a nuclear coactivator binding domain are evolutionarily conserved. Commun Biol 2022; 5:286. [PMID: 35354917 PMCID: PMC8967867 DOI: 10.1038/s42003-022-03217-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/08/2021] [Accepted: 03/02/2022] [Indexed: 12/21/2022] Open
Abstract
Evolution of proteins is constrained by their structure and function. While there is a consensus that the plasticity of intrinsically disordered proteins relaxes the structural constraints on evolution there is a paucity of data on the molecular details of these processes. The Nuclear Coactivator Binding Domain (NCBD) from CREB-binding protein is a protein interaction domain, which contains a hydrophobic core but is not behaving as a typical globular domain, and has been described as 'molten-globule like'. The highly dynamic properties of NCBD makes it an interesting model system for evolutionary structure-function investigation of intrinsically disordered proteins. We have here compared the structure and biophysical properties of an ancient version of NCBD present in a bilaterian animal ancestor living around 600 million years ago with extant human NCBD. Using a combination of NMR spectroscopy, circular dichroism and kinetics we show that although NCBD has increased its thermodynamic stability, it has retained its dynamic biophysical properties in the ligand-free state in the evolutionary lineage leading from the last common bilaterian ancestor to humans. Our findings suggest that the dynamic properties of NCBD have been maintained by purifying selection and thus are important for its function, which includes mediating several distinct protein-protein interactions.
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Affiliation(s)
- Elin Karlsson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Frieda A Sorgenfrei
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.,acib GmbH, Krenngasse 37, 8010 Graz c/o University of Graz, Institute of Chemistry, NAWI Graz, BioTechMed Graz, Heinrichstrasse 28, 8010, Graz, Austria
| | - Eva Andersson
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Jakob Dogan
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden
| | - Per Jemth
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
| | - Celestine N Chi
- Department of Medical Biochemistry and Microbiology, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden. .,Department of Pharmaceutical Biosciences, Uppsala University, BMC Box 582, SE-75123, Uppsala, Sweden.
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62
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Seim I, Posey AE, Snead WT, Stormo BM, Klotsa D, Pappu RV, Gladfelter AS. Dilute phase oligomerization can oppose phase separation and modulate material properties of a ribonucleoprotein condensate. Proc Natl Acad Sci U S A 2022; 119:e2120799119. [PMID: 35333653 PMCID: PMC9060498 DOI: 10.1073/pnas.2120799119] [Citation(s) in RCA: 42] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/16/2022] [Indexed: 01/02/2023] Open
Abstract
SignificanceA large subclass of biomolecular condensates are linked to RNA regulation and are known as ribonucleoprotein (RNP) bodies. While extensive work has identified driving forces for biomolecular condensate formation, relatively little is known about forces that oppose assembly. Here, using a fungal RNP protein, Whi3, we show that a portion of its intrinsically disordered, glutamine-rich region modulates phase separation by forming transient alpha helical structures that promote the assembly of dilute phase oligomers. These oligomers detour Whi3 proteins from condensates, thereby impacting the driving forces for phase separation, the protein-to-RNA ratio in condensates, and the material properties of condensates. Our findings show how nanoscale conformational and oligomerization equilibria can influence mesoscale phase equilibria.
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Affiliation(s)
- Ian Seim
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Ammon E. Posey
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Wilton T. Snead
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Benjamin M. Stormo
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Daphne Klotsa
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Applied Physical Sciences, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
| | - Rohit V. Pappu
- Department of Biomedical Engineering, Center for Science & Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130
| | - Amy S. Gladfelter
- Curriculum in Bioinformatics and Computational Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
- Department of Biology, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599
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63
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Liu L, Li H, Patterson AM, Plett PA, Sampson CH, Mohammad KS, Capitano ML, Singh P, Yao C, Orschell CM, Pelus LM. Upregulation of SIRT1 Contributes to dmPGE2-dependent Radioprotection of Hematopoietic Stem Cells. Stem Cell Rev Rep 2022; 18:1478-1494. [PMID: 35318613 DOI: 10.1007/s12015-022-10368-2] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/13/2022] [Indexed: 11/29/2022]
Abstract
Exposure to potentially lethal high-dose ionizing radiation results in bone marrow suppression, known as the hematopoietic acute radiation syndrome (H-ARS), which can lead to pancytopenia and possible death from hemorrhage or infection. Medical countermeasures to protect from or mitigate the effects of radiation exposure are an ongoing medical need. We recently reported that 16,16 dimethyl prostaglandin E2 (dmPGE2) given prior to lethal irradiation protects hematopoietic stem (HSCs) and progenitor (HPCs) cells and accelerates hematopoietic recovery by attenuating mitochondrial compromise, DNA damage, apoptosis, and senescence. However, molecular mechanisms responsible for the radioprotective effects of dmPGE2 on HSCs are not well understood. In this report, we identify a crucial role for the NAD+-dependent histone deacetylase Sirtuin 1 (Sirt1) downstream of PKA and CREB in dmPGE2-dependent radioprotection of hematopoietic cells. We found that dmPGE2 increases Sirt1 expression and activity in hematopoietic cells including HSCs and pharmacologic and genetic suppression of Sirt1 attenuates the radioprotective effects of dmPGE2 on HSC and HPC function and its ability to reduce DNA damage, apoptosis, and senescence and stimulate autophagy in HSCs. DmPGE2-mediated enhancement of Sirt1 activity in irradiated mice is accompanied by epigenetic downregulation of p53 activation and inhibition of H3K9 and H4K16 acetylation at the promoters of the genes involved in DNA repair, apoptosis, and autophagy, including p53, Ku70, Ku80, LC3b, ATG7, and NF-κB. These studies expand our understanding of intracellular events that are induced by IR but prevented/attenuated by dmPGE2 and suggest that modulation of Sirt1 activity may facilitate hematopoietic recovery following hematopoietic stress. Graphical Abstract.
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Affiliation(s)
- Liqiong Liu
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Hongge Li
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Andrea M Patterson
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA.,Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA
| | - P Artur Plett
- Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Carol H Sampson
- Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Khalid S Mohammad
- Department of Medicine/Endocrinology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Maegan L Capitano
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Pratibha Singh
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA.,Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA
| | - Chonghua Yao
- Shanghai Municipal Hospital of Traditional Chinese Medicine, NO.274, middle Zhijiang Road, Shanghai, China
| | - Christie M Orschell
- Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA.
| | - Louis M Pelus
- Department of Microbiology & Immunology, Indiana University School of Medicine, 950 West Walnut Street, Indianapolis, IN, 46202, USA. .,Department of Medicine/Hematology Oncology, Indiana University School of Medicine, 980 West Walnut Street, Indianapolis, IN, 46202, USA.
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64
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Balsalobre A, Drouin J. Pioneer factors as master regulators of the epigenome and cell fate. Nat Rev Mol Cell Biol 2022; 23:449-464. [PMID: 35264768 DOI: 10.1038/s41580-022-00464-z] [Citation(s) in RCA: 84] [Impact Index Per Article: 42.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 02/08/2022] [Indexed: 12/23/2022]
Abstract
Pioneer factors are transcription factors with the unique ability to initiate opening of closed chromatin. The stability of cell identity relies on robust mechanisms that maintain the epigenome and chromatin accessibility to transcription factors. Pioneer factors counter these mechanisms to implement new cell fates through binding of DNA target sites in closed chromatin and introduction of active-chromatin histone modifications, primarily at enhancers. As master regulators of enhancer activation, pioneers are thus crucial for the implementation of correct cell fate decisions in development, and as such, they hold tremendous potential for therapy through cellular reprogramming. The power of pioneer factors to reshape the epigenome also presents an Achilles heel, as their misexpression has major pathological consequences, such as in cancer. In this Review, we discuss the emerging mechanisms of pioneer factor functions and their roles in cell fate specification, cellular reprogramming and cancer.
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Affiliation(s)
- Aurelio Balsalobre
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada
| | - Jacques Drouin
- Laboratoire de génétique moléculaire, Institut de recherches cliniques de Montréal, Montreal, QC, Canada.
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65
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Mladek AC, Yan H, Tian S, Decker PA, Burgenske DM, Bakken K, Hu Z, He L, Connors MA, Carlson BL, Wilson J, Bommi-Reddy A, Conery A, Eckel-Passow JE, Sarkaria JN, Kitange GJ. RBBP4-p300 axis modulates expression of genes essential for cell survival and is a potential target for therapy in glioblastoma. Neuro Oncol 2022; 24:1261-1272. [PMID: 35231103 PMCID: PMC9340617 DOI: 10.1093/neuonc/noac051] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
BACKGROUND RBBP4 activates transcription by histone acetylation, but the partner histone acetyltransferases are unknown. Thus, we investigated the hypothesis that RBBP4 interacts with p300 in a complex in glioblastoma (GBM). METHODS shRNA silencing of RBBP4 or p300 and RNAseq was used to identify genes co-regulated by RBBP4 and p300 in GBM43 patient-derived xenograft (PDX). RBBP4/p300 complex was demonstrated using proximity ligation assay (PLA) and ChIPseq delineated histone H3 acetylation and RBBP4/p300 complex binding in promoters/enhancers. Temozolomide (TMZ)-induced DNA double strand breaks (DSBs) were evaluated by γ-H2AX and proliferation by CyQuant and live cell monitoring assays. In vivo efficacy was based on survival of mice with orthotopic tumors. RESULTS shRBBP4 and shp300 downregulated 4768 genes among which 1485 (31%) were commonly downregulated by both shRNAs, while upregulated genes were 2484, including 863 (35%) common genes. The pro-survival genes were the top-ranked among the downregulated genes, including C-MYC. RBBP4/p300 complex was demonstrated in the nucleus, and shRBBP4 or shp300 significantly sensitized GBM cells to TMZ compared to the control shNT in vitro (P < .05). Moreover, TMZ significantly prolonged the survival of mice bearing GBM22-shRBBP4 orthotopic tumors compared with control shNT tumors (median shNT survival 52 days vs. median shRBBP4 319 days; P = .001). CREB-binding protein (CBP)/p300 inhibitor CPI-1612 suppressed H3K27Ac and RBBP4/p300 complex target proteins, including C-MYC, and synergistically sensitized TMZ in vitro. Pharmacodynamic evaluation confirmed brain penetration by CPI-1612 supporting further investigation to evaluate efficacy to sensitize TMZ. CONCLUSIONS RBBP4/p300 complex is present in GBM cells and is a potential therapeutic target.
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Affiliation(s)
- Ann C Mladek
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Huihuang Yan
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Shulan Tian
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | - Paul A Decker
- Department of Quantitative Health Sciences, Mayo Clinic, Rochester, Minnesota, USA
| | | | - Katrina Bakken
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Zeng Hu
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Lihong He
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Margaret A Connors
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Brett L Carlson
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Jonathan Wilson
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | - Andy Conery
- Constellation Pharmaceuticals, Cambridge, Massachusetts, USA
| | | | - Jann N Sarkaria
- Department of Radiation Oncology, Mayo Clinic, Rochester, Minnesota, USA
| | - Gaspar J Kitange
- Corresponding Author: Gaspar J. Kitange, MD, PhD, Department of Radiation Oncology, Mayo Clinic, 200 First Street SW, Rochester, MN 55905, USA (/)
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66
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Sadanari H, Takemoto M, Ishida T, Otagiri H, Daikoku T, Murayama T, Kusano S. The Interferon-Inducible Human PLSCR1 Protein Is a Restriction Factor of Human Cytomegalovirus. Microbiol Spectr 2022; 10:e0134221. [PMID: 35138119 PMCID: PMC8826943 DOI: 10.1128/spectrum.01342-21] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 01/19/2022] [Indexed: 11/20/2022] Open
Abstract
Human phospholipid scramblase 1 (PLSCR1) is strongly expressed in response to interferon (IFN) treatment and viral infection, and it has been suggested to play an important role in IFN-dependent antiviral responses. In this study, we showed that the levels of human cytomegalovirus (HCMV) plaque formation in OUMS-36T-3 (36T-3) cells with high basal expression of PLSCR1 were significantly lower than those in human embryonic lung (HEL) cells with low basal expression of PLSCR1. In addition, the levels of HCMV plaque formation and replication in PLSCR1-knockout (KO) 36T-3 cells were significantly higher than those in parental 36T-3 cells and were comparable to those in HEL cells. Furthermore, compared to that in PLSCR1-KO cells, the expression of HCMV major immediate early (MIE) proteins was repressed and/or delayed in parental 36T-3 cells after HCMV infection. We also showed that PLSCR1 expression decreased the levels of the cAMP-responsive element (CRE)-binding protein (CREB)•HCMV immediate early protein 2 (IE2) and CREB-binding protein (CBP)•IE2 complexes, which have been suggested to play important roles in the IE2-mediated transactivation of the viral early promoter through interactions with CREB, CBP, and IE2. Interestingly, PLSCR1 expression repressed CRE- and HCMV MIE promoter-regulated reporter gene activities. These observations reveal, for the first time, that PLSCR1 negatively regulates HCMV replication by repressing the transcription from viral MIE and early promoters, and that PLSCR1 expression may contribute to the IFN-mediated suppression of HCMV infection. IMPORTANCE Because several IFN-stimulated genes (ISGs) have been reported to suppress HCMV replication, HCMV replication is thought to be regulated by an IFN-mediated host defense mechanism, but the mechanism remains unclear. PLSCR1 expression is induced in response to viral infection and IFN treatment, and PLSCR1 has been reported to play an important role in IFN-dependent antiviral responses. Here, we demonstrate that HCMV plaque formation and major immediate early (MIE) gene expression are significantly increased in PLSCR1-KO human fibroblast cells. PLSCR1 reduces levels of the CREB•IE2 and CBP•IE2 complexes, which have been suggested to play important roles in HCMV replication through its interactions with CREB, CBP, and IE2. In addition, PLSCR1 expression represses transcription from the HCMV MIE promoter. Our results indicate that PLSCR1 plays important roles in the suppression of HCMV replication in the IFN-mediated host defense system.
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Affiliation(s)
- Hidetaka Sadanari
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Masaya Takemoto
- Research Center for Pharmaceutical Education, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tomoki Ishida
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Hikaru Otagiri
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tohru Daikoku
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Tsugiya Murayama
- Department of Pharmaceutical Life Sciences, Faculty of Pharmaceutical Sciences, Hokuriku University, Ishikawa, Japan
| | - Shuichi Kusano
- Division of Biological Information Technology, Joint Research Center for Human Retrovirus Infection, Kagoshima University, Kagoshima, Japan
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67
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Maldotti M, Lauria A, Anselmi F, Molineris I, Tamburrini A, Meng G, Polignano IL, Scrivano MG, Campestre F, Simon LM, Rapelli S, Morandi E, Incarnato D, Oliviero S. The acetyltransferase p300 is recruited in trans to multiple enhancer sites by lncSmad7. Nucleic Acids Res 2022; 50:2587-2602. [PMID: 35137201 PMCID: PMC8934626 DOI: 10.1093/nar/gkac083] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 01/23/2022] [Accepted: 01/25/2022] [Indexed: 12/13/2022] Open
Abstract
The histone acetyltransferase p300 (also known as KAT3B) is a general transcriptional coactivator that introduces the H3K27ac mark on enhancers triggering their activation and gene transcription. Genome-wide screenings demonstrated that a large fraction of long non-coding RNAs (lncRNAs) plays a role in cellular processes and organ development although the underlying molecular mechanisms remain largely unclear (1,2). We found 122 lncRNAs that interacts directly with p300. In depth analysis of one of these, lncSmad7, is required to maintain ESC self-renewal and it interacts to the C-terminal domain of p300. lncSmad7 also contains predicted RNA-DNA Hoogsteen forming base pairing. Combined Chromatin Isolation by RNA precipitation followed by sequencing (ChIRP-seq) together with CRISPR/Cas9 mutagenesis of the target sites demonstrate that lncSmad7 binds and recruits p300 to enhancers in trans, to trigger enhancer acetylation and transcriptional activation of its target genes. Thus, these results unveil a new mechanism by which p300 is recruited to the genome.
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Affiliation(s)
- Mara Maldotti
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Andrea Lauria
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Francesca Anselmi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Ivan Molineris
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Annalaura Tamburrini
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Guohua Meng
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Isabelle Laurence Polignano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Mirko Giuseppe Scrivano
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Fabiola Campestre
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Lisa Marie Simon
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Stefania Rapelli
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
| | - Edoardo Morandi
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy
| | - Danny Incarnato
- Department of Molecular Genetics, Groningen Biomolecular Sciences and Biotechnology Institute (GBB), University of Groningen, Nijenborgh 7, 9747 AG Groningen, The Netherlands
| | - Salvatore Oliviero
- Dipartimento di Scienze della Vita e Biologia dei Sistemi and MBC, Università di Torino, Via Nizza 52, 10126 Torino, Italy.,Italian Institute for Genomic Medicine (IIGM), Sp142 Km 3.95, 10060 Candiolo (Torino), Italy
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Soto L, Li Z, Santoso CS, Berenson A, Ho I, Shen VX, Yuan S, Bass JIF. Compendium of human transcription factor effector domains. Mol Cell 2022; 82:514-526. [PMID: 34863368 PMCID: PMC8818021 DOI: 10.1016/j.molcel.2021.11.007] [Citation(s) in RCA: 40] [Impact Index Per Article: 20.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 10/16/2021] [Accepted: 11/03/2021] [Indexed: 02/08/2023]
Abstract
Transcription factors (TFs) regulate gene expression by binding to DNA sequences and modulating transcriptional activity through their effector domains. Despite the central role of effector domains in TF function, there is a current lack of a comprehensive resource and characterization of effector domains. Here, we provide a catalog of 924 effector domains across 594 human TFs. Using this catalog, we characterized the amino acid composition of effector domains, their conservation across species and across the human population, and their roles in human diseases. Furthermore, we provide a classification system for effector domains that constitutes a valuable resource and a blueprint for future experimental studies of TF effector domain function.
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Affiliation(s)
- Luis Soto
- Escuela Profesional de Genética y Biotecnología, Facultad de Ciencias Biológicas, Universidad Nacional Mayor de San Marcos, Lima 15081, Perú
| | - Zhaorong Li
- Bioinformatics Program, Boston University, Boston MA 02215
| | - Clarissa S Santoso
- Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215
| | - Anna Berenson
- Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215
| | - Isabella Ho
- Biology Department, Boston University, Boston MA 02215
| | - Vivian X Shen
- Biology Department, Boston University, Boston MA 02215
| | - Samson Yuan
- Biology Department, Boston University, Boston MA 02215
| | - Juan I Fuxman Bass
- Bioinformatics Program, Boston University, Boston MA 02215,Biology Department, Boston University, Boston MA 02215,Molecular Biology, Cellular Biology and Biochemistry Program, Boston University, Boston MA 02215,correspondence:
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69
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Staller MV, Ramirez E, Kotha SR, Holehouse AS, Pappu RV, Cohen BA. Directed mutational scanning reveals a balance between acidic and hydrophobic residues in strong human activation domains. Cell Syst 2022; 13:334-345.e5. [PMID: 35120642 PMCID: PMC9241528 DOI: 10.1016/j.cels.2022.01.002] [Citation(s) in RCA: 37] [Impact Index Per Article: 18.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/15/2021] [Revised: 10/20/2021] [Accepted: 01/05/2022] [Indexed: 01/01/2023]
Abstract
Acidic activation domains are intrinsically disordered regions of the transcription factors that bind coactivators. The intrinsic disorder and low evolutionary conservation of activation domains have made it difficult to identify the sequence features that control activity. To address this problem, we designed thousands of variants in seven acidic activation domains and measured their activities with a high-throughput assay in human cell culture. We found that strong activation domain activity requires a balance between the number of acidic residues and aromatic and leucine residues. These findings motivated a predictor of acidic activation domains that scans the human proteome for clusters of aromatic and leucine residues embedded in regions of high acidity. This predictor identifies known activation domains and accurately predicts previously unidentified ones. Our results support a flexible acidic exposure model of activation domains in which the acidic residues solubilize hydrophobic motifs so that they can interact with coactivators. A record of this paper’s transparent peer review process is included in the supplemental information. Transcriptional activation domains are poorly conserved, intrinsically disordered regions of the transcription factors that remain difficult to predict from protein sequences. A high-throughput method reveals how strong activation domains require a balance between acidic and hydrophobic residues. This balance powers an accurate predictor of activation domains on human transcription factors.
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Affiliation(s)
- Max V Staller
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA.
| | - Eddie Ramirez
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA
| | - Sanjana R Kotha
- Center for Computational Biology, University of California Berkeley, Berkeley, CA 94720, USA
| | - Alex S Holehouse
- Department of Biochemistry and Molecular Biophysics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Center for Science and Engineering of Living Systems, Washington University in St. Louis, St. Louis, MO 63130, USA; Department of Biomedical Engineering, Washington University in St. Louis, St. Louis, MO 63130, USA
| | - Barak A Cohen
- Edison Family Center for Genome Sciences and Systems Biology, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA; Department of Genetics, Washington University School of Medicine in St. Louis, Saint Louis, MO 63110, USA.
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70
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Multivalency enables unidirectional switch-like competition between intrinsically disordered proteins. Proc Natl Acad Sci U S A 2022; 119:2117338119. [PMID: 35012986 PMCID: PMC8784115 DOI: 10.1073/pnas.2117338119] [Citation(s) in RCA: 20] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 11/22/2021] [Indexed: 12/31/2022] Open
Abstract
Intrinsically disordered proteins must compete for binding to common regulatory targets to carry out their biological functions. Previously, we showed that the activation domains of two disordered proteins, the transcription factor HIF-1α and its negative regulator CITED2, function as a unidirectional, allosteric molecular switch to control transcription of critical adaptive genes under conditions of oxygen deprivation. These proteins achieve transcriptional control by competing for binding to the TAZ1 domain of the transcriptional coactivators CREB-binding protein (CBP) and p300 (CREB: cyclic-AMP response element binding protein). To characterize the mechanistic details behind this molecular switch, we used solution NMR spectroscopy and complementary biophysical methods to determine the contributions of individual binding motifs in CITED2 to the overall competition process. An N-terminal region of the CITED2 activation domain, which forms a helix when bound to TAZ1, plays a critical role in initiating competition with HIF-1α by enabling formation of a ternary complex in a process that is highly dependent on the dynamics and disorder of the competing partners. Two other conserved binding motifs in CITED2, the LPEL motif and an aromatic/hydrophobic motif that we term ϕC, function synergistically to enhance binding of CITED2 and inhibit rebinding of HIF-1α. The apparent unidirectionality of competition between HIF-1α and CITED2 is lost when one or more of these binding regions is altered by truncation or mutation of the CITED2 peptide. Our findings illustrate the complexity of molecular interactions involving disordered proteins containing multivalent interaction motifs and provide insight into the unique mechanisms by which disordered proteins compete for occupancy of common molecular targets within the cell.
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71
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Zug R. Developmental disorders caused by haploinsufficiency of transcriptional regulators: a perspective based on cell fate determination. Biol Open 2022; 11:bio058896. [PMID: 35089335 PMCID: PMC8801891 DOI: 10.1242/bio.058896] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/15/2022] Open
Abstract
Many human birth defects and neurodevelopmental disorders are caused by loss-of-function mutations in a single copy of transcription factor (TF) and chromatin regulator genes. Although this dosage sensitivity has long been known, how and why haploinsufficiency (HI) of transcriptional regulators leads to developmental disorders (DDs) is unclear. Here I propose the hypothesis that such DDs result from defects in cell fate determination that are based on disrupted bistability in the underlying gene regulatory network (GRN). Bistability, a crucial systems biology concept to model binary choices such as cell fate decisions, requires both positive feedback and ultrasensitivity, the latter often achieved through TF cooperativity. The hypothesis explains why dosage sensitivity of transcriptional regulators is an inherent property of fate decisions, and why disruption of either positive feedback or cooperativity in the underlying GRN is sufficient to cause disease. I present empirical and theoretical evidence in support of this hypothesis and discuss several issues for which it increases our understanding of disease, such as incomplete penetrance. The proposed framework provides a mechanistic, systems-level explanation of HI of transcriptional regulators, thus unifying existing theories, and offers new insights into outstanding issues of human disease. This article has an associated Future Leader to Watch interview with the author of the paper.
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Affiliation(s)
- Roman Zug
- Department of Biology, Lund University, 22362 Lund, Sweden
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72
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Alerasool N, Leng H, Lin ZY, Gingras AC, Taipale M. Identification and functional characterization of transcriptional activators in human cells. Mol Cell 2022; 82:677-695.e7. [PMID: 35016035 DOI: 10.1016/j.molcel.2021.12.008] [Citation(s) in RCA: 44] [Impact Index Per Article: 22.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Revised: 11/04/2021] [Accepted: 12/09/2021] [Indexed: 12/13/2022]
Abstract
Transcription is orchestrated by thousands of transcription factors (TFs) and chromatin-associated proteins, but how these are causally connected to transcriptional activation is poorly understood. Here, we conduct an unbiased proteome-scale screen to systematically uncover human proteins that activate transcription in a natural chromatin context. By combining interaction proteomics and chemical inhibitors, we delineate the preference of these transcriptional activators for specific co-activators, highlighting how even closely related TFs can function via distinct cofactors. We also identify potent transactivation domains among the hits and use AlphaFold2 to predict and experimentally validate interaction interfaces of two activation domains with BRD4. Finally, we show that many novel activators are partners in fusion events in tumors and functionally characterize a myofibroma-associated fusion between SRF and C3orf62, a potent p300-dependent activator. Our work provides a functional catalog of potent transactivators in the human proteome and a platform for discovering transcriptional regulators at genome scale.
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Affiliation(s)
- Nader Alerasool
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - He Leng
- Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada
| | - Zhen-Yuan Lin
- Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada
| | - Anne-Claude Gingras
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Lunenfeld-Tanenbaum Research Institute, Mount Sinai Hospital, Sinai Health System, Toronto, ON M5G 1X5, Canada.
| | - Mikko Taipale
- Department of Molecular Genetics, University of Toronto, Toronto, ON M5S 1A8, Canada; Donnelly Centre for Cellular and Biomolecular Research, University of Toronto, Toronto, ON M5S 3E1, Canada.
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73
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OUP accepted manuscript. Hum Mol Genet 2022; 31:2236-2261. [DOI: 10.1093/hmg/ddac029] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/08/2021] [Revised: 01/22/2022] [Accepted: 01/24/2022] [Indexed: 11/12/2022] Open
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74
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Larizza L, Calzari L, Alari V, Russo S. Genes for RNA-binding proteins involved in neural-specific functions and diseases are downregulated in Rubinstein-Taybi iNeurons. Neural Regen Res 2022; 17:5-14. [PMID: 34100419 PMCID: PMC8451555 DOI: 10.4103/1673-5374.314286] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
Taking advantage of the fast-growing knowledge of RNA-binding proteins (RBPs) we review the signature of downregulated genes for RBPs in the transcriptome of induced pluripotent stem cell neurons (iNeurons) modelling the neurodevelopmental Rubinstein Taybi Syndrome (RSTS) caused by mutations in the genes encoding CBP/p300 acetyltransferases. We discuss top and functionally connected downregulated genes sorted to “RNA processing” and “Ribonucleoprotein complex biogenesis” Gene Ontology clusters. The first set of downregulated RBPs includes members of hnRNHP (A1, A2B1, D, G, H2-H1, MAGOHB, PAPBC), core subunits of U small nuclear ribonucleoproteins and Serine-Arginine splicing regulators families, acting in precursor messenger RNA alternative splicing and processing. Consistent with literature findings on reduced transcript levels of serine/arginine repetitive matrix 4 (SRRM4) protein, the main regulator of the neural-specific microexons splicing program upon depletion of Ep300 and Crebbp in mouse neurons, RSTS iNeurons show downregulated genes for proteins impacting this network. We link downregulated genes to neurological disorders including the new HNRNPH1-related intellectual disability syndrome with clinical overlap to RSTS. The set of downregulated genes for Ribosome biogenesis includes several components of ribosomal subunits and nucleolar proteins, such NOP58 and fibrillarin that form complexes with snoRNAs with a central role in guiding post-transcriptional modifications needed for rRNA maturation. These nucleolar proteins are “dual” players as fibrillarin is also required for epigenetic regulation of ribosomal genes and conversely NOP58-associated snoRNA levels are under the control of NOP58 interactor BMAL1, a transcriptional regulator of the circadian rhythm. Additional downregulated genes for “dual specificity” RBPs such as RUVBL1 and METTL1 highlight the links between chromatin and the RBP-ome and the contribution of perturbations in their cross-talk to RSTS. We underline the hub position of CBP/p300 in chromatin regulation, the impact of its defect on neurons’ post-transcriptional regulation of gene expression and the potential use of epidrugs in therapeutics of RBP-caused neurodevelopmental disorders.
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Affiliation(s)
- Lidia Larizza
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Luciano Calzari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Valentina Alari
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
| | - Silvia Russo
- Cytogenetics and Molecular Genetics Laboratory, IRCCS Istituto Auxologico Italiano, Milano, Italy
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75
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Risør MW, Jansma AL, Medici N, Thomas B, Dyson HJ, Wright PE. Characterization of the High-Affinity Fuzzy Complex between the Disordered Domain of the E7 Oncoprotein from High-Risk HPV and the TAZ2 Domain of CBP. Biochemistry 2021; 60:3887-3898. [PMID: 34905914 PMCID: PMC8865373 DOI: 10.1021/acs.biochem.1c00669] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
The intrinsically disordered N-terminal region of the E7 protein from high-risk human papillomavirus (HPV) strains is responsible for oncogenic transformation of host cells through its interaction with a number of cellular factors, including the TAZ2 domain of the transcriptional coactivator CREB-binding protein. Using a variety of spectroscopic and biochemical tools, we find that despite its nanomolar affinity, the HPV16 E7 complex with TAZ2 is disordered and highly dynamic. The disordered domain of HPV16 E7 protein does not adopt a single conformation on the surface of TAZ2 but engages promiscuously with its target through multiple interactions involving two conserved motifs, termed CR1 and CR2, that occupy an extensive binding surface on TAZ2. The fuzzy nature of the complex is a reflection of the promiscuous binding repertoire of viral proteins, which must efficiently dysregulate host cell processes by binding to a variety of host factors in the cellular environment.
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Affiliation(s)
- Michael W. Risør
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Joint first author
| | - Ariane L. Jansma
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A.,Joint first author
| | - Natasha Medici
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A
| | - Brittany Thomas
- Department of Chemistry, Point Loma Nazarene University, San Diego, California, 92106, U.S.A
| | - H. Jane Dyson
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Author for correspondence: H. Jane Dyson, Phone: 1-858-784-2223, , Peter E. Wright, Phone: 1-858-784-9721,
| | - Peter E. Wright
- Department of Integrative Structural and Computational Biology and Skaggs Institute of Chemical Biology, The Scripps Research Institute, 10550 North Torrey Pines Road, La Jolla, California, 92037, U.S.A.,Author for correspondence: H. Jane Dyson, Phone: 1-858-784-2223, , Peter E. Wright, Phone: 1-858-784-9721,
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76
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Stati G, Passaretta F, Gindraux F, Centurione L, Di Pietro R. The Role of the CREB Protein Family Members and the Related Transcription Factors in Radioresistance Mechanisms. Life (Basel) 2021; 11:life11121437. [PMID: 34947968 PMCID: PMC8706059 DOI: 10.3390/life11121437] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/02/2021] [Accepted: 12/16/2021] [Indexed: 02/05/2023] Open
Abstract
In the framework of space flight, the risk of radiation carcinogenesis is considered a "red" risk due to the high likelihood of occurrence as well as the high potential impact on the quality of life in terms of disease-free survival after space missions. The cyclic AMP response element-binding protein (CREB) is overexpressed both in haematological malignancies and solid tumours and its expression and function are modulated following irradiation. The CREB protein is a transcription factor and member of the CREB/activating transcription factor (ATF) family. As such, it has an essential role in a wide range of cell processes, including cell survival, proliferation, and differentiation. Among the CREB-related nuclear transcription factors, NF-κB and p53 have a relevant role in cell response to ionising radiation. Their expression and function can decide the fate of the cell by choosing between death or survival. The aim of this review was to define the role of the CREB/ATF family members and the related transcription factors in the response to ionising radiation of human haematological malignancies and solid tumours.
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Affiliation(s)
- Gianmarco Stati
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
- Correspondence: ; Tel.: +39-08713554567
| | - Francesca Passaretta
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Florelle Gindraux
- Laboratoire de Nanomédecine, Imagerie, Thérapeutique EA 4662, Université Bourgogne Franche-Comté, 25030 Besançon, France;
- Service de Chirurgie Orthopédique, Traumatologique et Plastique, CHU, 25030 Besançon, France
| | - Lucia Centurione
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
| | - Roberta Di Pietro
- Department of Medicine and Ageing Sciences, G. d’Annunzio University of Chieti-Pescara, 66100 Chieti, Italy; (F.P.); (L.C.); (R.D.P.)
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77
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Tsai YJ, Ma MC, Wu PH, Wu WB. Novel involvement of PLD-PKCδ-CREB axis in regulating FGF-2-mediated pentraxin 3 production in human nasal fibroblast cells. J Cell Physiol 2021; 237:1871-1887. [PMID: 34897684 DOI: 10.1002/jcp.30657] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2021] [Revised: 11/26/2021] [Accepted: 11/29/2021] [Indexed: 01/27/2023]
Abstract
A higher expression level of mitogenic fibroblast growth factor-2 (FGF-2) has been reported in human nasal mucus of both chronic rhinosinusitis (CRS) with nasal polyps (CRSwNP) and CRS without nasal polyps (CRSsNP). Meanwhile, we have shown that long pentraxin 3 (PTX3), an essential component of humoral innate immunity that is produced at sites of infection and inflammation, was overproduced in human nasal mucosae and secretions of CRSsNP. Therefore, this study was aimed to investigate how FGF-2 regulates PTX3 expression in human CRSsNP nasal mucosa-derived fibroblast cells (hNMDFs). The FGF-2 treatment caused ptx3 mRNA expression and PTX3 protein induction and secretion. In parallel, a differential expression of FGF receptor (FGFR)-1 to FGFR-4 was observed in hNMDFs and human nasal tissues. While conventionally known PI3K/Akt/mTOR and AP-1 pathways following FGFR activation were shown to be involved, the protein kinase Cδ (PKCδ) and cAMP response element-binding protein (CREB) were also found to be as critical signaling molecules in FGF-2-induced PTX3 induction. The PKCδ and CREB activation could be detected in total cells and in the cell nucleus. Accordingly, a novel CREB binding sequence was detected in the human ptx3 promoter region and could interact with activated CREB in cells challenged with FGF-2. Surprisingly, the phospholipase D (PLD), but not phosphoinositide- and phosphatidylcholine-phospholipase C, was necessarily required for PKCδ and CREB activation. Therefore, we demonstrated here for the first time that FGF-2 mediates PTX3 production not only through PI-3K/Akt/mTOR and AP-1 activation, but also through a novel FGFR-PLD-PKCδ-CREB cellular signaling pathway.
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Affiliation(s)
- Yih-Jeng Tsai
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan.,Department of Otolaryngology Head and Neck Surgery, Shin Kong Wu Ho-Su Memorial Hospital, Taipei, Taiwan
| | - Ming-Chieh Ma
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Pi-Hui Wu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
| | - Wen-Bin Wu
- School of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan.,Graduate Institute of Biomedical and Pharmaceutical Science, College of Medicine, Fu Jen Catholic University, New Taipei City, Taiwan
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78
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Rota IA, Handel AE, Maio S, Klein F, Dhalla F, Deadman ME, Cheuk S, Newman JA, Michaels YS, Zuklys S, Prevot N, Hublitz P, Charles PD, Gkazi AS, Adamopoulou E, Qasim W, Davies EG, Hanson I, Pagnamenta AT, Camps C, Dreau HM, White A, James K, Fischer R, Gileadi O, Taylor JC, Fulga T, Lagerholm BC, Anderson G, Sezgin E, Holländer GA. FOXN1 forms higher-order nuclear condensates displaced by mutations causing immunodeficiency. SCIENCE ADVANCES 2021; 7:eabj9247. [PMID: 34860543 PMCID: PMC8641933 DOI: 10.1126/sciadv.abj9247] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 10/15/2021] [Indexed: 05/04/2023]
Abstract
The transcription factor FOXN1 is a master regulator of thymic epithelial cell (TEC) development and function. Here, we demonstrate that FOXN1 expression is differentially regulated during organogenesis and participates in multimolecular nuclear condensates essential for the factor’s transcriptional activity. FOXN1’s C-terminal sequence regulates the diffusion velocity within these aggregates and modulates the binding to proximal gene regulatory regions. These dynamics are altered in a patient with a mutant FOXN1 that is modified in its C-terminal sequence. This mutant is transcriptionally inactive and acts as a dominant negative factor displacing wild-type FOXN1 from condensates and causing athymia and severe lymphopenia in heterozygotes. Expression of the mutated mouse ortholog selectively impairs mouse TEC differentiation, revealing a gene dose dependency for individual TEC subtypes. We have therefore identified the cause for a primary immunodeficiency disease and determined the mechanism by which this FOXN1 gain-of-function mutant mediates its dominant negative effect.
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Affiliation(s)
- Ioanna A. Rota
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Adam E. Handel
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Nuffield Department of Clinical Neurosciences, University of Oxford, Oxford, UK
| | - Stefano Maio
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fabian Klein
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Fatima Dhalla
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Mary E. Deadman
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Stanley Cheuk
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Joseph A. Newman
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford, UK
| | - Yale S. Michaels
- Genome Engineering and Synthetic Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Saulius Zuklys
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
| | - Nicolas Prevot
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Philip Hublitz
- MRC Weatherall Institute of Molecular Medicine, Genome engineering services, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
| | - Philip D. Charles
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Athina Soragia Gkazi
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Eleni Adamopoulou
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Waseem Qasim
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Edward Graham Davies
- Great Ormond Street Hospital and Great Ormond Street Institute of Child Health, University College London, London WC1N 1EH, UK
| | - Imelda Hanson
- Department of Pediatrics, Section of Pediatric Immunology, Allergy, and Retrovirology, Baylor College of Medicine, Houston, TX, USA
| | - Alistair T. Pagnamenta
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Carme Camps
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Helene M. Dreau
- Department of Oncology, University of Oxford, Oxford OX3 7DQ, UK
| | - Andrea White
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Kieran James
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Roman Fischer
- Target Discovery Institute, University of Oxford, Oxford OX3 7FZ, UK
| | - Opher Gileadi
- Structural Genomics Consortium, University of Oxford, ORCRB, Roosevelt Drive, Oxford, UK
| | - Jenny C. Taylor
- National Institute for Health Research Biomedical Research Centre, Oxford, UK
- Wellcome Centre for Human Genetics, University of Oxford, Oxford OX3 7BN, UK
| | - Tudor Fulga
- Genome Engineering and Synthetic Biology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - B. Christoffer Lagerholm
- Wolfson Imaging Centre Oxford, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Headley Way, Oxford OX3 9DS, UK
| | - Graham Anderson
- Institute for Immunology and Immunotherapy, Medical School, University of Birmingham, Birmingham B15 2TT, UK
| | - Erdinc Sezgin
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
- MRC Human Immunology Unit, MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Georg A. Holländer
- Department of Paediatrics and the MRC Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
- Paediatric Immunology, Department of Biomedicine, University of Basel and University Children’s Hospital Basel, Basel, Switzerland
- Department of Biosystems Science and Engineering, ETH Zurich, Basel, Switzerland
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79
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Flanking Disorder of the Folded αα-Hub Domain from Radical Induced Cell Death1 Affects Transcription Factor Binding by Ensemble Redistribution. J Mol Biol 2021; 433:167320. [PMID: 34687712 DOI: 10.1016/j.jmb.2021.167320] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2021] [Revised: 09/28/2021] [Accepted: 10/13/2021] [Indexed: 11/22/2022]
Abstract
Protein intrinsic disorder is essential for organization of transcription regulatory interactomes. In these interactomes, the majority of transcription factors as well as their interaction partners have co-existing order and disorder. Yet, little attention has been paid to their interplay. Here, we investigate how order is affected by flanking disorder in the folded αα-hub domain RST from Radical-Induced Cell Death1 (RCD1), central in a large interactome of transcription factors. We show that the intrinsically disordered C-terminal tail of RCD1-RST shifts its conformational ensemble towards a pseudo-bound state through weak interactions with the ligand-binding pocket. An unfolded excited state is also accessible on the ms timescale independent of surrounding disordered regions, but its population is lowered by 50% in their presence. Flanking disorder additionally lowers transcription factor binding-affinity without affecting the dissociation rate constant, in accordance with similar bound-states assessed by NMR. The extensive dynamics of the RCD1-RST domain, modulated by flanking disorder, is suggestive of its adaptation to many different transcription factor ligands. The study illustrates how disordered flanking regions can tune fold and function through ensemble redistribution and is of relevance to modular proteins in general, many of which play key roles in regulation of genes.
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80
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Larizza L, Alari V, Calzari L, Russo S. Interconnected Gene Networks Underpin the Clinical Overlap of HNRNPH1-Related and Rubinstein-Taybi Intellectual Disability Syndromes. Front Neurosci 2021; 15:745684. [PMID: 34759793 PMCID: PMC8573106 DOI: 10.3389/fnins.2021.745684] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2021] [Accepted: 09/24/2021] [Indexed: 11/13/2022] Open
Affiliation(s)
- Lidia Larizza
- Laboratory of Medical Cytogenetics and Human Molecular Genetics, Biomedical & Technologies Research Center, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano, Milan, Italy
| | - Valentina Alari
- Laboratory of Medical Cytogenetics and Human Molecular Genetics, Biomedical & Technologies Research Center, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano, Milan, Italy
| | - Luciano Calzari
- Laboratory of Medical Cytogenetics and Human Molecular Genetics, Biomedical & Technologies Research Center, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano, Milan, Italy
| | - Silvia Russo
- Laboratory of Medical Cytogenetics and Human Molecular Genetics, Biomedical & Technologies Research Center, Istituto di Ricerca e Cura a Carattere Scientifico (IRCCS) Istituto Auxologico Italiano, Milan, Italy
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81
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Zhang J, Lu X, MoghaddamKohi S, Shi L, Xu X, Zhu WG. Histone lysine modifying enzymes and their critical roles in DNA double-strand break repair. DNA Repair (Amst) 2021; 107:103206. [PMID: 34411909 DOI: 10.1016/j.dnarep.2021.103206] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 07/24/2021] [Accepted: 08/05/2021] [Indexed: 10/20/2022]
Abstract
Cells protect the integrity of the genome against DNA double-strand breaks through several well-characterized mechanisms including nonhomologous end-joining repair, homologous recombination repair, microhomology-mediated end-joining and single-strand annealing. However, aberrant DNA damage responses (DDRs) lead to genome instability and tumorigenesis. Clarification of the mechanisms underlying the DDR following lethal damage will facilitate the identification of therapeutic targets for cancer. Histones are small proteins that play a major role in condensing DNA into chromatin and regulating gene function. Histone modifications commonly occur in several residues including lysine, arginine, serine, threonine and tyrosine, which can be acetylated, methylated, ubiquitinated and phosphorylated. Of these, lysine modifications have been extensively explored during DDRs. Here, we focus on discussing the roles of lysine modifying enzymes involved in acetylation, methylation, and ubiquitination during the DDR. We provide a comprehensive understanding of the basis of potential epigenetic therapies driven by histone lysine modifications.
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Affiliation(s)
- Jun Zhang
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Xiaopeng Lu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Sara MoghaddamKohi
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China
| | - Lei Shi
- Department of Biochemistry and Molecular Biology, School of Basic Medical Sciences, Tianjin Medical University, Tianjin, 300070, China.
| | - Xingzhi Xu
- Department of Cell Biology and Medical Genetics, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
| | - Wei-Guo Zhu
- Department of Biochemistry and Molecular Biology, School of Medicine, Shenzhen University, Shenzhen, 518055, China.
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82
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Healy KL, Morris AR, Liu AC. Circadian Synchrony: Sleep, Nutrition, and Physical Activity. FRONTIERS IN NETWORK PHYSIOLOGY 2021; 1:732243. [PMID: 35156088 PMCID: PMC8830366] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 11/11/2022]
Abstract
The circadian clock in mammals regulates the sleep/wake cycle and many associated behavioral and physiological processes. The cellular clock mechanism involves a transcriptional negative feedback loop that gives rise to circadian rhythms in gene expression with an approximately 24-h periodicity. To maintain system robustness, clocks throughout the body must be synchronized and their functions coordinated. In mammals, the master clock is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN is entrained to the light/dark cycle through photic signal transduction and subsequent induction of core clock gene expression. The SCN in turn relays the time-of-day information to clocks in peripheral tissues. While the SCN is highly responsive to photic cues, peripheral clocks are more sensitive to non-photic resetting cues such as nutrients, body temperature, and neuroendocrine hormones. For example, feeding/fasting and physical activity can entrain peripheral clocks through signaling pathways and subsequent regulation of core clock genes and proteins. As such, timing of food intake and physical activity matters. In an ideal world, the sleep/wake and feeding/fasting cycles are synchronized to the light/dark cycle. However, asynchronous environmental cues, such as those experienced by shift workers and frequent travelers, often lead to misalignment between the master and peripheral clocks. Emerging evidence suggests that the resulting circadian disruption is associated with various diseases and chronic conditions that cause further circadian desynchrony and accelerate disease progression. In this review, we discuss how sleep, nutrition, and physical activity synchronize circadian clocks and how chronomedicine may offer novel strategies for disease intervention.
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Affiliation(s)
| | | | - Andrew C. Liu
- Department of Physiology and Functional Genomics, University of Florida College of Medicine, Gainesville, FL, United States
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83
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Ruff KM, Pappu RV. AlphaFold and Implications for Intrinsically Disordered Proteins. J Mol Biol 2021; 433:167208. [PMID: 34418423 DOI: 10.1016/j.jmb.2021.167208] [Citation(s) in RCA: 226] [Impact Index Per Article: 75.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2021] [Revised: 08/11/2021] [Accepted: 08/12/2021] [Indexed: 10/20/2022]
Abstract
Accurate predictions of the three-dimensional structures of proteins from their amino acid sequences have come of age. AlphaFold, a deep learning-based approach to protein structure prediction, shows remarkable success in independent assessments of prediction accuracy. A significant epoch in structural bioinformatics was the structural annotation of over 98% of protein sequences in the human proteome. Interestingly, many predictions feature regions of very low confidence, and these regions largely overlap with intrinsically disordered regions (IDRs). That over 30% of regions within the proteome are disordered is congruent with estimates that have been made over the past two decades, as intense efforts have been undertaken to generalize the structure-function paradigm to include the importance of conformational heterogeneity and dynamics. With structural annotations from AlphaFold in hand, there is the temptation to draw inferences regarding the "structures" of IDRs and their interactomes. Here, we offer a cautionary note regarding the misinterpretations that might ensue and highlight efforts that provide concrete understanding of sequence-ensemble-function relationships of IDRs. This perspective is intended to emphasize the importance of IDRs in sequence-function relationships (SERs) and to highlight how one might go about extracting quantitative SERs to make sense of how IDRs function.
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Affiliation(s)
- Kiersten M Ruff
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA
| | - Rohit V Pappu
- Department of Biomedical Engineering and Center for Science & Engineering of Living Systems (CSELS), Washington University in St. Louis, Campus Box 1097, St. Louis, MO 63130, USA.
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84
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Healy KL, Morris AR, Liu AC. Circadian Synchrony: Sleep, Nutrition, and Physical Activity. FRONTIERS IN NETWORK PHYSIOLOGY 2021; 1:732243. [PMID: 35156088 PMCID: PMC8830366 DOI: 10.3389/fnetp.2021.732243] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2021] [Accepted: 09/20/2021] [Indexed: 08/01/2023]
Abstract
The circadian clock in mammals regulates the sleep/wake cycle and many associated behavioral and physiological processes. The cellular clock mechanism involves a transcriptional negative feedback loop that gives rise to circadian rhythms in gene expression with an approximately 24-h periodicity. To maintain system robustness, clocks throughout the body must be synchronized and their functions coordinated. In mammals, the master clock is located in the suprachiasmatic nucleus (SCN) of the hypothalamus. The SCN is entrained to the light/dark cycle through photic signal transduction and subsequent induction of core clock gene expression. The SCN in turn relays the time-of-day information to clocks in peripheral tissues. While the SCN is highly responsive to photic cues, peripheral clocks are more sensitive to non-photic resetting cues such as nutrients, body temperature, and neuroendocrine hormones. For example, feeding/fasting and physical activity can entrain peripheral clocks through signaling pathways and subsequent regulation of core clock genes and proteins. As such, timing of food intake and physical activity matters. In an ideal world, the sleep/wake and feeding/fasting cycles are synchronized to the light/dark cycle. However, asynchronous environmental cues, such as those experienced by shift workers and frequent travelers, often lead to misalignment between the master and peripheral clocks. Emerging evidence suggests that the resulting circadian disruption is associated with various diseases and chronic conditions that cause further circadian desynchrony and accelerate disease progression. In this review, we discuss how sleep, nutrition, and physical activity synchronize circadian clocks and how chronomedicine may offer novel strategies for disease intervention.
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85
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Direct photoresponsive inhibition of a p53-like transcription activation domain in PIF3 by Arabidopsis phytochrome B. Nat Commun 2021; 12:5614. [PMID: 34556672 PMCID: PMC8460787 DOI: 10.1038/s41467-021-25909-5] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 09/09/2021] [Indexed: 11/24/2022] Open
Abstract
Photoactivated phytochrome B (PHYB) binds to antagonistically acting PHYTOCHROME-INTERACTING transcription FACTORs (PIFs) to regulate hundreds of light responsive genes in Arabidopsis by promoting PIF degradation. However, whether PHYB directly controls the transactivation activity of PIFs remains ambiguous. Here we show that the prototypic PIF, PIF3, possesses a p53-like transcription activation domain (AD) consisting of a hydrophobic activator motif flanked by acidic residues. A PIF3mAD mutant, in which the activator motif is replaced with alanines, fails to activate PIF3 target genes in Arabidopsis, validating the functions of the PIF3 AD in vivo. Intriguingly, the N-terminal photosensory module of PHYB binds immediately adjacent to the PIF3 AD to repress PIF3’s transactivation activity, demonstrating a novel PHYB signaling mechanism through direct interference of the transactivation activity of PIF3. Our findings indicate that PHYB, likely also PHYA, controls the stability and activity of PIFs via structurally separable dual signaling mechanisms. Photoactivated phytochrome B regulates gene expression by interacting with PIF transcription factors. Here the authors show that PIF3 contains a p53-like transcription activation domain (AD) and that PHYB can directly suppress PIF3 transactivation activity by binding adjacent to the AD.
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86
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Beta-Genus Human Papillomavirus 8 E6 Destabilizes the Host Genome by Promoting p300 Degradation. Viruses 2021; 13:v13081662. [PMID: 34452526 PMCID: PMC8402844 DOI: 10.3390/v13081662] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2021] [Revised: 08/16/2021] [Accepted: 08/18/2021] [Indexed: 01/10/2023] Open
Abstract
The beta genus of human papillomaviruses infects cutaneous keratinocytes. Their replication depends on actively proliferating cells and, thus, they conflict with the cellular response to the DNA damage frequently encountered by these cells. This review focus on one of these viruses (HPV8) that counters the cellular response to damaged DNA and mitotic errors by expressing a protein (HPV8 E6) that destabilizes a histone acetyltransferase, p300. The loss of p300 results in broad dysregulation of cell signaling that decreases genome stability. In addition to discussing phenotypes caused by p300 destabilization, the review contains a discussion of the extent to which E6 from other β-HPVs destabilizes p300, and provides a discussion on dissecting HPV8 E6 biology using mutants.
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87
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Felli IC, Bermel W, Pierattelli R. Exclusively heteronuclear NMR experiments for the investigation of intrinsically disordered proteins: focusing on proline residues. MAGNETIC RESONANCE (GOTTINGEN, GERMANY) 2021; 2:511-522. [PMID: 37904768 PMCID: PMC10539766 DOI: 10.5194/mr-2-511-2021] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/27/2021] [Accepted: 06/02/2021] [Indexed: 11/01/2023]
Abstract
NMR represents a key spectroscopic technique that contributes to the emerging field of highly flexible, intrinsically disordered proteins (IDPs) or protein regions (IDRs) that lack a stable three-dimensional structure. A set of exclusively heteronuclear NMR experiments tailored for proline residues, highly abundant in IDPs/IDRs, are presented here. They provide a valuable complement to the widely used approach based on amide proton detection, filling the gap introduced by the lack of amide protons in proline residues within polypeptide chains. The novel experiments have very interesting properties for the investigations of IDPs/IDRs of increasing complexity.
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Affiliation(s)
- Isabella C. Felli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
| | - Wolfgang Bermel
- Bruker BioSpin GmbH, Silberstreifen 4, 76287 Rheinstetten, Germany
| | - Roberta Pierattelli
- CERM and Department of Chemistry “Ugo Schiff”, University of Florence, Via Luigi Sacconi 6, 50019 Sesto Fiorentino, Florence, Italy
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88
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Li L, Zhang YL, Liu XY, Meng X, Zhao RQ, Ou LL, Li BZ, Xing T. Periodontitis Exacerbates and Promotes the Progression of Chronic Kidney Disease Through Oral Flora, Cytokines, and Oxidative Stress. Front Microbiol 2021; 12:656372. [PMID: 34211440 PMCID: PMC8238692 DOI: 10.3389/fmicb.2021.656372] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2021] [Accepted: 04/01/2021] [Indexed: 12/25/2022] Open
Abstract
Periodontitis is a type of systemic immune inflammation that is caused by the complex infection of a variety of microorganisms in the subgingival plaque and the imbalance of the microbial ecological environment in the mouth. Periodontitis and chronic kidney disease (CKD) share many risk factors, such as obesity, smoking, and age. A growing body of data supports a strong correlation between periodontitis and kidney disease. Evidence supports the role of periodontal inflammation and elevated serum inflammatory mediators in renal atherosclerosis, renal deterioration, and end-stage renal disease (ESRD) development. Periodontitis is a risk factor for kidney disease. However, to our knowledge, there are few studies detailing the possible link between periodontitis and CKD. This review summarizes the possible mechanisms underlying periodontitis and CKD. More importantly, it highlights novel and potential pathogenic factors for CKD, including bacteria, pro-inflammatory mediators and oxidative stress. However, most research on the relationship between periodontitis and systemic disease has not determined causality, and these diseases are largely linked by bidirectional associations. Future research will focus on exploring these links to contribute to new treatments for CKD.
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Affiliation(s)
- Ling Li
- School of Stomatology, Anhui Medical University, Hefei, China
| | - Ya-Li Zhang
- School of Stomatology, Anhui Medical University, Hefei, China
| | - Xing-Yu Liu
- School of Stomatology, Anhui Medical University, Hefei, China
| | - Xiang Meng
- Key Laboratory of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, Hefei, China
| | - Rong-Quan Zhao
- School of Stomatology, Anhui Medical University, Hefei, China
| | - Lin-Lin Ou
- School of Stomatology, Anhui Medical University, Hefei, China
| | - Bao-Zhu Li
- Department of Epidemiology and Biostatistics, School of Public Health, Anhui Medical University, Hefei, China
| | - Tian Xing
- School of Stomatology, Anhui Medical University, Hefei, China.,Key Laboratory of Oral Diseases Research of Anhui Province, College and Hospital of Stomatology, Anhui Medical University, Hefei, China
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89
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Biddle JW, Martinez-Corral R, Wong F, Gunawardena J. Allosteric conformational ensembles have unlimited capacity for integrating information. eLife 2021; 10:65498. [PMID: 34106049 PMCID: PMC8189718 DOI: 10.7554/elife.65498] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2020] [Accepted: 04/30/2021] [Indexed: 12/24/2022] Open
Abstract
Integration of binding information by macromolecular entities is fundamental to cellular functionality. Recent work has shown that such integration cannot be explained by pairwise cooperativities, in which binding is modulated by binding at another site. Higher-order cooperativities (HOCs), in which binding is collectively modulated by multiple other binding events, appear to be necessary but an appropriate mechanism has been lacking. We show here that HOCs arise through allostery, in which effective cooperativity emerges indirectly from an ensemble of dynamically interchanging conformations. Conformational ensembles play important roles in many cellular processes but their integrative capabilities remain poorly understood. We show that sufficiently complex ensembles can implement any form of information integration achievable without energy expenditure, including all patterns of HOCs. Our results provide a rigorous biophysical foundation for analysing the integration of binding information through allostery. We discuss the implications for eukaryotic gene regulation, where complex conformational dynamics accompanies widespread information integration.
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Affiliation(s)
- John W Biddle
- Department of Systems Biology, Harvard Medical School, Boston, United States
| | | | - Felix Wong
- Institute for Medical Engineering and Science, Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, United States.,Infectious Disease and Microbiome Program, Broad Institute of MIT and Harvard, Cambridge, United States
| | - Jeremy Gunawardena
- Department of Systems Biology, Harvard Medical School, Boston, United States
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90
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Ramberger E, Sapozhnikova V, Kowenz-Leutz E, Zimmermann K, Nicot N, Nazarov PV, Perez-Hernandez D, Reimer U, Mertins P, Dittmar G, Leutz A. PRISMA and BioID disclose a motifs-based interactome of the intrinsically disordered transcription factor C/EBPα. iScience 2021; 24:102686. [PMID: 34189442 PMCID: PMC8220391 DOI: 10.1016/j.isci.2021.102686] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2021] [Revised: 05/17/2021] [Accepted: 05/30/2021] [Indexed: 01/27/2023] Open
Abstract
C/EBPα represents a paradigm intrinsically disordered transcription factor containing short linear motifs and post-translational modifications (PTM). Unraveling C/EBPα protein interaction networks is a prerequisite for understanding the multi-modal functions of C/EBPα in hematopoiesis and leukemia. Here, we combined arrayed peptide matrix screening (PRISMA) with BioID to generate an in vivo validated and isoform specific interaction map of C/EBPα. The myeloid C/EBPα interactome comprises promiscuous and PTM-regulated interactions with protein machineries involved in gene expression, epigenetics, genome organization, DNA replication, RNA processing, and nuclear transport. C/EBPα interaction hotspots coincide with homologous conserved regions of the C/EBP family that also score as molecular recognition features. PTMs alter the interaction spectrum of C/EBP-motifs to configure a multi-valent transcription factor hub that interacts with multiple co-regulatory components, including BAF/SWI-SNF or Mediator complexes. Combining PRISMA and BioID is a powerful strategy to systematically explore the PTM-regulated interactomes of intrinsically disordered transcription factors. Combining peptide arrays and BioID refines the C/EBPα interactome Hotspots of protein interactions in C/EBPα mostly occur in conserved regions The interaction with the BAF/SWI-SNF complex is modulated by C/EBPα methylation Experimental design suits interactome studies of intrinsically disordered proteins
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Affiliation(s)
- Evelyn Ramberger
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Valeria Sapozhnikova
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Elisabeth Kowenz-Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Karin Zimmermann
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Nathalie Nicot
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Petr V Nazarov
- Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Daniel Perez-Hernandez
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Ulf Reimer
- JPT Peptide Technologies GmbH, Volmerstrasse 5, 12489 Berlin, Germany
| | - Philipp Mertins
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany
| | - Gunnar Dittmar
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Quantitative Biology Unit, Luxembourg Institute of Health, 1a Rue Thomas Edison, 1445 Strassen, Luxembourg
| | - Achim Leutz
- Max Delbrück Center for Molecular Medicine in the Helmholtz Association, Robert-Rössle-Strasse 10, 13125 Berlin, Germany.,Institute of Biology, Humboldt University of Berlin, 10115 Berlin, Germany
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91
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Steroid receptor-coregulator transcriptional complexes: new insights from CryoEM. Essays Biochem 2021; 65:857-866. [PMID: 34061186 DOI: 10.1042/ebc20210019] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Revised: 05/04/2021] [Accepted: 05/06/2021] [Indexed: 01/14/2023]
Abstract
Steroid receptors activate gene transcription through recruitment of a number of coregulators to facilitate histone modification, chromatin remodeling, and general transcription machinery stabilization. Understanding the structures of full-length steroid receptor and coregulatory complexes has been difficult due to their large molecular sizes and dynamic structural conformations. Recent developments in cryo-electron microscopy (cryoEM) technology and proteomics have advanced the structural studies of steroid receptor complexes. Here, we will review the insights we learned from cryoEM studies of the estrogen and androgen receptor transcriptional complexes. Despite similar domain organizations, the two receptors have different coregulator interaction modes. The cryoEM structures now have revealed the fundamental differences between the two receptors and their functional mechanisms.
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92
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Henley MJ, Koehler AN. Advances in targeting 'undruggable' transcription factors with small molecules. Nat Rev Drug Discov 2021; 20:669-688. [PMID: 34006959 DOI: 10.1038/s41573-021-00199-0] [Citation(s) in RCA: 145] [Impact Index Per Article: 48.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/30/2021] [Indexed: 02/07/2023]
Abstract
Transcription factors (TFs) represent key biological players in diseases including cancer, autoimmunity, diabetes and cardiovascular disease. However, outside nuclear receptors, TFs have traditionally been considered 'undruggable' by small-molecule ligands due to significant structural disorder and lack of defined small-molecule binding pockets. Renewed interest in the field has been ignited by significant progress in chemical biology approaches to ligand discovery and optimization, especially the advent of targeted protein degradation approaches, along with increasing appreciation of the critical role a limited number of collaborators play in the regulation of key TF effector genes. Here, we review current understanding of TF-mediated gene regulation, discuss successful targeting strategies and highlight ongoing challenges and emerging approaches to address them.
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Affiliation(s)
- Matthew J Henley
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
| | - Angela N Koehler
- David H. Koch Institute for Integrative Cancer Research, Massachusetts Institute of Technology, Cambridge, MA, USA. .,The Broad Institute of MIT and Harvard, Cambridge, MA, USA. .,Department of Biological Engineering, Massachusetts Institute of Technology, Cambridge, MA, USA.
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93
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Oncogenic HPV promotes the expression of the long noncoding RNA lnc-FANCI-2 through E7 and YY1. Proc Natl Acad Sci U S A 2021; 118:2014195118. [PMID: 33436409 DOI: 10.1073/pnas.2014195118] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) play diverse roles in biological processes, but their expression profiles and functions in cervical carcinogenesis remain unknown. By RNA-sequencing (RNA-seq) analyses of 18 clinical specimens and selective validation by RT-qPCR analyses of 72 clinical samples, we provide evidence that, relative to normal cervical tissues, 194 lncRNAs are differentially regulated in high-risk (HR)-HPV infection along with cervical lesion progression. One such lncRNA, lnc-FANCI-2, is extensively characterized because it is expressed from a genomic locus adjacent to the FANCI gene encoding an important DNA repair factor. Both genes are up-regulated in HPV lesions and in in vitro model systems of HR-HPV18 infection. We observe a moderate reciprocal regulation of lnc-FANCI-2 and FANCI in cervical cancer CaSki cells. In these cells, lnc-FANCI-2 is transcribed from two alternative promoters, alternatively spliced, and polyadenylated at one of two alternative poly(A) sites. About 10 copies of lnc-FANCI-2 per cell are detected preferentially in the cytoplasm. Mechanistically, HR-HPVs, but not low-risk (LR)-HPV oncogenes induce lnc-FANCI-2 in primary and immortalized human keratinocytes. The induction is mediated primarily by E7, and to a lesser extent by E6, mostly independent of p53/E6AP and pRb/E2F. We show that YY1 interacts with an E7 CR3 core motif and transactivates the promoter of lnc-FANCI-2 by binding to two critical YY1-binding motifs. Moreover, HPV18 increases YY1 expression by reducing miR-29a, which targets the 3' untranslated region of YY1 mRNA. These data have provided insights into the mechanisms of how HR-HPV infections contribute to cervical carcinogenesis.
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94
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Zúñiga-Muñoz A, García-Niño WR, Carbó R, Navarrete-López LÁ, Buelna-Chontal M. The regulation of protein acetylation influences the redox homeostasis to protect the heart. Life Sci 2021; 277:119599. [PMID: 33989666 DOI: 10.1016/j.lfs.2021.119599] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Revised: 04/26/2021] [Accepted: 05/05/2021] [Indexed: 12/21/2022]
Abstract
The cellular damage caused by redox imbalance is involved in the pathogenesis of many cardiovascular diseases. Besides, redox imbalance is related to the alteration of protein acetylation processes, causing not only chromatin remodeling but also disturbances in so many processes where protein acetylation is involved, such as metabolism and signal transduction. The modulation of acetylases and deacetylases enzymes aids in maintaining the redox homeostasis, avoiding the deleterious cellular effects associated with the dysregulation of protein acetylation. Of note, regulation of protein acetylation has shown protective effects to ameliorate cardiovascular diseases. For instance, HDAC inhibition has been related to inducing cardiac protective effects and it is an interesting approach to the management of cardiovascular diseases. On the other hand, the upregulation of SIRT protein activity has also been implicated in the relief of cardiovascular diseases. This review focuses on the major protein acetylation modulators described, involving pharmacological and bioactive compounds targeting deacetylase and acetylase enzymes contributing to heart protection through redox homeostasis.
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Affiliation(s)
- Alejandra Zúñiga-Muñoz
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Wylly-Ramsés García-Niño
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Roxana Carbó
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Luis-Ángel Navarrete-López
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico
| | - Mabel Buelna-Chontal
- Department of Cardiovascular Biomedicine, National Institute of Cardiology, Ignacio Chávez, 14080 Mexico City, Mexico.
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95
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Liu X, Zhou F, Wang W, Chen G, Zhang Q, Lv R, Zhao Z, Li X, Yu Q, Meves JM, Hua H, Li X, Wang X, Sun H, Gao D. IL-9-triggered lncRNA Gm13568 regulates Notch1 in astrocytes through interaction with CBP/P300: contribute to the pathogenesis of experimental autoimmune encephalomyelitis. J Neuroinflammation 2021; 18:108. [PMID: 33971906 PMCID: PMC8112022 DOI: 10.1186/s12974-021-02156-5] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2021] [Accepted: 04/22/2021] [Indexed: 12/20/2022] Open
Abstract
Background Interleukin 9 (IL-9), produced mainly by T helper 9 (Th9) cells, has been recognized as an important regulator in multiple sclerosis (MS) and its animal model, experimental autoimmune encephalomyelitis (EAE). Astrocytes respond to IL-9 and reactive astrocytes always associate with blood-brain barrier damage, immune cell infiltration, and spinal injury in MS and EAE. Several long non-coding RNAs (lncRNAs) with aberrant expression have been identified in the pathogenesis of MS. Here, we examined the effects of lncRNA Gm13568 (a co-upregulated lncRNA both in EAE mice and in mouse primary astrocytes activated by IL-9) on the activation of astrocytes and the process of EAE. Methods In vitro, shRNA-recombinant lentivirus with glial fibrillary acidic protein (GFAP) promoter were performed to determine the relative gene expression and proinflammatory cytokines production in IL-9 treated-astrocytes using Western blot, real-time PCR, and Cytometric Bead Array, respectively. RIP and ChIP assays were analyzed for the mechanism of lncRNA Gm13568 regulating gene expression. Immunofluorescence assays was performed to measure the protein expression in astrocytes. In vivo, H&E staining and LFB staining were applied to detect the inflammatory cells infiltrations and the medullary sheath damage in spinal cords of EAE mice infected by the recombinant lentivirus. Results were analyzed by one-way ANOVA or Student’s t test, as appropriate. Results Knockdown of the endogenous lncRNA Gm13568 remarkably inhibits the Notch1 expression, astrocytosis, and the phosphorylation of signal transducer and activator of transcription 3 (p-STAT3) as well as the production of inflammatory cytokines and chemokines (IL-6, TNF-α, IP-10) in IL-9-activated astrocytes, in which Gm13568 associates with the transcriptional co-activators CBP/P300 which are enriched in the promoter of Notch1 genes. More importantly, inhibiting Gm13568 with lentiviral vector in astrocytes ameliorates significantly inflammation and demyelination in EAE mice, therefore delaying the EAE process. Conclusions These findings uncover that Gm13568 regulates the production of inflammatory cytokines in active astrocytes and affects the pathogenesis of EAE through the Notch1/STAT3 pathway. LncRNA Gm13568 may be a promising target for treating MS and demyelinating diseases. Supplementary Information The online version contains supplementary material available at 10.1186/s12974-021-02156-5.
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Affiliation(s)
- Xiaomei Liu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China.
| | - Feng Zhou
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Weixiao Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Guofang Chen
- Neurology Department, The Affiliated Xuzhou Center Hospital of Nanjing University of Chinese Medicine, Xuzhou, People's Republic of China.,Neurology Department, Xuzhou Central Hospital, Xuzhou, People's Republic of China.,Neurology Department, Xuzhou Clinical School of Xuzhou Medical University, Xuzhou, Jiangsu, 221009, People's Republic of China
| | - Qingxiu Zhang
- Department of Neurology, Second Affiliated Hospital of Xuzhou Medical University, Xuzhou, Jiangsu, 221006, People's Republic of China
| | - Ruixue Lv
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Zijun Zhao
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xiangyang Li
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Qian Yu
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Jessica M Meves
- Department of Psychiatry, University of Michigan Medicine, MI48109, Ann Arbor, Michigan, USA
| | - Hui Hua
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xiaocui Li
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Xiaotian Wang
- Jiangsu Key Laboratory of Immunity and Metabolism, Department of Pathogen Biology and Immunology and Laboratory of Infection and Immunity, Xuzhou Medical University, 209 Tongshan Road, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Hong Sun
- Department of Physiology, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China
| | - Dianshuai Gao
- Xuzhou Key Laboratory of Neurobiology, Department of Neurobiology and Anatomy, Xuzhou Medical University, Xuzhou, Jiangsu, 221004, People's Republic of China.
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96
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Khayachi A, Schorova L, Alda M, Rouleau GA, Milnerwood AJ. Posttranslational modifications & lithium's therapeutic effect-Potential biomarkers for clinical responses in psychiatric & neurodegenerative disorders. Neurosci Biobehav Rev 2021; 127:424-445. [PMID: 33971223 DOI: 10.1016/j.neubiorev.2021.05.002] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Revised: 03/14/2021] [Accepted: 05/03/2021] [Indexed: 01/03/2023]
Abstract
Several neurodegenerative diseases and neuropsychiatric disorders display aberrant posttranslational modifications (PTMs) of one, or many, proteins. Lithium treatment has been used for mood stabilization for many decades, and is highly effective for large subsets of patients with diverse neurological conditions. However, the differential effectiveness and mode of action are not fully understood. In recent years, studies have shown that lithium alters several protein PTMs, altering their function, and consequently neuronal physiology. The impetus for this review is to outline the links between lithium's therapeutic mode of action and PTM homeostasis. We first provide an overview of the principal PTMs affected by lithium. We then describe several neuropsychiatric disorders in which PTMs have been implicated as pathogenic. For each of these conditions, we discuss lithium's clinical use and explore the putative mechanism of how it restores PTM homeostasis, and thereby cellular physiology. Evidence suggests that determining specific PTM patterns could be a promising strategy to develop biomarkers for disease and lithium responsiveness.
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Affiliation(s)
- A Khayachi
- Montreal Neurological Institute, Department of Neurology & Neurosurgery, McGill University, Montréal, Quebec, Canada.
| | - L Schorova
- McGill University Health Center Research Institute, Montréal, Quebec, Canada
| | - M Alda
- Department of Psychiatry, Dalhousie University, Halifax, Nova Scotia, Canada
| | - G A Rouleau
- Montreal Neurological Institute, Department of Neurology & Neurosurgery, McGill University, Montréal, Quebec, Canada; Department of Human Genetics, McGill University, Montréal, Quebec, Canada.
| | - A J Milnerwood
- Montreal Neurological Institute, Department of Neurology & Neurosurgery, McGill University, Montréal, Quebec, Canada.
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97
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Chang M, Wilson CJ, Karunatilleke NC, Moselhy MH, Karttunen M, Choy WY. Exploring the Conformational Landscape of the Neh4 and Neh5 Domains of Nrf2 Using Two Different Force Fields and Circular Dichroism. J Chem Theory Comput 2021; 17:3145-3156. [PMID: 33861593 DOI: 10.1021/acs.jctc.0c01243] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Abstract
The nuclear factor erythroid 2-related factor 2 (Nrf2)-ARE transcriptional response pathway plays a critical role in protecting the cell from oxidative stresses via the upregulation of cytoprotective genes. Aberrant activation of Nrf2 in cancer cells can confer this cytoprotectivity, thereby reducing the efficacy of both chemotherapeutics and radiotherapies. Key to this antioxidant pathway is the interaction between Nrf2 and CREB binding protein (CBP), mediated by the Neh4 and Neh5 domains of Nrf2. Disruption of this interaction via small-molecule therapeutics could negate the effects of aberrant Nrf2 upregulation. Due to the disordered nature of these domains, there remains no three-dimensional structure of Neh4 or Neh5, making structure-based drug design a challenge. Here, we performed 48 μs of unbiased molecular dynamics (MD) simulations with the Amber99SB*-ILDNP and CHARMM36m force fields and circular dichroism (CD) spectropolarimetry experiments to elucidate the free-state structures of these domains; no previous data regarding their conformational landscapes exists. There are two main findings: First, we find Neh5 to be markedly more disordered than Neh4, which has nine residues in the middle of the domain showing α-helical propensity, thus pointing to Neh4 and Neh5 having different binding mechanisms. Second, the two force fields show strong differences for the glutamic acid-rich Neh5 peptide but are in reasonable agreement for Neh4, which has no glutamic acid. The CHARMM36m force field agrees more closely with the CD results.
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Affiliation(s)
- Megan Chang
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Carter J Wilson
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Nadun Chanaka Karunatilleke
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
| | - Mohamed Hesham Moselhy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada.,Department of Computer Science, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Mikko Karttunen
- Department of Applied Mathematics, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada.,Department of Chemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 3K7, Canada.,Centre for Advanced Materials and Biomaterials Research, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5B7, Canada
| | - Wing-Yiu Choy
- Department of Biochemistry, The University of Western Ontario, 1151 Richmond Street, London, Ontario N6A 5C1, Canada
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98
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Agelidis A, Turturice BA, Suryawanshi RK, Yadavalli T, Jaishankar D, Ames J, Hopkins J, Koujah L, Patil CD, Hadigal SR, Kyzar EJ, Campeau A, Wozniak JM, Gonzalez DJ, Vlodavsky I, Li JP, Perkins DL, Finn PW, Shukla D. Disruption of innate defense responses by endoglycosidase HPSE promotes cell survival. JCI Insight 2021; 6:144255. [PMID: 33621216 PMCID: PMC8119219 DOI: 10.1172/jci.insight.144255] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2020] [Accepted: 02/18/2021] [Indexed: 01/03/2023] Open
Abstract
The drive to withstand environmental stresses and defend against invasion is a universal trait extant in all forms of life. While numerous canonical signaling cascades have been characterized in detail, it remains unclear how these pathways interface to generate coordinated responses to diverse stimuli. To dissect these connections, we followed heparanase (HPSE), a protein best known for its endoglycosidic activity at the extracellular matrix but recently recognized to drive various forms of late-stage disease through unknown mechanisms. Using herpes simplex virus-1 (HSV-1) infection as a model cellular perturbation, we demonstrate that HPSE acts beyond its established enzymatic role to restrict multiple forms of cell-intrinsic defense and facilitate host cell reprogramming by the invading pathogen. We reveal that cells devoid of HPSE are innately resistant to infection and counteract viral takeover through multiple amplified defense mechanisms. With a unique grasp of the fundamental processes of transcriptional regulation and cell death, HPSE represents a potent cellular intersection with broad therapeutic potential.
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Affiliation(s)
- Alex Agelidis
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - Benjamin A. Turturice
- Department of Microbiology and Immunology
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | | | | | - Dinesh Jaishankar
- Department of Ophthalmology and Visual Sciences, and
- Department of Dermatology, Lurie Comprehensive Cancer Center, Northwestern University, Chicago, Illinois, USA
| | - Joshua Ames
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - James Hopkins
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | - Lulia Koujah
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
| | | | | | - Evan J. Kyzar
- Department of Psychiatry, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Anaamika Campeau
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - Jacob M. Wozniak
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - David J. Gonzalez
- Department of Pharmacology and
- Skaggs School of Pharmacy, UCSD, San Diego, La Jolla, California, USA
| | - Israel Vlodavsky
- Technion Integrated Cancer Center (TICC), Rappaport Faculty of Medicine, Technion, Haifa, Israel
| | - Jin-ping Li
- Department of Medical Biochemistry and Microbiology, University of Uppsala, Uppsala, Sweden
| | - David L. Perkins
- Division of Nephrology, Department of Medicine, and
- Department of Surgery, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Patricia W. Finn
- Department of Microbiology and Immunology
- Division of Pulmonary, Critical Care, Sleep, and Allergy, Department of Medicine, University of Illinois at Chicago, Chicago, Illinois, USA
| | - Deepak Shukla
- Department of Microbiology and Immunology
- Department of Ophthalmology and Visual Sciences, and
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99
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Li X, Song Y. Structure, function and inhibition of critical protein-protein interactions involving mixed lineage leukemia 1 and its fusion oncoproteins. J Hematol Oncol 2021; 14:56. [PMID: 33823889 PMCID: PMC8022399 DOI: 10.1186/s13045-021-01057-7] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2021] [Accepted: 03/05/2021] [Indexed: 12/13/2022] Open
Abstract
Mixed lineage leukemia 1 (MLL1, also known as MLL or KMT2A) is an important transcription factor and histone-H3 lysine-4 (H3K4) methyltransferase. It is a master regulator for transcription of important genes (e.g., Hox genes) for embryonic development and hematopoiesis. However, it is largely dispensable in matured cells. Dysregulation of MLL1 leads to overexpression of certain Hox genes and eventually leukemia initiation. Chromosome translocations involving MLL1 cause ~ 75% of acute leukemia in infants and 5–10% in children and adults with a poor prognosis. Targeted therapeutics against oncogenic fusion MLL1 (onco-MLL1) are therefore needed. Onco-MLL1 consists of the N-terminal DNA-interacting domains of MLL1 fused with one of > 70 fusion partners, among which transcription cofactors AF4, AF9 and its paralog ENL, and ELL are the most frequent. Wild-type (WT)- and onco-MLL1 involve numerous protein–protein interactions (PPI), which play critical roles in regulating gene expression in normal physiology and leukemia. Moreover, WT-MLL1 has been found to be essential for MLL1-rearranged (MLL1-r) leukemia. Rigorous studies of such PPIs have been performed and much progress has been achieved in understanding their structures, structure–function relationships and the mechanisms for activating gene transcription as well as leukemic transformation. Inhibition of several critical PPIs by peptides, peptidomimetic or small-molecule compounds has been explored as a therapeutic approach for MLL1-r leukemia. This review summarizes the biological functions, biochemistry, structure and inhibition of the critical PPIs involving MLL1 and its fusion partner proteins. In addition, challenges and perspectives of drug discovery targeting these PPIs for the treatment of MLL1-r leukemia are discussed.
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Affiliation(s)
- Xin Li
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA
| | - Yongcheng Song
- Department of Pharmacology and Chemical Biology, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA. .,Dan L. Duncan Comprehensive Cancer Center, Baylor College of Medicine, 1 Baylor Plaza, Houston, TX, 77030, USA.
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100
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Tooley JG, Catlin JP, Schaner Tooley CE. CREB-mediated transcriptional activation of NRMT1 drives muscle differentiation. Transcription 2021; 12:72-88. [PMID: 34403304 PMCID: PMC8555533 DOI: 10.1080/21541264.2021.1963627] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2021] [Revised: 07/28/2021] [Accepted: 07/29/2021] [Indexed: 12/29/2022] Open
Abstract
The N-terminal methyltransferase NRMT1 is an important regulator of protein/DNA interactions and plays a role in many cellular processes, including mitosis, cell cycle progression, chromatin organization, DNA damage repair, and transcriptional regulation. Accordingly, loss of NRMT1 results in both developmental pathologies and oncogenic phenotypes. Though NRMT1 plays such important and diverse roles in the cell, little is known about its own regulation. To better understand the mechanisms governing NRMT1 expression, we first identified its predominant transcriptional start site and minimal promoter region with predicted transcription factor motifs. We then used a combination of luciferase and binding assays to confirm CREB1 as the major regulator of NRMT1 transcription. We tested which conditions known to activate CREB1 also activated NRMT1 transcription, and found CREB1-mediated NRMT1 expression was increased during recovery from serum starvation and muscle cell differentiation. To determine how NRMT1 expression affects myoblast differentiation, we used CRISPR/Cas9 technology to knock out NRMT1 expression in immortalized C2C12 mouse myoblasts. C2C12 cells depleted of NRMT1 lacked Pax7 expression and were unable to proceed down the muscle differentiation pathway. Instead, they took on characteristics of C2C12 cells that have transdifferentiated into osteoblasts, including increased alkaline phosphatase and type I collagen expression and decreased proliferation. These data implicate NRMT1 as an important downstream target of CREB1 during muscle cell differentiation.
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Affiliation(s)
- John G. Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - James P. Catlin
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
| | - Christine E. Schaner Tooley
- Department of Biochemistry, Jacobs School of Medicine and Biomedical Sciences, State University of New York at Buffalo, Buffalo, NY, USA
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