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Comparing the transcriptional profiles of a Caulobacter crescentus phyR null mutant to a xylose-inducible phyR overexpression strain

ABSTRACT: phyR encodes a general stress regulator protein that is conserved among several alpha-proteobacteria. This experiment is quantifying transcription in two Caulobacter strains: one strain is overexpressing phyR (gene CC3477); the other carries a phyR in-frame deletion. Both strains were cultured in M2 defined medium with xylose as the sole carbon source. The first strain (FC626) carries a plasmid integrated into the xylX locus; phyR is fused to the xylX promoter in this plasmid, generating a xylose-inducible phyR overexpression strain. The second strain (FC799) carries an in-frame deletion at the chromosomal phyR locus.

ORGANISM(S): Caulobacter vibrioides

PROVIDER: GSE21205 | GEO | 2012/06/01

SECONDARY ACCESSION(S): PRJNA126291

REPOSITORIES: GEO

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Comparing the transcriptional profiles of a Caulobacter crescentus phyR null mutant to a xylose-inducible phyR overexpression strain

Project description:phyR encodes a general stress regulator protein that is conserved among several alpha-proteobacteria. This experiment is quantifying transcription in two Caulobacter strains: one strain is overexpressing phyR (gene CC3477); the other carries a phyR in-frame deletion. Both strains were cultured in M2 defined medium with xylose as the sole carbon source. The first strain (FC626) carries a plasmid integrated into the xylX locus; phyR is fused to the xylX promoter in this plasmid, generating a xylose-inducible phyR overexpression strain. The second strain (FC799) carries an in-frame deletion at the chromosomal phyR locus. Duplicate cultures of: 1) C. crescentus strain CB15 phyR in-frame deletion mutant , and 2) a xylose-inducible phyR overexpression strain, were cultured in M2 xylose defined medium and harvested at OD660=0.3

2012-05-31 | E-GEOD-21205 | biostudies-arrayexpress

Transcriptomic response of the xylose-selective strain derived from E. coli BL21(DE3) growing on xylose or glucose

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.

2024-10-01 | GSE277741 | GEO

The transcriptome comparison data between Saccharomyces cerevisiae cells in thi2p deletion strains and the control strains BSGX001 in xylose consumption phase after glucose depleted in glucose-xylose co-fermentation.

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

APJ1 and GRE3 Homologs Work in Concert to Allow Growth in Xylose in a Genetically Intractable Natural Saccharomyces sensu stricto Hybrid Yeast

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.

2012-07-19 | GSE35528 | GEO

Complete genome sequence and the expression pattern of plasmids of the model ethanologen Zymomonas mobilis ZM4 and its xylose-utilizing derivatives 8b and 2032

Project description:In this study, we reported the updated chromosome and plasmid sequence of ZM4, and its two engineered xylose-utilizing strains derivatives (strains 2032 and 8b). The majority of plasmid genes have either homologs from other organisms or some conserved domains. Our bioinformatics analysis suggested that several plasmid genes may be essential genes of ZM4. To further validate the function of these plasmid genes, an RNA-Seq pipeline was developed for Z. mobilis and used to compare the gene expression under various conditions, including anaerobic and aerobic conditions, and in different biomass hydrolysates. Overall, these plasmids genes are more responsive to different concentrated hydrolysates than the different oxygen concentrations tested (such as anaerobic vs. aerobic conditions). Moreover, our results also indicate that the plasmid copy number is affected by growth conditions and foreign gene insertion while the chromosomal gene expression is relatively stable across different conditions in different strain backgrounds.

2018-05-08 | GSE108890 | GEO

To study gene expression of PHO13 deleted Xylose isomerase (XI) harboring strain in xylose fermentation

Project description:The main objective is to improve xylose fermentation by deletion of PHO13 gene in Xylose isomerase (XI) harboring yeast strains. Microarray analysis was performed to investigate effects of PHO13 deletion on the gene expression prolife of xylose-fermenting strains.

2015-10-08 | GSE73814 | GEO

D-xylose catabolic pathways expressed in Herbaspirillum seropedicae

Project description:Herbaspirillum seropedicae are β-proteobacteria that establish as endophytes in various plants. They are able to consume diverse carbon sources, including hexoses and pentoses like D-xylose. D-xylose catabolism pathways have been described in some microorganisms, but databases of genes involved in these routes are limited. This is of special interest in biotechnology, considering that D-xylose is the second most abundant sugar in nature. Furthermore, it is found in some potential raw materials such as lignocellulosic biomass. In this work we present a study of D-xylose catabolism pathways in H. seropedicae strain Z69, using RNA-seq analysis and the subsequent study of phenotypes determined in targeted mutants in corresponding identified genes. G5B88_22805 gene, designated xylB, encodes a NAD+- dependent D-xylose dehydrogenase. Mutant Z69∆xylB was still able to grow on D-xylose, although at a reduced rate. This is due to expression of an L-arabinose dehydrogenase encoded by G5B88_05250 gene, and was thus able to use D-xylose as substrate. According to our results, H. seropedicae Z69 uses non-phosphorylative pathways to catabolize D-xylose. The lower portion of metabolism involves co-expression of two routes: Weimberg pathway that produces α-ketoglutarate and a novel pathway recently described that produces pyruvate and glycolate. This novel pathway seems to be essential since a mutant in the last step of this pathway, Z69∆G5B88_06410, was unable to grow on D‑xylose.

2021-03-01 | GSE162430 | GEO

Transcriptomic analysis of a novel Saccharomyces cerevisiae strain with improved xylose fermentation ability under heat and acid co-stress

Project description:Xylose-utilizing yeasts with tolerances to fermentation inhibitors (such as weak organic acids) and high temperature are needed for cost-effective simultaneous saccharification and co-fermentation (SSCF) of lignocellulosic materials. We constructed a novel xylose-assimilating Saccharomyces cerevisiae strain with improved fermentation performance under heat and acid co-stress using the genome shuffling technique. Two xylose-utilizing diploid yeasts with different genetic backgrounds were used as the parental strains for genome shuffling. The hybrid strain Hyb-8 showed significantly higher xylose fermentation ability than both parental strains (Sun049T-Z and Sun224T-K) under co-stress conditions of heat and acids. To screen for genes that might be important for fermentation under heat and acid co-stress, a transcriptomic analysis of hybrid strain Hyb-8 and its parental strains was performed.

2017-07-25 | GSE101786 | GEO

Aspergillus niger : Control (fructose) vs. xylose + arabinose (XA)

Project description:Transcriptional profiling of A. niger comparing different strains (WT, ΔXlnR, ΔaraR and ΔaraRΔXlnR) treated with 25mM xylose + 25mM arabinose for 2 and 8h. The main objective was to identifiy genes related to primary metabolism and carbohydrate metabolism in general, for instance, cellulases and hemicellulases. The study will compare the differences between WT strain and the strains with the disrupted xylanolytic transcriptional activator gene, XlnR, the arabinolytic transcriptional activator gene, AraR, and the double mutant,after treatment with xylose+arabinose (XA treatment). The experiment was further validated by real-time PCR and enzymatic assays.

2012-05-07 | GSE37760 | GEO

To study gene expression of PHO80-deleted yeast strain in xylose fermentation

Project description:The main objective is to improve xylose fermentation by deletion of PHO80 gene in recombinant xylose-fermenting yeast strains. Microarray analysis was performed to investigate effects of PHO80 deletion on the gene expression profile of xylose-fermenting strains. Samples for 2 strains (wild-type control, PHO80-deleted strain) were taken after 6h of xylose fermentation. Each sample was triplicated, resulting in a total of 6 samples.

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