Identification of candidate genes involved in fructooligosaccharides (FOS) utilization by Lactobacillus paracasei
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ABSTRACT:
ORGANISM(S): Lacticaseibacillus paracasei
PROVIDER: GSE5890 | GEO | 2006/12/06
SECONDARY ACCESSION(S): PRJNA97315
REPOSITORIES: GEO
Similar Datasets
Project description:A shotgun microarray-based approach was used to identify candidate genes encoding the FOS utilization pathway in L. paracasei 1195. Differential expression profiles between cells grown on FOS and glucose provided a basis for identifying genes specifically induced by FOS. In addition, transcriptional analysis of cells grown on FOS or FOS + glucose allowed us to investigate the effect of catabolite repression on the expression of the FOS-induced genes. For sugar induction experiment (FOS vs. glucose; FOS vs. fructose), L. paracasei were grown in modified MRS (mMRS) basal medium to a final OD625 nm of ca. 0.3, at which point all of the residual sugars in the medium were consumed (based on HPLC analysis of the supernatants). The culture was then divided into equal portions, where FOS or glucose was added to a 1% final concentration. Cells were collected for total RNA isolation after 30 min (OD625 nm ca. 0.3 â 0.4). For glucose repression experiment (FOS vs. FOS + glucose), cells were grown in mMRS supplemented with 2% FOS to an OD625 nm 0.6. The culture was split into equal portions, and glucose was added to one of the portions at a 2% final concentration. Both cultures were grown for another 60 min (OD625 nm ca. 1.0) before harvested for total RNA isolation. Both experiments were performed in independent replicates (two biological replicates per experiment) with incubation at 37 degree celsius in ambient atmosphere.
2010-06-30 | E-GEOD-5890 | biostudies-arrayexpress
Project description:In order to understand LBG derived galacto-manno-oligosaccharides utilization by a probiotic bacterium, Lactobacillus plantarum WCFS1, we have grown Lactobacillus plantarum WCFS1 (in duplicates) till mid log phase (OD600nm ~0.5, 10 h) in carbon free MRS (de Man, Rogosa Sharpe ) media containing either galacto-manno-oligosaccharides, mannose, glucose or galactose (1% w/v) as the sole carbon source.
2019-07-30 | GSE117591 | GEO
Project description:We have a cDNA microarray to investigate changes in gene expression following transfer of fungal cultures from growth on glucose to growth on pectin or no carbon source. Our goal was to asses the roles of release from carbon catabolite repression and specific induction on proteins needed for metabolism (or utilization) of a single class of complex polysaccharide. Keywords = Aspergillus Keywords = Pectin Keywords = central metabolism Keywords = pectin Keywords = carbon catabolite repression Keywords = polysaccharide Keywords = exopolygalacturonase Keywords: time-course
2006-01-01 | GSE2417 | GEO
Project description:We have a cDNA microarray to investigate changes in gene expression following transfer of fungal cultures from growth on glucose to growth on pectin or no carbon source. Our goal was to asses the roles of release from carbon catabolite repression and specific induction on proteins needed for metabolism (or utilization) of a single class of complex polysaccharide. Keywords = Aspergillus Keywords = Pectin Keywords = central metabolism Keywords = pectin Keywords = carbon catabolite repression Keywords = polysaccharide Keywords = exopolygalacturonase
2010-06-11 | E-GEOD-2417 | biostudies-arrayexpress
Project description:In the present study transcriptome and proteome of recombinant, xylose-utilising S. cerevisiae grown in aerobic batch cultures on xylose were compared with glucose-grown cells both in glucose repressed and derepressed states. The aim was to study at genome-wide level how signalling and carbon catabolite repression differed in cells grown on either glucose or xylose. The more detailed knowledge about is xylose sensed as a fermentable carbon source, capable of catabolite repression like glucose, or is it rather recognised as a non-fermentable carbon source is important in achieving understanding for further engineering this yeast for more efficient anaerobic fermentation of xylose.
2008-09-24 | GSE12890 | GEO
Project description:Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model.
2010-12-11 | GSE24472 | GEO
Project description:Mouse D1 dendritic cells treated with Lactobacillus Paracasei at different time points: 0h, 2h, 4h, 8h, 12h, 24h
2012-03-28 | E-MEXP-3157 | biostudies-arrayexpress
Project description:This experiment compares the transcriptional profiles of a WT yeast strain grown in either 2% glucose or 3% pyruvate. The goal was to identify genes whose expression is either induced or repressed by glucose (catabolite repression). Keywords: nutrient response
2007-08-22 | GSE3844 | GEO
Project description:Commensal (symbiont) bacteria form communities in various regions of the bodies of vertebrates. Phylogenetic analysis of gut communities is advanced, but the relationships, especially at the trophic level, between commensals that share gut habitats of monogastric animals have not been investigated to any extent. Lactobacillus reuteri strain 100-23 and Lactobacillus johnsonii strain 100-33 cohabit in the forestomach of mice. According to the niche exclusion principle, this should not be possible because both strains utilise the two main fermentable carbohydrates present in the stomach digesta: glucose and maltose. We show, based on gene transcription analysis, in vitro physiological assays, and in vivo experiments that the two strains can co-exist in the forestomach habitat because L. reuteri 100-23 transports maltose into its cells more efficiently than does L. johnsonii 100-33. Conversely, strain 100-33 transports glucose more efficiently than 100-23. As a result, 100-23 shows a preference for growth using maltose, whereas 100-33 prefers glucose. Mutation of the maltose phosphorylase gene (malA) of strain 100-23 prevented its growth on maltose-containing culture medium, and resulted in the numerical dominance of 100-33 in the forestomach. The fundamental niche of L. reuteri 100-23 in the mouse forestomach can be defined in terms of glucose and maltose fermentation. Its realised niche when L. johnsonii 100-33 is present is maltose fermentation. Hence nutritional adaptations provided niche differentiation that enabled cohabitation by the two strains through resource partitioning in the mouse forestomach. This real life, trophic phenomenon conforms to a mathematical model. Analysis of the microarray data was obtained from two independent biological replicates. A dye swap was included in the analysis
2010-12-11 | E-GEOD-24472 | 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