Ontology highlight
ABSTRACT:
PROVIDER: PRJNA783062 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR17023267.fastq.gz | Fastqsanger.gz | |||
| SRR17023267_1.fastq.gz | Fastqsanger.gz | |||
| SRR17023267_2.fastq.gz | Fastqsanger.gz |
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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: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: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:Pseudomonas alloputida KT2440 (previously misclassified as P. putida KT2440 based on 16S rRNA gene homology) has emerged as an ideal host strain for plan t biomass valorization. However, P. alloputida KT2440 is unable to natively utilize abundant pentose sugars (e.g., xylose and arabinose) in hydrolysate streams, which may account for up to 25% of lignocellulosic biomass. In the last decades, microbes have been engineered to utilize the pentose sugars. However, most of the engineered strains were either slow-growing or displayed phenotypes that could not be replicated. In this work, we successfully isolated five Pseudomonas species with the native capability to utilize glucose, xylose and p-coumarate as a sole carbon source. These isolates were in two clusters; one set of isolates (M2 and M5) and the second set of isolates (BP6 and BP7) showed 85.6% and 96.2% ANI, respectively, to P. alloputida KT24440. BP8 showed 84.6% ANI to P. putida KT2440 and does not belong to any neighboring type strains indicating a new species. Notably, the isolates showed robust growth solely on xylose and higher growth rates (m, 0.36-0.49 h-1) when compared to only known xylose-utilizing Pseudomonas taiwanenesis VLB120 (m, 0.28 h-1) as a control. Unexpectedly, among five isolates, M2 and M5 grew solely on arabinose as well. Comprehensive analysis of genomics, transcriptomics and proteomics revealed the isolates utilize xylose and arabinose via Weimberg pathway (xylD-xylX-xylA) and oxidative pathway (araD-araX-araA), respectively. Furthermore, a preliminary result demonstrated the production of flaviolin solely on xylose and arabinose in the isolate, showing noteworthy potential to be an alternative host for lignocellulosic feedstocks into valuable products. This is the first report on isolating Pseudomonas strains natively capable of utilizing all of the major carbon sources in lignocellulosic biomass, and leading to higher consumption of available substrates and therefore maximizing the product yield.
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Project description:The K. pneumoniae K2044, K2044-8Xyl-60G, K2044-ΔXylA and K2044-ΔXylB isolates were cultured overnight in MRS medium, then 1:200 diluted in MRS medium with 8% xylose to reach the exponential growth phase. The control group was K2044 treated with 8% xylose. The experiment was performed in triplicate.
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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
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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
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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:Creating Saccharomyces yeasts capable of efficient fermentation of pentoses such as xylose remains a key challenge in the production of ethanol from lignocellulosic biomass. Metabolic engineering of industrial Saccharomyces cerevisiae strains has yielded xylose-fermenting strains, but these strains have not yet achieved industrial viability due largely to xylose fermentation being prohibitively slower than that of glucose. Recently, it has been shown that naturally occurring xylose-utilizing Saccharomyces species exist. Uncovering the genetic architecture of such strains will shed further light on xylose metabolism, suggesting additional engineering approaches or possibly even the development of xylose-fermenting yeasts that are not genetically modified. We previously identified a hybrid yeast strain, the genome of which is largely Saccharomyces uvarum, which has the ability to grow on xylose as the sole carbon source. Despite the sterility of this hybrid strain, we were able to develop novel methods to genetically characterize its xylose utilization phenotype, using bulk segregant analysis in conjunction with high-throughput sequencing. We found that its growth in xylose is governed by at least two genetic loci: one of the loci maps to a known xylose-pathway gene, a novel allele of the aldo-keto reductase gene GRE3, while a second locus maps to an allele of APJ1, a chaperonin gene not previously connected to xylose metabolism. Our work demonstrates that the power of sequencing combined with bulk segregant analysis can also be applied to a non-genetically-tractable hybrid strain that contains a complex, polygenic trait, and it identifies new avenues for metabolic engineering as well as for construction of non-genetically modified xylose-fermenting strains.
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