Optogenetic control of the horizontally acquired region A reveal its importance to prevent stuck fermentations in a wine yeast
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ABSTRACT:
PROVIDER: PRJEB73885 | ENA |
REPOSITORIES: ENA
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Project description:Emergence of resistance to novel β-lactam β-lactamase inhibitor combinations due to horizontally-acquired AmpC (FOX-4) in Pseudomonas aeruginosa
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Project description:ToxR Antagonizes H-NS Regulation of Horizontally Acquired Genes to Drive Host Colonization.
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Project description:To assess the impact of a higher oligopeptide assimilation mediated by Fot1/2, oligopeptides transporters acquired by HGT on wine yeast cell metabolism in winemaking conditions,we carried out a comparison of transcriptomic profiles of the wine wild type strain 59A and the deletion mutant of FOT1/2 genes during exponential growth.
2016-01-19 | GSE62446 | GEO
Project description:SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to post-transcriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in non-pathogenic Escherichia coli where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of ptsG mRNA which encodes the major glucose transporter. We have discovered new SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli, which recently acquired a quarter of all genes by horizontal gene transfer. We demonstrate that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella-specific sopD mRNA of a secreted virulence protein. The SgrS-sopD interaction is exceptionally selective; we find that sopD2 mRNA whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS owing to a non-productive G:U pair in the potential SgrS-sopD2 RNA duplex versus G:C in SgrS-sopD. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens employ their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing post-transcriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity, and argue that target predictions must consider all-or-none decisions by individual seed nucleotides.
2012-01-20 | GSE34851 | GEO
Project description:SgrS RNA is a model for the large class of Hfq-associated small RNAs that act to post-transcriptionally regulate bacterial mRNAs. The function of SgrS is well-characterized in non-pathogenic Escherichia coli where it was originally shown to counteract glucose-phosphate stress by acting as a repressor of ptsG mRNA which encodes the major glucose transporter. We have discovered new SgrS targets in Salmonella Typhimurium, a pathogen related to E. coli, which recently acquired a quarter of all genes by horizontal gene transfer. We demonstrate that the conserved short seed region of SgrS that recognizes ptsG was recruited to target the Salmonella-specific sopD mRNA of a secreted virulence protein. The SgrS-sopD interaction is exceptionally selective; we find that sopD2 mRNA whose gene arose from sopD duplication during Salmonella evolution, is deaf to SgrS owing to a non-productive G:U pair in the potential SgrS-sopD2 RNA duplex versus G:C in SgrS-sopD. In other words, SgrS discriminates the two virulence factor mRNAs at the level of a single hydrogen bond. Our study suggests that bacterial pathogens employ their large suites of conserved Hfq-associated regulators to integrate horizontally acquired genes into existing post-transcriptional networks, just as conserved transcription factors are recruited to tame foreign genes at the DNA level. The results graphically illustrate the importance of the seed regions of bacterial small RNAs to select new targets with high fidelity, and argue that target predictions must consider all-or-none decisions by individual seed nucleotides. To determine the targets of the small regulatory RNA SgrS in S. Typhimurium, we looked at the effect of a short pulse of SgrS over-expression on the Salmonella transcriptome. To achieve over-expression, the sgrS gene was cloned in the pBAD plasmid and induced with 0.2% L-arabinose for 10 min. We then extracted the total RNA for transcriptional profiling. A strain carrying the pBAD plasmid w/o insert was used as negative control. 3 biological replicates were performed. This sRNA target identification strategy has been described in Papenfort et al; Molecular Microbiology (2006) 62(6), 1674–1688.
2012-01-20 | E-GEOD-34851 | biostudies-arrayexpress
Project description:To assess the impact of a higher oligopeptide assimilation mediated by Fot1/2, oligopeptides transporters acquired by HGT on wine yeast cell metabolism in winemaking conditions,we carried out a comparison of transcriptomic profiles of the wine wild type strain 59A and the deletion mutant of FOT1/2 genes during exponential growth. Two strains (59A and 59A FOT-deleted) at 2 released CO2 time point (5g/L and 10g/L) are analyzed. Each condition are in quadriplicate.
2016-01-19 | E-GEOD-62446 | biostudies-arrayexpress
Project description:Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease. Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C and successive recovery at 46°C were targeted for sampling. Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.
2018-12-31 | GSE118890 | GEO
Project description:TsrA regulates gene expression of horizontally acquired elements in Vibrio cholerae via both H-NS dependent and independent mechanisms
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Project description:Cold acclimation of the thermoacidophilic red alga Galdieria sulphuraria - changes in gene expression and involvement of horizontally acquired genes
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Project description:Vibrio cholerae, the causative agent of the diarrheal disease cholera, poses an ongoing health threat due to its wide repertoire of horizontally acquired elements (HAEs) and virulence factors. New clinical isolates of the bacterium with improved fitness abilities, often associated with HAEs, frequently emerge. The appropriate control and expression of such genetic elements is critical for the bacteria to thrive in different environments. H-NS, the histone-like nucleoid structuring protein, is the best studied xenogeneic silencer of HAEs in gamma-proteobacteria. Although H-NS and other highly abundant nucleoid-associated proteins (NAPs) have been shown to play important roles in regulating HAEs and virulence in model bacteria, we still lack a comprehensive understanding of how different NAPs modulate transcription in V. cholerae. By obtaining genome-wide measurements of protein occupancy and active transcription in a clinical isolate of V. cholerae, harboring recently-discovered HAEs encoding for phage defense systems, we show that lack of H-NS causes a robust increase on the expression of genes found in many HAEs. We further found that TsrA, a protein with partial homology to H-NS, regulates virulence genes primarily through modulation of H-NS activity, but we also found a few sites that are affected by TsrA independently of H-NS. Our results demonstrate how the combinatorial activity of NAPs is employed by a clinical isolate of an important pathogen to regulate recently-discovered HAEs.
2024-02-09 | GSE250405 | GEO