Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1199164 | ENA |
REPOSITORIES: ENA
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Project description:The screen for genes involved in the spontaneous loss of heterozygosity mutagenesis (SLM) in diploid cells was done on the collections of deletion strains of Saccharomyces cerevisiae created by the Saccharomyces Genome Deletion Project (http://www-sequence.stanford.edu/group/yeast_deletion_project/). Screens were performed on the pools of clones. Barcode microarrays were used to detect the increased SLM frequency leading to relative increase in abundance of deletion clone in a pool. Collections used were: Homozygous Diploid (HD) and Essential (E) mixed to create single HDE pool. Three mutagenesis markers were used: (1) naturally existing mating type locus, and two newly introduced markers, (2) CAN1/can1delta, (3) URA3/ura3delta. <br>1. To detect the increased SLM frequency at the mating type locus HDE pool was crossed to MATa or MATalpha strain. Deletion clones that gained mating competence due to loss of heterozygosity (LOH) at the mating type locus gave rise to clones with the ability to grow on minimal medium. The relative abundance of these clones was compared to the abundance in the original HDE pool.<br>2. To detect the increased SLM frequency at the CAN1/can1delta locus the derivative HDE pool was created. Every cell of this pool had one of two copies of CAN1 gene deleted. The increased SLM frequency led to increased relative abundance of respective deletion clone under canavanine selection and could be estimated by comparing it to the abundance when pool was grown without selection.<br>3. To detect the increased SLM frequency at the URA3/ura3delta locus the derivative HDE pool was created. Every cell of this pool had one of two copies of URA3 gene deleted. The increased SLM frequency led to increased relative abundance of respective deletion clone under 5M-^R-fluoroorotic acid selection and could be estimated by comparing it to the abundance when pool was grown without selection.<br>4. For screens of SLM at CAN1 and URA3 markers the resistance control experiments were performed to detect genes whose deletion is sufficient to enable yeast cells with functional CAN1 or URA3 to grow in the presence of canavanine or 5M-^R- fluoroorotic acid respectively.<br>5. To include in the analysis slow-growing deletion clones control hybridizations were performed to detect genes whose deletion extends the doubling time of yeast cells.<br>
2011-06-28 | E-MEXP-2685 | biostudies-arrayexpress
Project description:Transcriptional regulation plays an important role in the control of gene expression during aging. However, translation efficiency likely plays an equally important role in determining protein abundance, but has been relatively under studied in this context. Here we used RNA-seq and ribosome profiling to investigate the role of translational regulation in lifespan extension by CAN1 gene deletion in yeast. Through comparison of the transcriptional and translational changes in cells lacking CAN1 with other long-lived mutants, we were able to identify critical regulatory factors, including transcription factors and mRNA-binding proteins, that coordinate transcriptional and translational responses. Together, our data support a model in which deletion of CAN1 extends replicative lifespan through increased translation of proteins that facilitate cellular response to stress. This study extends our understanding of the importance of translational control in regulating stress resistance and longevity.
2017-02-20 | GSE85198 | GEO
Project description:Ionophores are antibacterial compounds that affect bacterial growth by changing intracellular concentrations of the essential cations, sodium and potassium. They are extensively used in animal husbandry to increase productivity and reduce infectious diseases. Given their widespread usage, it is important to determine the potential negative consequences of ionophore use on human and animal health. In this study, we demonstrate that exposure to the ionophore monensin can select for resistant mutants in the human and animal pathogen Staphylococcus aureus, with a majority of the resistant mutants showing increased growth rates in vitro and/or in mice. Whole-genome sequencing and proteomics analysis of the resistant mutants show that the resistance phenotype is associated with de-repression of de novo purine synthesis, which could be achieved through mutations in different transcriptional regulators including mutations in the gene purR, the repressor of the purine de novo synthesis pathway. This study shows that mutants with reduced susceptibility to the ionophore monensin can be readily selected and highlights an unexplored link between ionophore resistance, purine metabolism and fitness in pathogenic bacteria.
2024-01-09 | PXD047199 | Pride
Project description:We treated C. albicans reference strain SC5314 with 20ng/ml of aureobasidin A, and obtained two mutants which were resistant to aureobasidin A. Then we did whole genome sequencing of these two mutants.
2020-04-09 | E-MTAB-8942 | biostudies-arrayexpress
Project description:This project aimed to investigate the effects of glyphosate-based herbicide Roundup LB Plus on bacteria. For this, ten environmental strains of Salmonella enterica were exposed to the increasing concentrations of Roundup over several passages to obtain Roundup-resistant mutants. Four stable re-sequenced resistant mutants and their respective ancestors were characterized by global proteomics in the presence and absence of sub-inhibitory (1/4xMIC) concentrations of the herbicide. By comparing the proteomes of the Roundup-challenged ancestors with constitutive non-challenged ancestors, it became possible to deepen the understanding of how Roundup stress affects naïve bacteria. Similarly, comparing Mutants versus Ancestors in the absence of Roundup allowed to understand how Roundup resistance constitutively affects bacterial physiology, while the comparison of Roundup-challenged mutants versus constitutive mutants helped improve the understanding of the inducible responses in the resistant background.
2020-09-22 | PXD019463 | Pride
Project description:Discovery of the genome-wide location of proteins using ChIP-Seq has allowed global mapping of the key transcription factors and chromatin regulators that control gene expression programs in various cells. Many DNA-associated processes are targeted for disease therapy. This study investigates the functions of small molecule therapeutics that target DNA-associated processes involved of CDK9 and BRD4. Genomic DNA was enriched by chromatin immunoprecipitation (ChIP) and analyzed by Solexa sequencing. ChIP was performed using an antibody against RNAP2, BRD4, CDK9, and CTCF using whole cell extract (WCE) as a background control.
2013-04-23 | E-GEOD-43743 | biostudies-arrayexpress
Project description:All yeast strains were in the genetic background W303-1A (MATa leu2-3,112 trp1-1 ura3-1 can1-100 ade2-1 his3-11,15). Gene expression profiles of the following mutant strains were compared with WT: YIA29 (mdl1::HIS3); YIA30 (yme1::KAN); YIA31 (mdl1::HIS3 yme1::KAN); 2 independent RNA preparations per strain were used (A and B); 2 independent array hybridisations per RNA preparation were performed (color switch experiments).
2005-12-31 | E-EMBL-5 | biostudies-arrayexpress
Project description:We investigated the effect of canavanine (toxic Arg analogue) treatment on U251MG and U87MG cell lines using a variety of methods including proteomics. Since 3rd isotope of unmodified peptide cannot be resolved from canavanine containing peptide even at extremely high resolutions of 480K we incorporated R13C615N4 into peptides to avoid MS1 overlap of Arg signals.
2020-10-19 | PXD019044 | Pride
Project description:Aflatoxin contamination caused by Aspergillus flavus in peanut is a serious constraint for food safety and human health. However, molecular mechanism/s underlying the defense response is poorly understood. A comparative proteomic analysis was carried out between two contrasting peanut genotypes, JL24 (WT-susceptible) and a near-isogenic transgenic event (OE-Def) in the same background expressing defensin gene (resistant) with different time points, To understand the proteome changes in OE-Def and WT control lines, a label-free quantitative proteomics analysis was performed at 0, 24, 40, 56 and 72 h after A. flavus inoculation using UPLC-ESI-MS/MS. Several resistance proteins in the secondary metabolic pathways related to phenylpropanoids, flavonoids, and fatty acid biosynthesis were strongly induced in the resistant genotype.
2021-07-15 | PXD027315 | JPOST Repository