Dataset Information

Adaptive Laboratory Evolution of E. coli towards usage of fluoroindole

ABSTRACT: Although fluorine is abundant in the earth’s crust, it is scarcely found in biomolecules. Adaptive laboratory evolution (ALE) experiments were conducted to introduce organofluorine into living microorganisms. By cultivating Escherichia coli with fluorinated indole analogs, microbial cells evolved that relinquished their dependence on indole and are instead capable of utilizing either 6-fluoroindole (6Fi) or 7-fluoroindole (7Fi) for growth (TrpS-catalyzed in-situ conversion of fluoroindole into fluorotryptophan (FTrp) and TrpRS-catalyzed incorporation of FTrp in context of protein biosynthesis). Consistent and complete adaptation of microbial populations was achieved and the quantitative proteome-wide replacement of Trp by either 6FTrp or 7FTrp was confirmed by nano-LC-MSMS. The dataset comprises the ancestral strain TUB00, two positive controls W-TUB165 and Ind-TUB165 (adapted to grow on tryptophan and indole), three 6Fi adapted lineages 6TUB128-OC, 6TUB165-MB4, 6TUB165-MB3 and two 7Fi adapted lineages 7TUB165-OC and 7TUB165-MB.

INSTRUMENT(S): LTQ Orbitrap Velos

ORGANISM(S): Escherichia Coli

SUBMITTER: Lorenz Adrian

LAB HEAD: Beate Koksch

PROVIDER: PXD048225 | Pride | 2024-01-08

REPOSITORIES: Pride

ACCESS DATA

Similar Datasets

Project description:Background: Malignant ascites is often present at diagnostic in women with advanced ovarian cancer (OC) and its presence is associated with a worse outcome. Human peritoneal mesothelial cells (HPMCs) are key components of malignant ascites. Although the interplay between HPMCs and OC cells is believed to be critical for tumor progression, it has not been well characterized. The purpose of this study was to assess the effect of ascites on HPMCs and clarify the role of HPMCs in OC progression. Methods: Human OC ascites and benign peritoneal fluids were assessed for their ability to stimulate HPMC proliferation. Conditioned medium from ascites- and benign fluid-stimulated HPMCs were compared for their ability to attenuate apoptosis induced by TNF-related apoptosis-inducing ligand (TRAIL). We conducted a comparative analysis of global expression changes in ascites-stimulated HPMCs using Agilent oligonucleotide microarrays. Results: As compared to benign peritoneal fluids, malignant ascites stimulated the proliferation of HPMCs. TRAIL-induced apoptosis was attenuated in OC cells exposed to conditioned medium from ascites-stimulated HPMCs as compared to OC cells exposed to conditioned medium from benign fluid-stimulated HPMCs. A total of 649 genes were differentially expressed in ascites-stimulated HPMCs. Based on a ratio of more than 1.5-fold and a P < 0.05, 484 genes were up-regulated and 165 genes were down-regulated in ascites-exposed HPMCs. Stimulation of HPMCs with OC ascites resulted in differential expression of genes mainly associated with the regulation of cell growth and proliferation, cell death, cell cycle and cell assembly and organization, compared to benign peritoneal fluids. Top networks up-regulated by OC ascites included Akt and NF-M-NM-:B survival pathways whereas vascular endothelial growth factor (VEGF) pathway was down-regulated. Conclusions: The results of this study not only provide evidence supporting the importance of the interplay between cancer cells and HPMCs but also define the role that the tumor environment plays in these interactions. The expression profiles from human peritoneal mesothelial cells (HPMC) cultures exposed to peritoneal fluids and ovarian cancer ascites were compared using the Agilent Whole Human Genome Oligonucleotide microarrays, containing 44,000 genes. Microarrays were performed on HPMCs exposed to 3 malignant ascites from women with advanced (stage III/IV) serous OC and two benign peritoneal fluids. First, we generated lists of significantly up-regulated and down-regulated genes that were differentially expressed between OC ascites (OVC346, OVC508 and OVC509) and control OV370 peritoneal fluid. Then, the set of genes that were commonly expressed between control peritoneal fluids (OV370 and OV401) were subtracted from the first list of genes to generate a dataset of differentially expressed genes between malignant ascites and benign peritoneal fluids.

Dataset Information

Adaptive Laboratory Evolution of E. coli towards usage of fluoroindole

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure