Global transcriptional analysis of S. mutans sugar transporters in biofilm
Ontology highlight
ABSTRACT:
ORGANISM(S): Streptococcus mutans UA159
SUBMITTER: Dragana Ajdic
PROVIDER: E-GEOD-35605 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:In this study we showed that one PTS of S. mutans is specific for biofilm mode of growth in the presence of sucrose. Our data indicates that this PTS is involved in transport and metabolism of disaccharides and possibly oligosaccharides synthesized by GtfI and GtfSI.
2012-09-01 | GSE35605 | GEO
Project description:The transport of carbohydrates by Streptococcus mutans is accomplished by the phosphoenolpyruvate-phosphotrasferase system (PTS) and ATP-binding cassette (ABC) transporters. To undertake a global transcriptional analysis of all S. mutans sugar transporters simultaneously, we used a whole-genome expression microarray. Global transcription profiles of S. mutans UA159 were determined for several carbohydrates. The results revealed that PTSs were responsible for transport of monosaccharides, disaccharides and sugar alcohols. Six PTSs were transcribed only if a specific sugar was present in the growth medium, thus they were regulated at the transcriptional level. These included transporters for fructose, lactose, cellobiose, trehalose, and two transporters for mannitol. Three PTSs were repressed under all conditions tested. Interestingly, five PTSs were always highly expressed regardless of the sugar source used, presumably suggesting their availability for immediate uptake of most common dietary sugars (glucose, fructose, maltose and sucrose). The ABC transporters were found to be specific for polysaccharides, raffinose, stachyose and isomaltosaccharides. Compared to the PTS, the ABC transporters showed higher transcription under several tested conditions, suggesting that they might be transporting multiple substrates. Keywords: carbohydrate response
2007-06-15 | GSE6973 | GEO
Project description:Short-chain fructooligosaccharides (scFOS) and other prebiotics are used to selectively stimulate the growth and activity of lactobacilli and bifidobacteria in the colon. However, there is little information on the mechanisms whereby prebiotics exert their specific effects upon such microorganisms. To study the genomic basis of scFOS metabolism in Lactobacillus plantarum WCFS1, two-colour microarrays were used to screen for differentially expressed genes when grown on scFOS as compared to glucose (not a prebiotic). A significant up-regulation (8 to 60-fold) was observed with a set of only five genes located in a single locus and predicted to encode a sucrose phosphoenolpyruvate transport system (PTS), a â-fructofuranosidase, a fructokinase, an á-glucosidase and a sucrose operon repressor. Several other genes were slightly overexpressed, including pyruvate dehydrogenase. For the latter, no detectable activity in L. plantarum under various growth conditions, has been previously reported. A mannose-PTS likely to encode glucose uptake was 50-fold down-regulated as well as, to a lower extent, other PTS. Chemical analysis of the different moieties of scFOS that were depleted in the growth medium revealed that the trisaccharide 1-kestose present in scFOS was preferentially utilized, in comparison with the tetrasaccharide nystose and the pentasaccharide fructofuranosylnystose. The main end-products of scFOS fermentation were lactate and acetate. This is the first example in lactobacilli of the association of a sucrose PTS and a â-fructofuranosidase for scFOS degradation. Keywords: comparative transcriptomics, carbohydrate metabolism
2007-02-13 | GSE5882 | GEO
Project description:Sucrose is a major carbon source for industrial bioethanol production by Saccharomyces cerevisiae. In yeasts, two modes of sucrose metabolism occur: (i) extracellular hydrolysis by invertase, followed by uptake and metabolism of glucose and fructose, and (ii) uptake via sucrose-H+ symport followed by intracellular hydrolysis and metabolism. Although alternative start codons in the SUC2 gene enable synthesis of extracellular and intracellular invertase isoforms, sucrose hydrolysis in S. cerevisiae predominantly occurs extracellularly. In anaerobic cultures, intracellular hydrolysis theoretically enables a 9 % higher ethanol yield than extracellular hydrolysis, due to energy costs of sucrose-proton symport. This prediction was tested by engineering the promoter and 5’ coding sequences of SUC2, resulting in relocation of invertase to the cytosol. In anaerobic sucrose-limited chemostats, this iSUC2-strain showed an only 4% increased ethanol yield and high residual sucrose concentrations indicated suboptimal sucrose-transport kinetics. To improve sucrose-uptake affinity, it was subjected to 95 generations of anaerobic, sucrose-limited chemostat cultivation, resulting in a 20-fold decrease of residual sucrose concentrations and a 10-fold increase of the sucrose-transport capacity. A single-cell isolate showed an 11 % higher ethanol yield on sucrose in chemostat and batch cultures than an isogenic SUC2 reference strain, while transcriptome analysis revealed elevated expression of AGT1, encoding a disaccharide-proton symporter, and other maltose-related genes. Deletion of AGT1, which had been duplicated during laboratory evolution, restored the growth characteristics of the unevolved iSUC2 strain. This study demonstrates that engineering the topology of sucrose metabolism is an attractive strategy to improve ethanol yields in industrial processes.
2011-09-06 | GSE30535 | GEO
Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants
2009-12-01 | GSE18363 | GEO
Project description:Identification of the major PEP-phosphotransferase systems (PTS) for glucose, mannose and cellobiose of Listeria monocytogenes, and their significance for extra- and intracellular growth. Transcriptional profile of prfA, the dependent genes and the PTS genes after growth in MM (minimal medium (Premaratne et al. 2001)) (supplemented with 10 mM Glucose). Listeria monocytogenes EGD-e possesses 86 pts genes encoding 29 complete and several incomplete PEP-dependent phosphotransferase systems (PTS) for the transport of carbohydrates and sugar alcohols. By a systematic deletion analysis we identified the major PTS involved in glucose, mannose and cellobiose transport, when L. monocytogenes grows in a defined minimal medium in the presence of either of these carbohydrates. Under these conditions two of the four PTSMan and at least one of the five PTSGlc function as glucose transporter with different affinities. Cellobiose is transported (with different efficiencies) mainly by two of the six PTSLac and by a PTSGlc that also transports glucose. One of the PTSMan and both PTSLac are regulated by LevR-homologous PRD containing transcriptional activators, detected with PRD deletion mutants. The growth rates of mutants that are lacking these PTS are drastically reduced compared to the wild-type strain upon growth in a defined medium with low concentrations of glucose and cellobiose, respectively. In contrast, replication of these PTS mutants within epithelial cells or macrophages is as efficient as that of the wild-type strain. Keywords: pts and prd deletion mutants A total of three independently isolated RNA samples from each condition were used for the analysis. PTS Samples: GSM458191-GSM458208 PRD Samples: GSM458209-GSM458214
2010-05-19 | E-GEOD-18363 | biostudies-arrayexpress
Project description:imbibed Col-0 seeds were sown on ? X MS medium supplemented with 0.8% agar and 1% sucrose. The plates were first exposed to continuous light for 12 h to stimulate germination and then wrapped with two layers of aluminum foil and placed in the growth chamber for 5 d. Once the plant material was uniformly germinated, the experimental conditions were applied. 5-d-old, dark-grown seedlings were washed seven times with sterile water followed by a wash with ? X MS liquid medium without sucrose to remove residual exogenous sugar and the plant material was kept in ? X MS liquid without sucrose in the dark for all subsequent steps. Cultures were shaken at 140 rpm at 22 C for 24 h and then treated with ? X MS without glucose or ½ X MS supplemented with BR (100 nM), glucose (3%), or glucose (3%) + BR (100 nM) for 3 h. Seedlings were harvested after 3h and preceded for RNA isolation and microarray analysis.
2012-08-10 | E-MEXP-3545 | biostudies-arrayexpress
Project description:We have demonstrated that the etiology of preeclampsia (PE) is associated with protein aggregation, a pathologic paradigm observed in neurodegenerative diseases, and that impaired autophagy contributes to accumulation of protein aggregates. In search of therapeutic options for preeclampsia that inhibit protein aggregation and restore autophagy, we screened several small molecules and identified a class of disaccharides that may prove to be highly efficacious to treat and prevent this severe pregnancy complication. We used the human serum-based humanized PE mouse model to assess the effect of disaccharides on the onset of the syndrome. Mice were i.p. injected with vehicle, disaccharides (2g/kg) at gd9, gd11, and gd14. At gd17, urine was collected, blood pressure was measured, fetal weight was recorded, and placenta was collected and subjected to immunostaining and RNA sequencing. Trehalose and Lactotrehalose inhibited hypoxia-induced accumulation of aggregates and restored impaired autophagy-lysosomal machinery. Disaccharide administration significantly restored normal pregnancy features in PE mice as characterized by normalization of hypertension, proteinuria, growth restriction, and kidney injury. RNA-seq analysis identified some novel genes and pathways that are related to preeclampsia and normalized by disaccharides.
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Project description:Sucrose is a major carbon source for industrial bioethanol production by Saccharomyces cerevisiae. In yeasts, two modes of sucrose metabolism occur: (i) extracellular hydrolysis by invertase, followed by uptake and metabolism of glucose and fructose, and (ii) uptake via sucrose-H+ symport followed by intracellular hydrolysis and metabolism. Although alternative start codons in the SUC2 gene enable synthesis of extracellular and intracellular invertase isoforms, sucrose hydrolysis in S. cerevisiae predominantly occurs extracellularly. In anaerobic cultures, intracellular hydrolysis theoretically enables a 9 % higher ethanol yield than extracellular hydrolysis, due to energy costs of sucrose-proton symport. This prediction was tested by engineering the promoter and 5’ coding sequences of SUC2, resulting in relocation of invertase to the cytosol. In anaerobic sucrose-limited chemostats, this iSUC2-strain showed an only 4% increased ethanol yield and high residual sucrose concentrations indicated suboptimal sucrose-transport kinetics. To improve sucrose-uptake affinity, it was subjected to 95 generations of anaerobic, sucrose-limited chemostat cultivation, resulting in a 20-fold decrease of residual sucrose concentrations and a 10-fold increase of the sucrose-transport capacity. A single-cell isolate showed an 11 % higher ethanol yield on sucrose in chemostat and batch cultures than an isogenic SUC2 reference strain, while transcriptome analysis revealed elevated expression of AGT1, encoding a disaccharide-proton symporter, and other maltose-related genes. Deletion of AGT1, which had been duplicated during laboratory evolution, restored the growth characteristics of the unevolved iSUC2 strain. This study demonstrates that engineering the topology of sucrose metabolism is an attractive strategy to improve ethanol yields in industrial processes. The goal of the present study was to investigate whether a relocation of sucrose hydrolysis to the cytosol can be used to improve ethanol yields on sucrose and which additional steps may be required to improve sucrose utilization by strains that only express intracellular invertase. To this end, the SUC2 gene was modified to cause an exclusive intracellular localization. Growth and product formation by the engineered strain were compared with that of the parental strain in anaerobic sucrose-limited chemostat cultures. Subsequently, evolutionary engineering was used to improve sucrose uptake kinetics and an evolved strain was characterized for growth and product formation in chemostat cultures. Transcriptome analysis and gene deletion studies were used to identify genetic changes in the evolved strain that contribute to its improved sucrose-uptake kinetics.
2011-09-05 | E-GEOD-30535 | biostudies-arrayexpress
Project description:Expression data comparing typical E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 to L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G. Keywords: one time point DNA microarray analysis of E.coli colonies grown on BHI and BHI+Sucrose+MgSO4 (controls) with L-form colonies grown on BHI+Sucrose+MgSO4+Penicillin G (experimental). An isolated colony of fresh W3110 was grown for 5hrs to log phase, dilutions of the inoculmn were spread onto three media: BHI, BHI+Sucrose+MgSO4, and BHI+Sucrose+MgSO4+Penicillin G to yield isolated colonies. Isolated control colonies which grow overnight were harvested the next day while isolated L-form colonies which do not grow until 48-72 hrs were harvested after 72hrs. All colonies were harvest with a PBS moistened sterile swab and dipped into a sterile microcentrifuge tube containing 500ul of PBS. RNA was isolated from pelleted cells using MasterPure RNA Purification Kit and reverse transcribed for making probes for array hybridization on E.coli Genome 2.0 Affymetrix microarrays.
2010-02-21 | E-GEOD-14796 | biostudies-arrayexpress