Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR26504034_1.fastq.gz | Fastqsanger.gz | |||
| SRR26504034_2.fastq.gz | Fastqsanger.gz | |||
| SRR26504035_1.fastq.gz | Fastqsanger.gz | |||
| SRR26504035_2.fastq.gz | Fastqsanger.gz | |||
| SRR26504036_1.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:We conducted whole genome sequencing on eight evolved E. coli strains (S1–S8) and the parental wild-type (WT) strain to identify mutations arising from ofloxacin treatments. These strains (S1-S8), generated through fluoroquinolone-mediated adaptive laboratory evolution (ALE), exhibited varying levels of tolerance and resistance. The ALE experiment involved intermittent antibiotic treatments of eight independent cultures over 22 days. The untreated WT strain served as a baseline to pinpoint mutations in the evolved strains.
2024-12-23 | E-MTAB-14682 | biostudies-arrayexpress
Project description:A strain of Acetivibrio thermocellus (colloquially, Clostridium thermocellum) DSM 1313 capable of growing in xylose was created by both rational engineering and adaptive laboratory evolution (ALE) approaches. This RNA-seq experiment compares the transcriptomes of the pre-ALE strain on native substrate with the pre-ALE and post-ALE strains growing in xylose (or xylose plus xylan). These data show the progression of the initially engineered strain from normal growth with a native substrate, to debilitated growth in the new engeered substrate, to improved growth on the engineered substrate after ALE. Genes of various biological functions are found to undergo coordinated changes at various stages of the engineering & ALE campaign. These correlations shed light on the state of the cell at each stage. All together, these data paint a picture of the strain initially undergoing a stress state, which is eventually overcome through ALE. Many of these changes dissipate in the fast growing strain, leaving only permanent changes that enable growth on xylose.
2025-08-31 | GSE276070 | GEO
Project description:Fuel ethanol is now considered a global energy commodity that is fully competitive with gasoline. We have determined genome copy number differences that are common to five industrially important fuel ethanol yeast strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. The fuel strains used were CAT1, BG1, PE2, SA1, and VR1 (note that two independent isolates were analyzed, denoted by "-1" and "-2"). These array-CGH data were compared with array-CGH data from nine other non-fuel industrial yeasts: An ale brewing strain ("Sc-ale"), four wine strains (GSY2A, GSY3A, GSY10A, GSY11B), and 4 bakers' yeast strains (GSY149, GSY150, GSY154, GSY155). Our results reveal significant amplifications of the telomeric SNO and SNZ genes only in the fuel strains, whose protein products are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that these amplifications allow these yeasts to grow efficiently, especially at high sugar concentrations, regardless of the presence or absence of either of the two vitamins. Our results reveal important genetic adaptations that have been selected for in the industrial environment, which may be required for the efficient fermentation of biomass-derived sugars from other renewable feedstocks. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Strain Name: fuel strains used for aCGH
2009-09-24 | GSE13875 | GEO
Project description:Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named “LAbrini”, exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain “LAbrini” to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
2024-06-12 | GSE225123 | GEO
Project description:Fuel ethanol is now considered a global energy commodity that is fully competitive with gasoline. We have determined genome copy number differences that are common to five industrially important fuel ethanol yeast strains responsible for the production of billions of gallons of fuel ethanol per year from sugarcane. The fuel strains used were CAT1, BG1, PE2, SA1, and VR1 (note that two independent isolates were analyzed, denoted by "-1" and "-2"). These array-CGH data were compared with array-CGH data from nine other non-fuel industrial yeasts: An ale brewing strain ("Sc-ale"), four wine strains (GSY2A, GSY3A, GSY10A, GSY11B), and 4 bakers' yeast strains (GSY149, GSY150, GSY154, GSY155). Our results reveal significant amplifications of the telomeric SNO and SNZ genes only in the fuel strains, whose protein products are involved in the biosynthesis of vitamins B6 (pyridoxine) and B1 (thiamin). We show that these amplifications allow these yeasts to grow efficiently, especially at high sugar concentrations, regardless of the presence or absence of either of the two vitamins. Our results reveal important genetic adaptations that have been selected for in the industrial environment, which may be required for the efficient fermentation of biomass-derived sugars from other renewable feedstocks. A strain or line experiment design type assays differences between multiple strains, cultivars, serovars, isolates, lines from organisms of a single species. Strain Name: fuel strains used for aCGH Strain_or_line_design
2010-06-25 | E-GEOD-13875 | biostudies-arrayexpress
Project description:Microbes able to convert gaseous one-carbon (C1) waste feedstocks are increasingly important to transition to the sustainable production of renewable chemicals and fuels. Acetogens are interesting biocatalysts since gas fermentation using Clostridium autoethanogenum has been commercialised. However, most acetogen strains need complex nutrients, display slow growth, and are not robust for bioreactor fermentations. In this work, we used three different and independent adaptive laboratory evolution (ALE) strategies to evolve the wild-type C. autoethanogenum to grow faster, without yeast extract and to be robust in operating continuous bioreactor cultures. Multiple evolved strains with improved phenotypes were isolated on minimal media with one strain, named “LAbrini”, exhibiting superior performance regarding the maximum specific growth rate, product profile, and robustness in continuous cultures. Whole-genome sequencing of the evolved strains identified 25 mutations. Of particular interest are two genes that acquired seven different mutations across the three ALE strategies, potentially as a result of convergent evolution. Reverse genetic engineering of mutations in potentially sporulation-related genes CLAU_3129 (spo0A) and CLAU_1957 recovered all three superior features of our ALE strains through triggering significant proteomic rearrangements. This work provides a robust C. autoethanogenum strain “LAbrini” to accelerate phenotyping and genetic engineering and to better understand acetogen metabolism.
2024-06-12 | PXD047330 | Pride
Project description:Gas-fermenting acetogens, such as Clostridium autoethanogenum, have emerged as promising biocatalysts capable of converting CO and CO2-containing gases into fuels and chemicals relevant for a circular economy. However, functionalities of the majority of genes in acetogens remain uncharacterised, hindering the development of acetogen cell factories through targeted genetic engineering. We previously identified gene targets through adaptive laboratory evolution (ALE) that potentially realise enhanced autotrophic phenotypes in C. autoethanogenum. In this study, we deleted one of the targets – CLAU_0471 (proposed amino acid permease) – with high mutation occurrence in ALE isolates and extensively characterised autotrophic growth of strain RE3 in batch bottle and bioreactor continuous cultures. In addition, we characterized two previously reverse-engineered strains RE1 (deletion of CLAU_3129; putative sporulation transcriptional activator Spo0A) and RE2 (SNP in CLAU_1957; proposed two component transcriptional regulator winged helix family). Strikingly, the strains recovered the superior phenotypes of ALE isolates, including faster autotrophic growth, no need for yeast extract, and robustness in bioreactor operation (e.g. low sensitivity to gas ramping, high biomass, and dilution rates). Notably, RE3 exhibited elevated 2,3-butanediol production while RE1 performed similar to the best-performing previously characterised ALE isolate LAbrini. The three reverse-engineered strains showed similarities in proteome expression and bioinformatic analyses suggest that the targeted genes may be involved in overlapping regulatory networks. Our work provides insights into genotype-phenotype relationships for a better understanding of the metabolism of an industrially-relevant acetogen.
2025-08-12 | PXD062027 | Pride
Project description:To broaden microbial cell factories´ substrate scope towards renewable substrates, rational genetic interventions are often combined with adaptive laboratory evolution (ALE). However, comprehensive studies enabling a holistic understanding of adaptation processes primed by detailed knowledge of metabolism remain scarce, especially for non-model organisms. The industrial workhorse Pseudomonas putida was engineered to utilize the non-native sugar D-xylose, but its assimilation into the bacterial biochemical network via the exogenous pathway remained unresolved. Here, we elucidated the xylose metabolism and established a foundation for further engineering followed by ALE. By de-repressing native glycolysis, we unlocked the route for xylose-derived carbon and obtained a strain with a substantially reduced lag phase on xylose. We then enhanced the pentose phosphate pathway in two lag-shortened strains and allowed ALE to fine-tune the rewired metabolism. Following the metabolism tuning, we employed multi-level analysis that provided unique insights into the parallel paths of bacterial adaptation to the non-native carbon source.
2024-03-06 | PXD047537 | Pride
Project description:Genome sequencing data of evolved strains from ALE experiments
| PRJDB6152 | ENA
Project description:Fit phenotypes are achieved through optimal transcriptomic allocation. Here, we performed a high-resolution, multi-scale study of the transcriptomic tradeoff between two key fitness phenotypes, stress response (fear) and growth (greed), in Escherichia coli. We introduced 12 RNA polymerase (RNAP) mutations commonly acquired during adaptive laboratory evolution (ALE) and found that single mutations could result in large shifts in this fear vs. greed tradeoff likely through destabilizing the rpoB-rpoC interface. RpoS and GAD regulons drive the fear response while ribosomal proteins and the ppGpp regulon underlie greed. Growth rate selection pressure during ALE results in endpoint strains that universally have RNAP mutations, with synergistic mutations reflective of particular conditions. A phylogenetic analysis found the tradeoff in numerous bacteria species and one archaea species. The results suggest that the tradeoff represents a general principle of transcriptome allocation in bacteria where small genetic changes can result in large phenotypic adaptations to growth conditions.
2023-08-07 | GSE227624 | GEO