Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR25406939_1.fastq.gz | Fastqsanger.gz | |||
| SRR25406939_2.fastq.gz | Fastqsanger.gz | |||
| SRR25406940_1.fastq.gz | Fastqsanger.gz | |||
| SRR25406940_2.fastq.gz | Fastqsanger.gz | |||
| SRR25406941_1.fastq.gz | Fastqsanger.gz |
Items per page: 5 1 - 5 of 8 |
Similar Datasets
Project description:E. Coli DHFR Deep Mutational Scanning
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Project description:Gene variants leading to insertions or deletions of amino acid residues (indels) often have detrimental consequences for the folding of the encoded protein. Yet at some positions indels are tolerated or only result in partial unfolding. Typically unfolded proteins are targeted for protein quality control (PQC) degradation via ubiquitin-proteasome system, which in yeast is mediated by specific E3 ubiquitin-protein ligases, including Ubr1 and San1. Here we systematically probed the folding of a library of indel variants in the DHFR protein using sensitive yeast-based protein folding reporter. We show that deletion of Ubr1 and San1 leads to a greater fraction of folded DHFR indel variants, primarily positioned towards the N- and C-termini regions in DHFR. Intriguingly, most of the DHFR indels that are structurally stabilized in the E3 knockout strains, are also stabilized at lowered temperatures and upon binding the DHFR inhibitor methotrexate. This suggests that blocking PQC degradation can restore function to partially unfolded hypomorph variants, thus providing a potential therapeutic avenue for protein misfolding diseases.
2025-12-22 | GSE302176 | GEO
Project description:Dihydrofolate reductase (DHFR) is a prominent molecular target in antitumor, antibacterial and antiprotozoan chemotherapies. Our in silico amino acid sequence and 3D structure analyses revealed the presence of several putative CK2 phosphorylation sites. Indeed, CK2α subunit phosphorylated DHFR in vitro. In order to identify phosphorylation site we used site-directed mutagenesis to obtain several DHFR mutants with predicted CK2-phosphorylable serine or threonine residues substituted with alanines. All enzyme forms were subjected to in vitro phosphorylation by CK2α subunit. The results pointed to serine 168. Mass spectrometry analyses revealed the presence of additional phosphoserine 145. Phosphorylation by CK2α of S145A mutant and lack of phosphorylation of S145A/S168A double mutant may indicate that S145 phosphorylation may occur only when serine 168 is already phosphorylated. The effect of these and other mutations on enzyme catalytic activity was also investigated.
2019-04-15 | PXD011853 | Pride
Project description:Pseudovirus deep mutational scanning system mutant library of HIV Env TRO11
| PRJNA1217050 | ENA
Project description:The goal of this study was to determine how the method of pooling (combining mutants) for bacteral Tn libraries affected mutant distribution. Previously we generated a pooled version of a~6,800 Tn mutant library in Enterococcus faecalis OG1RF by plating and scraping individual mutants. Here, we combined liquid cultures grown in deep well plates. DNA from the new pooled library was extracted, and TnSeq was used to compare mutant distribution between the old (plate scraping) and new (liquid pooling) Tn library formats. This is important because it will guide best practices for handling large collections of bacterial mutants.
2023-05-22 | GSE233193 | GEO
Project description:We investigated the influence of genome position on propensity to amplify. First, we integrated a mutant form of DHFR into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells. We observed site specific differences in methotrexate sensitivity, organization of amplicons and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site. We introduced a mutant form of DHFR (L22F), which confers greater resistance to methotrexate than the wild type (endogenous) gene into HCT116+chr3 cells and isolated independent clones containing DHFR* at different positions in the genome and identified genome sequences flanking the integration site of DHFR* using inverse PCR. For further analysis, we selected only clones, which were considered to have a single insertion of DHFR* by inverse PCR (13 independent insertion sites). The individual insertion site clones were further characterized with respect to genome copy number profiles. To select methotrexate resistant colonies, we exposed cells to a concentration of methotrexate that was three to four times the IC-50 for each integration site. Genomic copy number profiles were obtained for isolated resistant colonies (GSE6262) by using UCSF HumArray platform (GPL4421). Twelve methotrexate resistant colonies (four different integration sites) were selected for microarray analysis of gene expression at the mRNA level. The untreated integration site clone was used as the reference (Cy5 labeled cDNA) for each of the hybridizations with its respective resistant colonies (Cy3 labeled cDNA). Hybridizations were carried out on arrays of printed long oligonucleotides (70mers) containing 21,000 elements (Operon V2.0, printed in J. David Gladstone Institutes, Genomics Core Laboratory).
2007-10-08 | E-GEOD-6361 | biostudies-arrayexpress
Project description:To identify whether DHFR deficiency affects neurogenesis by modulating H3K4me3 methylation marks.
2022-12-31 | GSE206407 | GEO