New xylose transporters support the simultaneous consumption of glucose and xylose in Escherichia coli
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PROVIDER: PRJNA776155 | ENA |
REPOSITORIES: ENA
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Project description:RNA-seq libraries were constructed for six samples, including AE1.0, AE2.0, PS1.0, PS2.0, REV1.0, REV2.0 . For preparation of RNA samples, Co-utilization were assessed using AM1 mineral salt media supplemented with glucose and xylose at each concentration of 50 g·L-1. Seed culture were grown overnight (16 h) in AM1 medium supplemented with 2% sugar. For each experiment, E. coli was grown at 37 ℃ in a pH-controlled fermentation vessel with the initial cell density at OD550nm of 0.1.Total RNA for samples were isolated using TRIzol reagent (Invitrogen, Grand Island, USA), then used for high-throughput RNA sequencing. The 150-nt paired-end RNA-seq libraries were generated commercially at Novogene Biotechnology Co. Ltd (Tianjin, China) by using Illumina’s Hiseq X Ten platform (Illumina, San Diego, USA).
2022-10-01 | GSE186804 | GEO
Project description:Yeast sugar transporters are highly evolved for optimized glucose transport, a major roadblock when it comes to utilizing non-glucose sugars in renewable feedstocks such as lignocellulosic biomass. The AtSWEET7p transporter has been identified for simultaneous transport of glucose and xylose, prevalent in plant cell wall hydrolysates. Here, we replaced endogenous hexose transporters with AtSWEET7 to construct an engineered Saccharomyces cerevisiae capable of multiple sugars with no glucose repression. The resulting strain (NKSW7-1) gained the capacity to simultaneously co-ferment glucose, xylose, mannose, and fructose in a synthetic medium, as well as the sugars in mixtures of bagasse hydrolysate and cane juice. Notably, the replacement of native sugar transporters by AtSWEET7 led to reprogramming of central carbon metabolism, activating glucose-repressed genes even in the presence of substantial amounts of glucose. Continuous culture experiments with the NKSW7-1 strain demonstrated feasibility of AtSWEET7 to disable glucose repression on other hexose or/and pentose sugar uptake. The broad transport capacity of AtSWEET7p can be utilized for achieving co-consumption of all sugars, especially in the case of emerging, underutilized, and renewable substrates.
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Project description:The xylose fermentation rate during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage) was much lower than that when xylose was the sole carbon source (defined as X stage). BSGX001 and XH7 are two engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between GX stage and X stage of BSGX001 and XH7, respectively.
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Project description:The xylose fermentation rate of thi2p deletion strains was higher than the control strains BSGX001 during xylose consumption phase after glucose depleted in glucose-xylose co-fermentation (defined as GX stage). BSGX001 was derived from the haploid strain CEN.PK113-5D, which is a engineered strains that have the xylose-utilizing capacity. Here,we investigate the transcriptional differences between BSGX001 (thi2Δ) and BSGX001 in GX stage.
2018-10-01 | GSE119333 | GEO
Project description:As advances are made toward the industrial feasibility of mass-producing biofuels and commodity chemicals with sugar-fermenting microbes, high feedstock costs continue to inhibit commercial application. Hydrolyzed lignocellulosic biomass represents an ideal feedstock for these purposes as it is cheap and prevalent. However, many microbes, including Escherichia coli, struggle to efficiently utilize this mixture of hexose and pentose sugars due to the regulation by the carbon catabolite repression (CCR) system. CCR causes a sequential utilization of sugars, rather than simultaneous utilization, resulting in reduced carbon yield and complex process implications in fed-batch fermentation. A mutation in the gene encoding the cyclic AMP receptor protein, Crp*, has been shown to disable CCR and improve co-utilization of mixed sugar substrates. Here, we present the strain construction and characterization of a site specific crp* chromosomal mutant in E. coli BL21 starTM (DE3). The crp* mutant strain demonstrates simultaneous consumption of glucose and xylose, suggesting a deregulated CCR system. The proteomic analysis further showed that cells link xylose consumption to energy production through the de novo nucleotide synthesis pathway, explaining the relatively slower growth of the crp* mutant strain. This highly characterized strain can be particularly beneficial for chemical production by simultaneously utilizing both C5 and C6 substrates from lignocellulosic biomass.
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Project description:Different genetic engineering strategies have been proposed to obtain E. coli strains that selectively consume xylose. In this study, a previously reported strategy for obtaining a xylose-selective strain in E. coli K12 was applied to E. coli BL21 (DE3). While this approach resulted in the expected xylose-selective phenotype, a low xylose consumption rate was recorded when the strain was grown on a mixture of xylose and glucose. To enhance xylose consumption, a variant of the transcriptional activator XylR was expressed. The resulting strain not only exhibited an improved capacity to consume xylose but also slightly recovered the ability to consume glucose. The aim of the microarray analysis was to identify the transcriptional changes associated with glucose assimilation in the BL21(DE3) derived xylose-selective strain.
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Project description:Saccharomyces cerevisiae cannot metabolize xylodextrins in nature. One engineered S. cerevisiae strain, which expresses XYL1 (xylose reductase gene), XYL2 (xylitol dehydrogenase gene), and XKS1 (xylulose kinase gene) from Scheffersomyces stipitis, and cdt-2 (coding for cellodextrin transporter 2), gh43-2 (coding for β-xylosidase) and gh43-7 (coding for a xylosyl-xylitol-specific β-xylosidase) from N. crassa, can utilize xylodextrins in aerobic condtions but not anaerobic conditions. We sequenced mRNA from anaerobically fed-batch cultures of the engineered S. cerevisiae grown on xylodextrins with or without the continuous feeding of xylose in biological duplicate. Dynamic changes of gene expression during xylose feeding experiment revealed by RNA deep sequencing indicated that xylose helps anaerobically xylodextrin-grown cells to recover mithondrial function thereby resuming xylodextrin consumption. Furthermore, different portions of genes involved in ribosome biogenesis showed either decreased or increased transcriptions. The underlying mechanism remains to be elucidated.
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Project description:HMF and furfural were pulse added to xylose-utilizing Saccharomyces cerevisiae during either the glucose consumption phase or the xylose consumption phase. Transcriptome samples were collected before and one hour after pulsing of inhibitors.
2013-11-25 | GSE50182 | GEO
Project description:Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. An increase in xylose concentration to 2 and 4 g/L in a medium containing 1 g/L glucose resulted in a growth rate of 0.082 and 0.085 h-1. However, increasing glucose concentration by 2 and 4 g/L when xylose concentration was maintained at 1 g/L decreased the growth rate to 0.062 and 0.052 h-1 respectively. S. acidocaldarius appeared to be utilizing the sugars at a rate roughly proportional to their concentration in the medium, resulting in complete utilization of these sugars at same time. The organism did not show preference for either glucose or xylose when it was grown on both sugars. Similar results were obtained with a combination of glucose, arabinose and galactose. These observations strongly suggest that S. acidocaldarius does not regulate utilization of the sugars tested herein using carbon catabolite repression (CCR) commonly found in most bacteria. The mechanism by which the organism utilized a mixture of sugar is yet to be elucidated. However, we were able to identify genes encoding for the putative glucose ABC transporters; but the putative xylose transporter was not identified. A study of S. acidocaldarius grown in glucose, xylose, or the two carbon sources combined in mid-log. Analyzed on Nimblegen 4-plex S. acidocaldarius DSM 639 array weblink: http://microbesonline.org/cgi-bin/microarray/viewExp.cgi?expId=1723
2010-07-31 | E-GEOD-21695 | biostudies-arrayexpress
Project description:Sulfolobus acidocaldarius has been previously reported to grow on a broad range of sugars, but there is limited information on the ability of the organism to metabolize multiple sugars simultaneously. We report here the ability of S. acidocaldarius to utilize glucose and xylose simultaneously without di-auxie effect. The organism utilized a mixture of 1 g/L glucose and 1 g/L xylose with a growth rate of 0.079 h-1 compared to 0.074 h-1 and 0.22 h-1 when the organism was grown on xylose 2 g/L and 2 g/L glucose respectively as sole carbon sources. An increase in xylose concentration to 2 and 4 g/L in a medium containing 1 g/L glucose resulted in a growth rate of 0.082 and 0.085 h-1. However, increasing glucose concentration by 2 and 4 g/L when xylose concentration was maintained at 1 g/L decreased the growth rate to 0.062 and 0.052 h-1 respectively. S. acidocaldarius appeared to be utilizing the sugars at a rate roughly proportional to their concentration in the medium, resulting in complete utilization of these sugars at same time. The organism did not show preference for either glucose or xylose when it was grown on both sugars. Similar results were obtained with a combination of glucose, arabinose and galactose. These observations strongly suggest that S. acidocaldarius does not regulate utilization of the sugars tested herein using carbon catabolite repression (CCR) commonly found in most bacteria. The mechanism by which the organism utilized a mixture of sugar is yet to be elucidated. However, we were able to identify genes encoding for the putative glucose ABC transporters; but the putative xylose transporter was not identified.
2010-07-31 | GSE21695 | GEO