Development of novel molecular tools for targeting protein degradation
Ontology highlight
ABSTRACT:
ORGANISM(S): Homo Sapiens
SUBMITTER: 
Fengli Qu
PROVIDER: PXD063360 | iProX | Fri Apr 25 00:00:00 BST 2025
REPOSITORIES: iProX
Similar Datasets
Project description:Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval of information on the metabolic net. Information on gene localization from genome surveys was correlated to signals of putative hosts to generate phylogenetic community information. Hence, this novel array system was validated using genomic DNA of genome sequenced bacterial strains hosting biodegradation functions and applied to genomic DNA and RNA extracted from environmental samples under aromatic pollution pressure.
2012-12-31 | GSE30303 | GEO
Project description:Despite various efforts to develop tools to detect and compare the activity and catabolic potential and activity for pollutant degradation of microorganisms in environmental samples, an open-source, curated and reliable method is still required. Here we report on a customize normalization system that can be applied to any microarray design, allowing the assessment of reliability of signals and enabling cross-experiment comparisons. Probes for the underlying catabolic gene array were designed based on manually curated databases for catabolic key genes. Signals were assigned to the respective catabolic protein subfamily that allows to inferring the functions and substrate specificity. The placement of probes for critical degradation nodes and subsequent metabolic steps allows the retrieval of information on the metabolic net. Information on gene localization from genome surveys was correlated to signals of putative hosts to generate phylogenetic community information. Hence, this novel array system was validated using genomic DNA of genome sequenced bacterial strains hosting biodegradation functions and applied to genomic DNA and RNA extracted from environmental samples under aromatic pollution pressure. Catabolic microarray was optimized for detection and expression of catabolic genes involved in the degradation of pollutant compounds using genome genomic DNA of type strains: Burkholderia xenovorans LB400, Cupriavidus necator JMP134, Pseudomonas putida F1 and Sphingomonas wittichii RW1. Afterwards, this microarray was applied for environmental samples. For microcosm experiments, 200 ml of each groundwater were incubated in closed 1 l Erlenmeyer flasks at 20 degree C and 50 rpm. Second sets of 200 ml microcosms were supplemented with naphthalene (100 mg), which had above been identified as a contaminant present in both groundwaters in similar amounts. Naphthalene was supplied via the vapor phase and incubated under identical conditions as the control microcosms. After 4 days of incubations, 50 ml of each of the 4 microcosms were subjected to genomic DNA extraction and another 50 ml to RNA extraction.
2012-12-31 | E-GEOD-30303 | biostudies-arrayexpress
Project description:The study aims essentially at the characterisation of suberin degradation mechanisms by Aspergillus nidulans, at a fundamental level. Suberin is an important protective barrier in plant, thus the study of its biodegradation significantly impacts on phytopatology. In addition, fungal suberin degrading enzymes might provide important insights to develop new waste management, bioremediation and biodeterioration prevention strategies.
2014-07-31 | GSE54427 | GEO
Project description:As a member of the 11S proteasome family, REGγ facilitates ubiquitin-independent protein degradation. Previous studies have largely concentrated on the effects of substrate protein degradation. However, the mechanism by which REGγ recognizes substrate proteins and the substrate selectivity of REGγ remained unclear. In this study, we discovered that the multiple substrate proteins of REGγ contain the RKRR conserved sequence. Subsequently, the degron of REGγ, RR(K)R(K)R, was ascertained through site mutation, BLI, and Cryo-EM analysis. Consequently, the recognition mechanism of REGγ and its substrate proteins was clarified. Simultaneously, the number of substrates was expanded through a combination of interactome and degron analysis. Moreover, we successfully constructed a targeted protein degradation system that utilizes the degron of REGγ, thereby providing a novel approach for targeted protein degradation.
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Project description:Introduction: Emerging evidence suggests long non-coding RNA (lncRNA) H19 is associated with osteoarthritis (OA) pathology. However, how H19 contributes to OA has not been reported. This study aims to investigate the biological function of H19 in OA subchondral bone remodeling and OA progression. Methods: Clinical joint samples and OA animal models induced by medial meniscus destabilization (DMM) surgery were used to verify the causal relationship between osteocyte H19 and OA subchondral bone and cartilage changes. MLO-Y4 osteocyte cells subjected to fluid shear stress were used to verify the mechanism underlying H19-mediated mechano-response. Finally, the antisense oligonucleotide (ASO) against H19 was delivered to mice knee joints by magnetic metal-organic framework (MMOF) nanoparticles in order to develop a site-specific delivery method for targeting osteocyte H19 for OA treatment. Results: Both clinical OA subchondral bone and wildtype mice with DMM-induced OA exhibit aberrant higher subchondral bone mass with more H19 expressing osteocytes. On the contrary, osteocyte-specific deletion of H19 mice is less vulnerable to DMM-induced OA phenotype. In MLO-Y4 cells, H19-mediated osteocyte mechano-response through PI3K/AKT/GSK3 signals activation by EZH2-induced H3K27me3 regulation on PP2A inhibition. Targeted inhibition of H19 (using ASO-loaded MMOF) substantially alleviates subchondral bone remodeling and OA phenotype. Discussion: In summary, our results provide new evidence that the elevated H19 expression in osteocytes may contribute to aberrant subchondral bone remodeling and OA progression. H19 appears to be required for the osteocyte response to mechanical stimulation, and targeting H19 represents a new promising approach for OA treatment.
2025-03-05 | GSE254053 | GEO
Project description:Brown rot fungi have great potential in biorefinery wood conversion systems, because they are the primary wood decomposers in coniferous forests and have an efficient lignocellulose degrading system. Their initial wood degradation mechanism is thought to consist of an oxidative radical-based system that acts sequentially with an enzymatic saccharification system, but the complete molecular mechanism of this system has not yet been elucidated. Some studies have shown that wood degradation mechanisms of brown rot fungi have diversity in their substrate selectivity. Gloeophyllum trabeum, one of the most studied brown rot species, has broad substrate selectivity and even can degrade some grasses. However, the basis for this broad substrate specificity is poorly understood. In this study, we performed RNA-seq analyses on G. trabeum grown on media containing glucose, cellulose, or Japanese cedar (Cryptomeria japonica) as the sole carbon source. Beyond the gene expression on glucose, 1129 genes were upregulated on cellulose and 1516 genes were upregulated on cedar. Carbohydrate Active enZyme (CAZyme) genes upregulated on cellulose and cedar media by G. trabeum included GH12, GH131, CE1, AA3_1, AA3_2, AA3_4 and AA9, which is a newly reported expression pattern for brown rot fungi. The upregulation of both terpene synthase and cytochrome P450 genes on cedar media suggests the potential importance of these genes in the production of secondary metabolites associated with the chelator-mediated Fenton reaction. These results provide new insights into the inherent wood degradation mechanism of G. trabeum and the diversity of brown rot mechanisms.
2020-08-05 | GSE155681 | GEO
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2025-08-04 | PXD063179 | Pride
Project description:E3 ubiquitin ligases of the Cullin RING Ligase (CRL) family assemble into multiprotein complexes to diversify substrate adaptors and ensure selectivity in substrate engagement for degradation. Here we show a novel mechanism whereby mutations in substrate adaptors can drive neo-substrate degradation in cancer. KBTBD4 is a CRL3 substrate adaptor harbouring recurrent indel mutations in a subset of non-WNT/non-SHH medulloblastomas. We show that these mutations, arising in the substrate recognition domain of KBTBD4, promote the recruitment and ubiquitylation of the REST Corepressor (CoREST), which forms a complex to modulate chromatin accessibility and transcriptional programmes. We observe that this neomorphic activity of KBTBD4 mutants induces changes in epigenetic markers and significant alterations in transcription, diverting normal cellular programmes towards increased stemness. These results highlight mutation-driven neomorphic E3 ligase activity as a previously unrecognised mechanism in tumorigenesis, with implications for medulloblastoma pathogenesis and treatment.
2022-03-30 | GSE197240 | GEO
Project description:Regulation of the stability of epigenetic regulators offers unique opportunities for epigenetic therapies. However, this strategy has been poorly explored. Here we report that the E3 ubiquitin ligase UBE3A binds and ubiquitylates the histone H3-lysine 4-methyltransferase MLL4 (aka KMT2D) as a new substrate for degradation. Using Ube3a knockout and UBE3A-overexpressing transgenic mouse models, we show that, in the liver, UBE3A levels are inversely correlated with levels of MLL4, its functional surrogate marker H3-lysine 4-monomethylation, and expression of the recently identified steatosis target genes of MLL4. Consistently, Ube3a knockout mice are highly susceptible to high-fat diet-induced steatosis relative to their littermate control mice, and this phenotype is rescued by deletion of a copy of Mll4. Therefore, UBE3A indirectly exerts an epigenetic gene regulation activity through targeting MLL4 for degradation. Also this UBE3A-MLL4 axis presents a novel therapeutic venue for treating various MLL4-directed pathogeneses.
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