Effect of luxS gene mutation on Streptococcus pneumonaie biofilm gene expression
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ABSTRACT:
ORGANISM(S): Streptococcus pneumoniae R6 Streptococcus pneumoniae D39
PROVIDER: GSE109347 | GEO | 2018/05/17
REPOSITORIES: GEO
Similar Datasets
Project description:Genes differentially regulated by the LuxS/AI-2 system in E. feacalis VE14089
2014-10-01 | GSE52374 | GEO
Project description:We were interested in determining if the LuxS signaling system contributed to the regulation of pneumococcal genes. To accomplish this, we compared the in vitro transcriptional profiles over time of S. pneumoniae D39, a serotype 2 strain of pneumococcus, with that of an isogenic deletion mutant, (delta)luxS, using a spotted S. pneumoniae- specific DNA microarray. For in vitro time course experiments, broth cultures of D39 and (delta)luxS were grown to low density (optical densities between ~0.01- 0.02), the cells were collected by centrifugation, washed 1x with sterile PBS, back diluted to ~3x105CFU/ ml into fresh broth, and immediately incubated at 37oC in a 5% CO2 chamber for 45 minutes. At this point, the first sample was collected. Subsequently, growth was monitored for approximately 8 generations by measuring both the optical density (OD600) and determining viable counts every 30 to 45 minutes. At these points samples were also harvested by centrifugation for RNA isolation and stored at -80oC until processing. For microarray probe synthesis, experimental samples were generated using 0.5ug total bacterial RNA isolated from either D39 or (delta)luxS strains at the various time points throughout the growth curve. These RNAs were used as templates for reverse transcription, and the resulting cDNAs were labelled with Cy5. The reference sample for each time course was generated from the D39 time zero RNA. Subsequent to reverse transcription, the resulting cDNAs were labelled with Cy3. The probes were mixed in hybridization buffer, heated to 99oC for at least 2 minutes, centrifuged briefly, and applied to the microarray. Hybridizations were carried out at 60oC for at least 24 hours. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Keywords: Logical Set
2005-08-03 | GSE3046 | GEO
Project description:We were interested in determining if the LuxS signaling system contributed to the regulation of pneumococcal genes. To accomplish this, we compared the in vitro transcriptional profiles over time of S. pneumoniae D39, a serotype 2 strain of pneumococcus, with that of an isogenic deletion mutant, (delta)luxS, using a spotted S. pneumoniae- specific DNA microarray. For in vitro time course experiments, broth cultures of D39 and (delta)luxS were grown to low density (optical densities between ~0.01- 0.02), the cells were collected by centrifugation, washed 1x with sterile PBS, back diluted to ~3x105CFU/ ml into fresh broth, and immediately incubated at 37oC in a 5% CO2 chamber for 45 minutes. At this point, the first sample was collected. Subsequently, growth was monitored for approximately 8 generations by measuring both the optical density (OD600) and determining viable counts every 30 to 45 minutes. At these points samples were also harvested by centrifugation for RNA isolation and stored at -80oC until processing. For microarray probe synthesis, experimental samples were generated using 0.5ug total bacterial RNA isolated from either D39 or (delta)luxS strains at the various time points throughout the growth curve. These RNAs were used as templates for reverse transcription, and the resulting cDNAs were labelled with Cy5. The reference sample for each time course was generated from the D39 time zero RNA. Subsequent to reverse transcription, the resulting cDNAs were labelled with Cy3. The probes were mixed in hybridization buffer, heated to 99oC for at least 2 minutes, centrifuged briefly, and applied to the microarray. Hybridizations were carried out at 60oC for at least 24 hours. Set of arrays organized by shared biological context, such as organism, tumors types, processes, etc. Computed
2005-08-03 | E-GEOD-3046 | biostudies-arrayexpress
Project description:The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions. Keywords: Genetic modification
2007-11-14 | GSE9582 | GEO
Project description:The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions. Keywords: Genetic modification
2007-11-14 | GSE9587 | GEO
Project description:Yersinia pestis, the etiological agent of plague, is able to sense cell density by quorum sensing. The function of quorum sensing in Y. pestis is not clear. Here, the process of autoinducer 2 (AI-2) quorum sensing was investigated by comparing transcript profiles when luxS gene was knocked out. The luxS gene encodes S-ribosylhomocysteinase which can produce DPD, a precursor of AI-2. The strain ∆pgm (pigmentation-negative) mutant R88 was called wild type. The ∆pgm ∆luxS mutant was called control.
2013-09-05 | GSE22849 | GEO
Project description:The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions. Experiment Overall Design: Total RNA was extracted from E. coi W3110 wild type and luxS mutant grown in LB plus 0.8% glucose at OD 1.0. The genomic expression was compared between the two strains using Affymetrix E. Coli antisense genome array.
2008-06-16 | E-GEOD-9587 | biostudies-arrayexpress
Project description:The bacterial quorum-sensing autoinducer 2 (AI-2) has received intense interest because the gene for its synthase, luxS, is common among a large number of bacterial species. We have identified luxS-controlled genes in Escherichia coli under two different growth conditions using DNA microarrays. Twenty-three genes were affected by luxS deletion in the presence of glucose, and 63 genes were influenced by luxS deletion in the absence of glucose. Minimal overlap among these gene sets suggests the role of luxS is condition dependent. Under the latter condition, the metE gene, the lsrACDBFG operon, and the flanking genes of the lsr operon (lsrR, lsrK, tam, and yneE) were among the most significantly induced genes by luxS. The E. coli lsr operon includes an additional gene, tam, encoding an S-adenosyl-l-methionine-dependent methyltransferase. Also, lsrR and lsrK belong to the same operon, lsrRK, which is positively regulated by the cyclic AMP receptor protein and negatively regulated by LsrR. lsrK is additionally transcribed by a promoter between lsrR and lsrK. Deletion of luxS was also shown to affect genes involved in methionine biosynthesis, methyl transfer reactions, iron uptake, and utilization of carbon. It was surprising, however, that so few genes were affected by luxS deletion in this E. coli K-12 strain under these conditions. Most of the highly induced genes are related to AI-2 production and transport. These data are consistent with the function of LuxS as an important metabolic enzyme but appear not to support the role of AI-2 as a true signal molecule for E. coli W3110 under the investigated conditions. Experiment Overall Design: Total RNA was extracted from E. coi W3110 wild type and luxS mutant grown in LB at OD 2.4. The genomic expression was compared between the two strains using Affymetrix E. Coli antisense genome array.
2008-06-16 | E-GEOD-9582 | biostudies-arrayexpress
Project description:Autoinducer-2 (AI-2)-mediated quorum sensing has been extensively studied in relation to the regulation of microbial behaviour. There are however two potential roles for the AI-2 synthase (LuxS). The first is in the production of AI-2 and the second is as an enzyme in the activated methyl cycle where it catalyses the conversion of S-ribosylhomocysteine to homocysteine. The by-product of the reaction catalysed by LuxS is (S)-4,5-dihydroxy-2,3-pentanedione (DPD), which spontaneously forms the furanones known collectively as AI-2. The mammalian gastrointestinal tract contains a complex collection of bacterial species so a method of interspecies communication might influence community structure and function. Lactobacillus reuteri 100-23 is an autochthonous inhabitant of the rodent forestomach where it adheres to the non-secretory epithelium of the forestomach forming a biofilm. Microarray comparisons of gene expression profiles of the L. reuteri 100-23 wild type and a luxS mutant under different culture conditions revealed altered transcription of genes encoding proteins involved in cysteine biosynthesis, the oxidative stress response and cell wall proteins. Metabolomic analysis revealed that the luxS mutation affected cellular levels of fermentation products, fatty acids and amino acids. Cell density-dependent changes (log phase versus stationary phase growth) in gene transcription were not detected. Overall, the results indicated that AI-2 was unlikely to be involved in gene regulation in L. reuteri 100-23 in a classical quorum-sensing type manner.
2011-10-01 | GSE32520 | GEO
Project description:The AI-2 quorum-sensing system has been linked to diverse phenotypes and regulatory changes in pathogenic bacteria. In strain CO92, the AI-2 signal is produced in a luxS-dependent manner, reaching maximal levels of 2.5 μM in late logarithmic growth, and both wild type and pigmentation mutant strains made equivalent levels of AI-2. Y. pestis CO92 possesses a chromosomal lsr locus encoding factors involved in the binding and import of AI-2, and confirming this assignment, an lsr deletion increased extracellular pools of AI-2. To assess the functional role of AI-2 sensing in Y. pestis, microarray study was conducted comparing the ∆Pgm strain R88 to a ∆Pgm ∆luxS mutant at 30°C to mimic the flea gut.
2016-01-01 | GSE30108 | GEO