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ABSTRACT: Genome resequencing of adaptive laboratory evolved Vibrio sp. dhg for xylose utilization

PROVIDER: PRJNA720008 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR14150276_1.fastq.gz	Fastqsanger.gz
	SRR14150276_2.fastq.gz	Fastqsanger.gz
	SRR14150277_1.fastq.gz	Fastqsanger.gz
	SRR14150277_2.fastq.gz	Fastqsanger.gz
	SRR14150278_1.fastq.gz	Fastqsanger.gz

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Project description:Genome resequencing of adaptive evolved Vibrio sp. dhg for raffinose utilization

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Transcriptomic analysis of Vibrio sp. dhg in different sugar media.

Project description:Brown macroalgae holds an enormous potential as a future feedstock because it rapidly forms large biomasses and has high carbohydrate content (35% of its dry weight consists of alginate and mannitol). However, utilization of brown macroalgae by conventional microbial platforms (e.g., Escherichia coli and Saccharomyces cerevisiae) has been limited due to the inability of these platforms to metabolize alginate. Although recent studies engineered them to utilize alginate, their growth rates and metabolic activities are still too low for industrial applications, likely due to the unoptimized expression of multiple xenogeneic genes. Here, we isolated Vibrio sp. dhg, a novel, fast-growing bacterium that has been naturally evolved for efficient alginate assimilation (growth rate = 0.98 h-1). Especially, both the growth rate and sugar uptake rate of V. sp. dhg are substantially higher than the rates of E. coli for most biomass-derivable sugars. Based on our systematic characterization of its metabolism and gene expression architecture, we were able to develop a genetic toolbox for its engineering. By using this microorganism, we successfully demonstrated its ability to produce a broad spectrum of chemicals from alginate-mannitol mixtures with high productivities (1.1 g ethanol/L/h, 1.3 g 2,3-butanediol and acetoin/L/h, and 0.69 mg lycopene/L/h). Collectively, the V. sp. dhg strain is a powerful platform for the conversion of brown macroalgae sugars whose usage will dramatically accelerate the production of value-added biochemicals in the future.

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Vibrio sp. dhg

Project description:Vibrio sp. dhg Genome sequencing

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Expression data from parental and evolved Saccharomyces cerevisiae F12 cells in the presence of insoluble solids at high concentration and lignocellulose-derived inhibitors

Project description:Increasing yeast robustness against biomass-derived inhibitors and insoluble solids is essential for the realization of a bio-based economy. The xylose-fermenting Saccharomyces cereivisiae F12 strain was subjected to an adaptive laboratory evolution experiment in the presence of these stressors. The resulting evolved strain exhibit better fermentation performance in terms of xylose consumption and ethanol yields than the parental strain. The overexpression of genes related to cell wall integrity and the stress response, together with the downregulation of protein synthesis and iron transport and homeostasis were highlighted as the major biological processes responsible for the improved phenotype.

2022-01-11 | GSE159167 | GEO

Genome resequencing data of adaptive laboratory evolved E. coli W

Project description:Genome resequencing data of adaptive laboratory evolved E. coli W

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Transcriptomes of evolved Pseudomonas putida KT2440 on non-native sugars

Project description:Efficient utilization of lignocellulosic biomass-derived sugars is essential to improve the economics of biorefinery. While Pseudomonas putida is a promising microbial host, its usage is limited because this strain cannot utilize xylose or galactose as a sole carbon source. To address this issue, we heterologously introduced a xylose utilizing gene (xylD) from Caulobacter crescentus and a galactose operon (galETKM) from E. coli MG1655. To improve the utilization further, we evolved the engineered strains in minimal medium conditions. After the evolution, they acquired better fitnesses on the non-native sugars. To understand transcriptional changes after the evolution, the transcriptomes of few evolved isolates were analyzed.

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Generation of Escherichia coli Enhanced Acetate Utilization through Compensatory ATP Consumption via Adaptive Laboratory Evolution

Project description:We carried out adaptive laboratory evolution of an E. coli strain lacking four genes (adhE, pta, ldhA, frdA) involved in acetyl-CoA consumption, allowing the efficient utilization of acetate as its sole carbon and energy source. The transcriptomes according to the medium status (M9 aceate, M9 glucose) of the evolved strain (SBA01) and its parent strain (DSM01) were compared using RNA-seq.

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Project description:Transcriptomic analysis of strains evolved for anaerobic xylose utilization

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Project description:Carotenoids are a large family of health-beneficial compounds that have been widely used in the food and nutraceutical industries. There have been extensive studies to engineer Saccharomyces cerevisiae for the production of carotenoids, which already gained high level. However, it was difficult to discover new targets that were relevant to the accumulation of carotenoids. Herein, a new, ethanol-induced adaptive laboratory evolution was applied to boost carotenoid accumulation in a carotenoid producer BL03-D-4, subsequently, an evolved strain M3 was obtained with a 5.1-fold increase in carotenoid yield. Through whole-genome resequencing and reverse engineering, loss-of-function mutation of phosphofructokinase 1 (PFK1) was revealed as the major cause of increased carotenoid yield. Transcriptome analysis was conducted to reveal the potential mechanisms for improved yield, and strengthening of gluconeogenesis and downregulation of cell wall-related genes were observed in M3. This study provided a classic case where the appropriate selective pressure could be employed to improve carotenoid yield using adaptive evolution and elucidated the causal mutation of evolved strain.

2021-01-09 | GSE164470 | GEO

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