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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 -
Journal of Cellular Biochemistry Dec 2016Transcription factors represent the point of convergence of multiple signaling pathways within eukaryotic cells. Deregulated transcription factors contribute to the... (Review)
Review
Transcription factors represent the point of convergence of multiple signaling pathways within eukaryotic cells. Deregulated transcription factors contribute to the pathogenesis of a plethora of human diseases, ranging from diabetes, inflammatory disorders and cardiovascular disease to many cancers, and thus these proteins hold great therapeutic potential. Direct modulation of transcription factor function by small molecules is no longer regarded a Sisyphean task, as recent work in drug discovery has revealed that transcription factors are amenable to drug inhibition. Here in we summarize, recent advances regarding the significance of transcription factors in human diseases and we discuss emerging pharmacological strategies to modulate transcription factor function. J. Cell. Biochem. 117: 2693-2696, 2016. © 2016 Wiley Periodicals, Inc.
Topics: Animals; Drugs, Investigational; Gene Expression Regulation; Humans; Signal Transduction; Transcription Factors
PubMed: 27191703
DOI: 10.1002/jcb.25605 -
Seminars in Cell & Developmental Biology Mar 2020Biophysical parameters that govern transcription factors activity are binding locations across the genome, dwelling time at these regulatory elements and specific... (Review)
Review
Biophysical parameters that govern transcription factors activity are binding locations across the genome, dwelling time at these regulatory elements and specific protein-protein interactions. Most molecular strategies used to develop small compounds that block transcription factors activity have been based on biochemistry and cell biology methods that that do not take into consideration these key biophysical features. Here, we review the advance in the field of transcription factor biology and describe how their interactome and transcriptional regulation on a genome wide scale have been deciphered. We suggest that this new knowledge has the potential to be used to implement innovative research drug discovery program.
Topics: Animals; Gene Regulatory Networks; Humans; Protein Binding; Protein Interaction Maps; Transcription Factors
PubMed: 30172762
DOI: 10.1016/j.semcdb.2018.07.019 -
Sheng Wu Gong Cheng Xue Bao = Chinese... Mar 2021Transcription factor-based biosensors (TFBs) play an essential role in metabolic engineering and synthetic biology. TFBs sense the metabolite concentration signals and... (Review)
Review
Transcription factor-based biosensors (TFBs) play an essential role in metabolic engineering and synthetic biology. TFBs sense the metabolite concentration signals and convert them into specific signal output. They hold high sensitivity, strong specificity, brief analysis speed, and are widely used in response to target metabolites. Here we reviewe the principles of TFBs, the application examples, and challenges faced in recent years in microbial cells, including detecting target metabolite concentrations, high-throughput screening, adaptive laboratory evolutionary selection, and dynamic control. Simultaneously, to overcome the challenges in the application, we also focus on reviewing the performance tuning strategies of TFBs, mainly including traditional and computer-aided tuning strategies. We also discuss the opportunities and challenges that TFBs may face in practical applications, and propose the future research trend.
Topics: Biosensing Techniques; Gene Expression Regulation; Metabolic Engineering; Synthetic Biology; Transcription Factors
PubMed: 33783157
DOI: 10.13345/j.cjb.200641 -
Biotechnology Advances 2024As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental... (Review)
Review
As a sustainable and renewable alternative to petroleum fuels, advanced biofuels shoulder the responsibility of energy saving, emission reduction and environmental protection. Traditional engineering of cell factories for production of advanced biofuels lacks efficient high-throughput screening tools and regulating systems, impeding the improvement of cellular productivity and yield. Transcription factor-based biosensors have been widely applied to monitor and regulate microbial cell factory products due to the advantages of fast detection and in-situ screening. This review updates the design and application of transcription factor-based biosensors tailored for advanced biofuels and related intermediates. The construction and genetic parts selection principle of biosensors are discussed. Strategies to enhance the performance of biosensor, including regulating promoter strength and RBS strength, optimizing plasmid copy number, implementing genetic amplifier, and modulating the structure of transcription factor, have also been summarized. We further review the application of biosensors in high-throughput screening of new metabolic engineering targets, evolution engineering, confirmation of protein function, and dynamic regulation of metabolic flux for higher production of advanced biofuels. At last, we discuss the current limitations and future trends of transcription factor-based biosensors.
Topics: Transcription Factors; Biofuels; Metabolic Engineering; Gene Expression Regulation; Biosensing Techniques
PubMed: 38508427
DOI: 10.1016/j.biotechadv.2024.108339 -
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 -
Experientia Oct 1993Xenopus transcription factor, termed TFIIIA, is the first eukaryotic transcription factor purified to homogeneity and one of the most extensively characterized... (Review)
Review
Xenopus transcription factor, termed TFIIIA, is the first eukaryotic transcription factor purified to homogeneity and one of the most extensively characterized polymerase III gene factors at the levels both of the protein and its gene. It is an abundant protein in oocytes and is specifically required for the 5S RNA gene transcription. It promotes the formation of a stable transcription complex by first binding to the internal control region of the 5S RNA gene through its zinc finger motifs. It contains two structural domains and associates with 5S RNA to form 7S ribonucleoprotein particles in oocytes. Its expression is developmentally controlled at the level of transcription and translation. It participates in the assembly of active chromatin templates and, at least in part, is responsible for the differential expression of two kinds of 5S RNA genes in Xenopus.
Topics: Amino Acid Sequence; Animals; Binding Sites; DNA; Gene Expression Regulation; Molecular Sequence Data; RNA, Ribosomal, 5S; Transcription Factor TFIIIA; Transcription Factors; Xenopus
PubMed: 8224095
DOI: 10.1007/BF01952592 -
BioEssays : News and Reviews in... Apr 2000RNA chain elongation by RNA polymerase II (pol II) is a complex and regulated process which is coordinated with capping, splicing, and polyadenylation of the primary... (Review)
Review
RNA chain elongation by RNA polymerase II (pol II) is a complex and regulated process which is coordinated with capping, splicing, and polyadenylation of the primary transcript. Numerous elongation factors that enable pol II to transcribe faster and/or more efficiently have been purified. SII is one such factor. It helps pol II bypass specific blocks to elongation that are encountered during transcript elongation. SII was first identified biochemically on the basis of its ability to enable pol II to synthesize long transcripts. ((1)) Both the high resolution structure of SII and the details of its novel mechanism of action have been refined through mutagenesis and sophisticated in vitro assays. SII engages transcribing pol II and assists it in bypassing blocks to elongation by stimulating a cryptic, nascent RNA cleavage activity intrinsic to RNA polymerase. The nuclease activity can also result in removal of misincorporated bases from RNA. Molecular genetic experiments in yeast suggest that SII is generally involved in mRNA synthesis in vivo and that it is one type of a growing collection of elongation factors that regulate pol II. In vertebrates, a family of related SII genes has been identified; some of its members are expressed in a tissue-specific manner. The principal challenge now is to understand the isoform-specific functional differences and the biology of regulation exerted by the SII family of proteins on target genes, particularly in multicellular organisms.
Topics: Animals; Humans; Protein Conformation; Protein Isoforms; Transcription Factors; Transcription Factors, General; Transcriptional Elongation Factors
PubMed: 10723030
DOI: 10.1002/(SICI)1521-1878(200004)22:4<327::AID-BIES3>3.0.CO;2-4 -
Immunology and Cell Biology Apr 1996Transcription factors function to regulate gene transcription. They may be constitutively expressed or may only be activated during specific situations. Activator... (Review)
Review
Transcription factors function to regulate gene transcription. They may be constitutively expressed or may only be activated during specific situations. Activator protein-1 (AP-1) is an inducible transcription factor, and is comprised of multiple protein complexes that include the gene products of the fos and jun gene families. Numerous cellular and viral genes contain AP-1 binding sites within their promoters and, accordingly, AP-1 has been shown to play a role in the regulation of both basal and inducible transcription of these genes. fos-related antigen-2 (fra-2) has been found to have both similar and unique properties to that of other fos gene members in terms of its regulation and expression. The analysis and determination of the function of Fra-2 will provide further information on the role of AP-1.
Topics: Animals; DNA-Binding Proteins; Fos-Related Antigen-2; Gene Expression Regulation; Genes, fos; Genes, jun; Humans; Transcription Factor AP-1; Transcription Factors
PubMed: 8723999
DOI: 10.1038/icb.1996.17 -
Methods in Molecular Biology (Clifton,... 2023Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques, such as chromatin...
Reconstruction of gene regulatory networks is a very important but difficult issue in plant sciences. Recently, numerous high-throughput techniques, such as chromatin immunoprecipitation sequencing (ChIP-seq) and DNA affinity purification sequencing (DAP-seq), have been developed to identify the genomic binding landscapes of regulatory factors. To understand the relationships among transcription factors (TFs) and their corresponding binding sites on target genes is usually the first step for elucidating gene regulatory mechanisms. Therefore, a good database for plant TFs and transcription factor binding sites (TFBSs) will be useful for starting a series of complex experiments. In this chapter, PlantPAN (version 3.0) is utilized as an example to explain how bioinformatics systems advance research on gene regulation.
Topics: Binding Sites; Protein Binding; Plants; Transcription Factors; DNA
PubMed: 36264496
DOI: 10.1007/978-1-0716-2815-7_13