PROTein Evolution Using Selection (PROTEUS)
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1054169 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR27276546_1.fastq.gz | Fastqsanger.gz | |||
| SRR27276547_1.fastq.gz | Fastqsanger.gz | |||
| SRR27276548_1.fastq.gz | Fastqsanger.gz | |||
| SRR27276549_1.fastq.gz | Fastqsanger.gz | |||
| SRR27276550_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 148 |
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Project description:Directed evolution (DE) is a process of mutation and iterative artificial selection to breed biomolecules with new or improved activity. DE platforms are primarily prokaryotic or yeast-based, and stable highly mutagenic mammalian systems have been challenging to establish and apply. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform, consisting of a minimal modified Semliki Forest virus genome controlling expression of the Indiana vesiculovirus G coat protein, is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a novel DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is a robust, efficient, and stable platform to direct evolution of biomolecules within mammalian cells.
2025-04-03 | GSE250500 | GEO
Project description:Directed evolution (DE) is a process of mutation and iterative artificial selection to breed biomolecules with new or improved activity. DE platforms are primarily prokaryotic or yeast-based, and stable highly mutagenic mammalian systems have been challenging to establish and apply. To this end, we developed PROTein Evolution Using Selection (PROTEUS), a new platform that uses chimeric virus-like vesicles (VLVs) to enable extended mammalian DE campaigns without loss of system integrity. This platform, consisting of a minimal modified Semliki Forest virus genome controlling expression of the Indiana vesiculovirus G coat protein, is stable and can generate sufficient diversity for DE in mammalian systems. Using PROTEUS, we altered the doxycycline responsiveness of tetracycline-controlled transactivators, generating a more sensitive TetON-4G tool for gene regulation. PROTEUS is also compatible with intracellular nanobody evolution, and we use it to design a novel DNA damage-responsive anti-p53 nanobody. Overall, PROTEUS is a robust, efficient, and stable platform to direct evolution of biomolecules within mammalian cells.
2025-04-03 | GSE250501 | GEO
Project description:PROTein Evolution Using Selection (PROTEUS) [Illumina]
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Project description:PROTein Evolution Using Selection (PROTEUS) [Nanopore]
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Project description:This SuperSeries is composed of the SubSeries listed below.
2025-04-03 | GSE250502 | GEO
Project description:Sexually dimorphic traits are subject to diversifying selection. Also genes with a male biased gene expression are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in rate of evolution for genes with a male biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male biased genes, our data imply a radically different selection regime in D. pseudoobscura. Keywords: SAGE Male and female SAGE libraries of D. pseudoobscura were developed for analyzing the gene expression pattern.
2006-07-27 | E-GEOD-2840 | biostudies-arrayexpress
Project description:Sexually dimorphic traits are subject to diversifying selection. Also genes with a male biased gene expression are probably affected by sexual selection and have a high rate of protein evolution. We used SAGE to measure sex biased gene expression in Drosophila pseudoobscura. Consistent with previous results from D. melanogaster, a larger number of genes were male biased (402 genes) than female biased (138 genes). About 34% of the genes changed the sex related expression pattern between D. melanogaster and D. pseudoobscura. Combining gene expression with protein divergence between both species, we observed a striking difference in rate of evolution for genes with a male biased gene expression in one species only. Contrary to expectations, D. pseudoobscura genes in this category showed no accelerated rate of protein evolution, while D. melanogaster genes did. If sexual selection is driving molecular evolution of male biased genes, our data imply a radically different selection regime in D. pseudoobscura. Keywords: SAGE
2006-07-27 | GSE2840 | GEO
Project description:Directed biomolecular evolution is widely used to tailor and enhance proteins but has hitherto not been applied in the reprogramming of mammalian cells. Here we describe a novel method to identify artificially enhanced and evolved reprogramming factors by pooled screens with randomised protein libraries, cell selection based on phenotypic readouts and genotyping by amplicon sequencing. We benchmark this approach by identifying artificially enhanced Sox2 and Sox17 factors in pluripotency reprogramming.
2018-07-12 | GSE107987 | GEO
Project description:We report a new platform for the rapid phenotypic selection of protein aggregation inhibitors from genetically encoded cyclic peptide libraries in E. coli based on phage-assisted continuous evolution (PACE). Here, we developed a new PACE-compatible selection for protein aggregation inhibition and employed it to identify cyclic peptides that suppress amyloid-β42 (Aβ42) and human islet amyloid polypeptide (hIAPP) aggregation. Additionally, we integrated a negative selection that removes false positives and off-target hits, significantly improving cyclic peptide selectivity. We show that selected inhibitors are active when chemically re-synthesized in in vitro assays. Our platform provides a powerful new approach for the rapid discovery of cyclic peptide inhibitors of protein aggregation and may serve as the basis for the future evolution of cyclic peptides with a broad spectrum of inhibitory activities. Data deposited here are HTS data critical to the conclusions of this study.
2024-10-25 | GSE279094 | GEO
Project description:This series of microarrays compares gene expression by the bacterial pathogen Proteus mirabilis when the transcriptional regulator mrpJ is deleted or induced to levels found during experimental urinary tract infection. The enteric bacterium Proteus mirabilis is associated with a significant number of catheter-associated urinary tract infections. Strict regulation of the antagonistic processes of adhesion and motility, mediated by fimbriae and flagella, respectively, is essential for successful disease progression. Previously, the transcriptional regulator MrpJ, which is encoded by the mrp fimbrial operon, has been shown to repress both swimming and swarming motility. Here we show that MrpJ affects a wide array of cellular processes beyond adherence and motility. Microarray analysis found that expression of mrpJ mimicking expression levels that occur during UTI leads to differential expression of 217 genes related to, among others, bacterial virulence, type VI secretion and metabolism. We probed the molecular mechanism of transcriptional regulation through MrpJ using reporter assays and chromatin immunoprecipitation (ChIP). Two virulence-associated target genes, the flagellar master regulator flhDC and mrp itself, appear to be regulated through a binding site proximal to the transcriptional start, complemented by a more distantly situated enhancer site. Furthermore, an mrpJ deletion mutant colonized the bladders of mice at significantly lower levels in a transurethral model of infection. Additionally, we observe that mrpJ is widely conserved in a collection of recent clinical isolates, leading us to conclude that our results elucidate an unanticipated role of MrpJ as a global regulator of P. mirabilis virulence. Four biological replicates were analyzed for each set of arrays (P. mirabilis HI4320 wild type vs. ΔmrpJ, and vector pLX3607 vs. mrpJ plasmid pLX3805).
2015-04-13 | E-GEOD-63321 | biostudies-arrayexpress