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EBioMedicine Dec 2022The E2F family of transcription factors play a crucial role in the development of various cancers. However, E2F members lack targetable binding pockets and are typically...
BACKGROUND
The E2F family of transcription factors play a crucial role in the development of various cancers. However, E2F members lack targetable binding pockets and are typically considered "undruggable". Unlike canonical small-molecule therapeutics, molecular glues mediate new E3 ligase-protein interactions to induce selective proteasomal degradation, which represents an attractive option to overcome these limitations.
METHODS
Human proteome microarray was utilized to identify a natural product-derived molecular glue for targeting E2F2 degradation. Co-IP analysis with stable isotope labeling of amino acids in cell culture (SILAC)-based quantitative proteomics was carried out to further explore the E3 ligase for E2F2 degradation.
FINDINGS
In this study, we identified a molecular glue bufalin, which significantly promoted E2F2 degradation. Unexpectedly, E2F2 underwent ubiquitination and proteasomal degradation via a previously undisclosed atypical E3 ligase, zinc finger protein 91 (ZFP91). In particular, we observed that bufalin markedly promoted E2F2-ZFP91 complex formation, thereby leading to E2F2 polyubiquitination via K48-linked ubiquitin chains for degradation. E2F2 degradation subsequently caused transcriptional suppression of multiple oncogenes including c-Myc, CCNE1, CCNE2, MCM5 and CDK1, and inhibited hepatocellular carcinoma growth in vitro and in vivo.
INTERPRETATION
Collectively, our findings open up a new direction for transcription factors degradation by targeting atypical E3 ligase ZFP91. Meanwhile, the chemical knockdown strategy with molecular glue may promote innovative transcription factor degrader development in cancer therapy.
FUNDING
This work was financially supported by the National Key Research and Development Project of China (2022YFC3501601), National Natural Sciences Foundation of China (81973505, 82174008, 82030114), and China Postdoctoral Science Foundation (2019M650396), the Fundamental Research Funds for the Central Universities.
Topics: Humans; E2F2 Transcription Factor; Neoplasms; Proteolysis; Transcription Factors; Ubiquitin-Protein Ligases; Ubiquitination
PubMed: 36375317
DOI: 10.1016/j.ebiom.2022.104353 -
Genes & DevelopmentTranscription factors are defined by their sequence-specific binding to DNA and by their selective impacts on gene expression, depending on specific binding sites. The... (Review)
Review
Transcription factors are defined by their sequence-specific binding to DNA and by their selective impacts on gene expression, depending on specific binding sites. The factor binding motifs in the DNA should thus represent a blueprint of regulatory logic, suggesting that transcription factor binding patterns on the genome (e.g., measured by ChIP-seq) should indicate which target genes the factors are directly controlling. However, although genetic data confirm high impacts of transcription factor perturbation in embryology, transcription factors bind to far more sites than the number of genes they dynamically regulate, when measured by direct perturbation in a given cell type. Also, deletion of carefully chosen transcription factor binding sites often gives disappointingly weak results. In a new study in the previous issue of , Lo and colleagues (pp. 1079-1095) reconcile these contradictions by using an elegant experimental system to directly compare the roles of transcription factor-binding site interaction in gene regulation maintenance with roles of the same factor-site interactions in gene regulation through developmental change. They examine Oct4:Sox2 shared target genes under maintained versus reinduced pluripotency conditions within the same cell clone. The results show that the same factor-site interaction impacts can appear modest in assays in developmental steady-state but are far more important as regulatory catalysts of developmental change.
Topics: Transcription Factors; Embryonic Stem Cells; Gene Expression Regulation; Binding Sites; Octamer Transcription Factor-3; DNA; SOXB1 Transcription Factors; Cell Differentiation
PubMed: 36622807
DOI: 10.1101/gad.350308.122 -
Blood Reviews Jan 2017Recent years have seen increasing recognition of a subgroup of inherited platelet function disorders which are due to defects in transcription factors that are required... (Review)
Review
Recent years have seen increasing recognition of a subgroup of inherited platelet function disorders which are due to defects in transcription factors that are required to regulate megakaryopoiesis and platelet production. Thus, germline mutations in the genes encoding the haematopoietic transcription factors RUNX1, GATA-1, FLI1, GFI1b and ETV6 have been associated with both quantitative and qualitative platelet abnormalities, and variable bleeding symptoms in the affected patients. Some of the transcription factor defects are also associated with an increased predisposition to haematologic malignancies (RUNX1, ETV6), abnormal erythropoiesis (GATA-1, GFI1b, ETV6) and immune dysfunction (FLI1). The persistence of MYH10 expression in platelets is a surrogate marker for FLI1 and RUNX1 defects. Characterisation of the transcription factor defects that give rise to platelet function disorders, and of the genes that are differentially regulated as a result, are yielding insights into the roles of these genes in platelet formation and function.
Topics: Blood Platelet Disorders; Blood Platelets; Disease Susceptibility; Gene Expression Regulation; Germ-Line Mutation; Hemostasis; Humans; Structure-Activity Relationship; Thrombopoiesis; Transcription Factors
PubMed: 27450272
DOI: 10.1016/j.blre.2016.07.002 -
Biosensors Mar 2023Transcription factor (TF)-based biosensors are widely used for the detection of metabolites and the regulation of cellular pathways in response to metabolites. Several... (Review)
Review
Transcription factor (TF)-based biosensors are widely used for the detection of metabolites and the regulation of cellular pathways in response to metabolites. Several challenges hinder the direct application of TF-based sensors to new hosts or metabolic pathways, which often requires extensive tuning to achieve the optimal performance. These tuning strategies can involve transcriptional or translational control depending on the parameter of interest. In this review, we highlight recent strategies for engineering TF-based biosensors to obtain the desired performance and discuss additional design considerations that may influence a biosensor's performance. We also examine applications of these sensors and suggest important areas for further work to continue the advancement of small-molecule biosensors.
Topics: Transcription Factors; Metabolic Engineering; Biosensing Techniques
PubMed: 37185503
DOI: 10.3390/bios13040428 -
Microbiology (Reading, England) Aug 2023Evolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Transcription factors can gain or...
Evolutionary innovation of transcription factors frequently drives phenotypic diversification and adaptation to environmental change. Transcription factors can gain or lose connections to target genes, resulting in novel regulatory responses and phenotypes. However the frequency of functional adaptation varies between different regulators, even when they are closely related. To identify factors influencing propensity for innovation, we utilise a SBW25 strain rendered incapable of flagellar mediated motility in soft-agar plates via deletion of the flagellar master regulator (). This bacterium can evolve to rescue flagellar motility via gene regulatory network rewiring of an alternative transcription factor to rescue activity of FleQ. Previously, we have identified two members (out of 22) of the RpoN-dependent enhancer binding protein (RpoN-EBP) family of transcription factors (NtrC and PFLU1132) that are capable of innovating in this way. These two transcription factors rescue motility repeatably and reliably in a strict hierarchy – with NtrC the only route in a ∆ background, and PFLU1132 the only route in a ∆∆ background. However, why other members in the same transcription factor family have not been observed to rescue flagellar activity is unclear. Previous work shows that protein homology cannot explain this pattern within the protein family (RpoN-EBPs), and mutations in strains that rescued motility suggested high levels of transcription factor expression and activation drive innovation. We predict that mutations that increase expression of the transcription factor are vital to unlock evolutionary potential for innovation. Here, we construct titratable expression mutant lines for 11 of the RpoN-EBPs in . We show that in five additional RpoN-EBPs (FleR, HbcR, GcsR, DctD, AauR and PFLU2209), high expression levels result in different mutations conferring motility rescue, suggesting alternative rewiring pathways. Our results indicate that expression levels (and not protein homology) of RpoN-EBPs are a key constraining factor in determining evolutionary potential for innovation. This suggests that transcription factors that can achieve high expression through few mutational changes, or transcription factors that are active in the selective environment, are more likely to innovate and contribute to adaptive gene regulatory network evolution.
Topics: Transcription Factors; Transcription, Genetic; Gene Expression Regulation; Pseudomonas fluorescens; Gene Expression Regulation, Bacterial; Bacterial Proteins
PubMed: 37584667
DOI: 10.1099/mic.0.001378 -
Molecular Cell Nov 2022Many principles of bacterial gene regulation have been foundational to understanding mechanisms of eukaryotic transcription. However, stark structural and functional... (Review)
Review
Many principles of bacterial gene regulation have been foundational to understanding mechanisms of eukaryotic transcription. However, stark structural and functional differences exist between eukaryotic and bacterial transcription factors that complicate inferring properties of the eukaryotic system from that of bacteria. Here, we review those differences, focusing on the impact of intrinsically disordered regions on the thermodynamic and kinetic parameters governing eukaryotic transcription factor interactions-both with other proteins and with chromatin. The prevalence of unstructured domains in eukaryotic transcription factors as well as their known impact on function call for more sophisticated knowledge of what mechanisms they support. Using the evidence available to date, we posit that intrinsically disordered regions are necessary for the complex and integrative functions of eukaryotic transcription factors and that only by understanding their rich biochemistry can we develop a deep molecular understanding of their regulatory mechanisms.
Topics: Transcription Factors; Eukaryota; Eukaryotic Cells; Gene Expression Regulation; Intrinsically Disordered Proteins
PubMed: 36265487
DOI: 10.1016/j.molcel.2022.09.021 -
Journal of Virology Oct 2020Viruses commonly antagonize the antiviral type I interferon response by targeting signal transducer and activator of transcription 1 (STAT1) and STAT2, key mediators of... (Review)
Review
Viruses commonly antagonize the antiviral type I interferon response by targeting signal transducer and activator of transcription 1 (STAT1) and STAT2, key mediators of interferon signaling. Other STAT family members mediate signaling by diverse cytokines important to infection, but their relationship with viruses is more complex. Importantly, virus-STAT interaction can be antagonistic or stimulatory depending on diverse viral and cellular factors. While STAT antagonism can suppress immune pathways, many viruses promote activation of specific STATs to support viral gene expression and/or produce cellular conditions conducive to infection. It is also becoming increasingly clear that viruses can hijack noncanonical STAT functions to benefit infection. For a number of viruses, STAT function is dynamically modulated through infection as requirements for replication change. Given the critical role of STATs in infection by diverse viruses, the virus-STAT interface is an attractive target for the development of antivirals and live-attenuated viral vaccines. Here, we review current understanding of the complex and dynamic virus-STAT interface and discuss how this relationship might be harnessed for medical applications.
Topics: Cytokines; Gene Expression; Host-Pathogen Interactions; Immune Evasion; STAT Transcription Factors; STAT1 Transcription Factor; STAT2 Transcription Factor; STAT4 Transcription Factor; STAT6 Transcription Factor; Signal Transduction; Viruses
PubMed: 32847860
DOI: 10.1128/JVI.00856-20 -
Current Genetics Feb 2022The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies... (Review)
Review
The role of general transcription factor TFIIB in transcription extends well beyond its evolutionarily conserved function in initiation. Chromatin localization studies demonstrating binding of TFIIB to both the 5' and 3' ends of genes in a diverse set of eukaryotes strongly suggested a rather unexpected role of the factor in termination. TFIIB indeed plays a role in termination of transcription. TFIIB occupancy of the 3' end is possibly due to its interaction with the termination factors residing there. Interaction of the promoter-bound TFIIB with factors occupying the 3' end of a gene may be the basis of transcription-dependent gene looping. The proximity of the terminator-bound factors with the promoter in a gene loop has the potential to terminate promoter-initiated upstream anti-sense transcription thereby conferring promoter directionality. TFIIB, therefore, is emerging as a factor with pleiotropic roles in the transcription cycle. This could be the reason for preferential targeting of TFIIB by viruses. Further studies are needed to understand the critical role of TFIIB in viral pathogenesis in the context of its newly identified roles in termination, gene looping and promoter directionality.
Topics: Eukaryota; Promoter Regions, Genetic; RNA Polymerase II; Transcription Factor TFIIB; Transcription Factors; Transcription, Genetic
PubMed: 34797379
DOI: 10.1007/s00294-021-01223-x -
The Journal of Experimental Medicine Nov 2010A relatively small cadre of lineage-restricted transcription factors largely orchestrates erythropoiesis, but how these nuclear factors interact to regulate this complex... (Review)
Review
A relatively small cadre of lineage-restricted transcription factors largely orchestrates erythropoiesis, but how these nuclear factors interact to regulate this complex biology is still largely unknown. However, recent technological advances, such as chromatin immunoprecipitation (ChIP) paired with massively parallel sequencing (ChIP-seq), gene expression profiling, and comprehensive bioinformatic analyses, offer new insights into the intricacies of red cell molecular circuits.
Topics: Animals; Basic Helix-Loop-Helix Transcription Factors; Chromatin Immunoprecipitation; Computational Biology; Erythropoiesis; GATA1 Transcription Factor; Gene Expression Profiling; Humans; Kruppel-Like Transcription Factors; Proto-Oncogene Proteins; T-Cell Acute Lymphocytic Leukemia Protein 1; Transcription Factors
PubMed: 21098097
DOI: 10.1084/jem.20102260 -
The Journal of Biological Chemistry May 2023The conversion of signal transducer and activator of transcription (STAT) proteins from latent to active transcription factors is central to cytokine signaling....
The conversion of signal transducer and activator of transcription (STAT) proteins from latent to active transcription factors is central to cytokine signaling. Triggered by their signal-induced tyrosine phosphorylation, it is the assembly of a range of cytokine-specific STAT homo- and heterodimers that marks a key step in the transition of hitherto latent proteins to transcription activators. In contrast, the constitutive self-assembly of latent STATs and how it relates to the functioning of activated STATs is understood less well. To provide a more complete picture, we developed a co-localization-based assay and tested all 28 possible combinations of the seven unphosphorylated STAT (U-STAT) proteins in living cells. We identified five U-STAT homodimers-STAT1, STAT3, STAT4, STAT5A, and STAT5B-and two heterodimers-STAT1:STAT2 and STAT5A:STAT5B-and performed semi-quantitative assessments of the forces and characterizations of binding interfaces that support them. One STAT protein-STAT6-was found to be monomeric. This comprehensive analysis of latent STAT self-assembly lays bare considerable structural and functional diversity in the ways that link STAT dimerization before and after activation.
Topics: Cytokines; Gene Expression Regulation; Phosphorylation; STAT1 Transcription Factor; STAT2 Transcription Factor; STAT3 Transcription Factor; STAT4 Transcription Factor; STAT5 Transcription Factor; Trans-Activators; STAT Transcription Factors; Protein Multimerization
PubMed: 37059181
DOI: 10.1016/j.jbc.2023.104703