Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA253056 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR1425200.fastq.gz | Fastqsanger.gz | |||
| SRR1425201.fastq.gz | Fastqsanger.gz | |||
| SRR1425202.fastq.gz | Fastqsanger.gz | |||
| SRR1425203.fastq.gz | Fastqsanger.gz | |||
| SRR1425204.fastq.gz | Fastqsanger.gz |
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Similar Datasets
Project description:Braun’s lipoprotein (Lpp) plays a major role in stabilizing the integrity of the cell envelope in E. coli, as it provides a covalent crosslink between the outer membrane and the peptidoglycan layer. Here, using atomic force microscopy, we visualized Lpp directly on peptidoglycan sacculi. Lpp is homogeneously distributed over the outer surface of the sacculus at a high density.
2022-11-17 | PXD037277 | Pride
Project description:In enteric bacteria, the transcription factor ?E maintains membrane homeostasis by inducing expression of proteins involved in membrane repair and of two small, regulatory RNAs (sRNAs) that downregulate synthesis of abundant membrane porins. Here, we describe the discovery of a third ?E-dependent sRNA, MicL, transcribed from a promoter located within the coding sequence of the cutC gene. MicL is synthesized as a 308 nt primary transcript that is processed to an 80 nt form. Both forms possess features typical of Hfq-binding sRNAs, but surprisingly only target a single mRNA, which encodes the outer membrane lipoprotein Lpp, the most abundant protein of the cell. We show that the copper sensitivity phenotype previously ascribed to inactivation of the cutC gene is actually derived from the loss of MicL and elevated Lpp levels. This observation raises the possibility that other phenotypes currently attributed to protein defects are due to deficiencies in unappreciated regulatory RNAs. We also report that ?E activity is sensitive to Lpp abundance and that MicL and Lpp comprise a new ?E regulatory loop that opposes membrane stress. Together MicA, RybB and MicL allow ?E to repress the expression of all abundant outer membrane proteins in response to stress. 12 samples mRNA-seq data, 2 samples ribosome profiling data. For mRNA-seq data, samples were gathered at the indicated time (in min) after induction of either vector (WT), long (MicL), and short (MicL-S) forms of MicL.
2014-07-17 | E-GEOD-58637 | biostudies-arrayexpress
Project description:In enteric bacteria, the transcription factor σE maintains membrane homeostasis by inducing expression of proteins involved in membrane repair and of two small, regulatory RNAs (sRNAs) that downregulate synthesis of abundant membrane porins. Here, we describe the discovery of a third σE-dependent sRNA, MicL, transcribed from a promoter located within the coding sequence of the cutC gene. MicL is synthesized as a 308 nt primary transcript that is processed to an 80 nt form. Both forms possess features typical of Hfq-binding sRNAs, but surprisingly only target a single mRNA, which encodes the outer membrane lipoprotein Lpp, the most abundant protein of the cell. We show that the copper sensitivity phenotype previously ascribed to inactivation of the cutC gene is actually derived from the loss of MicL and elevated Lpp levels. This observation raises the possibility that other phenotypes currently attributed to protein defects are due to deficiencies in unappreciated regulatory RNAs. We also report that σE activity is sensitive to Lpp abundance and that MicL and Lpp comprise a new σE regulatory loop that opposes membrane stress. Together MicA, RybB and MicL allow σE to repress the expression of all abundant outer membrane proteins in response to stress.
2014-07-17 | GSE58637 | GEO
Project description:Braun/murein lipoprotein (Lpp) is one of the major outer membrane components of gram-negative bacteria belonging to the enterobacteriaceae family that that is involved in inflammatory responses and septic shock. We previously characterized a delta-lpp isogenic mutant of Yersinia pestis CO92 and found that this mutant was defective in surviving in macrophages and was attenuated in a mouse inhalation model of plague when compared to the highly virulent wild-type (WT) bacterium. To better understand how deletion of the lpp gene might affect Yersinia virulence, we performed global transcriptional profiling of the genes in the WT Y. pestis CO92 and its delta-lpp mutant by using microarrays. The organisms were cultured at both 26 and 37 degrees Celsius to simulate the flea vector and mammalian host environments, respectively. Our data revealed vastly different effects of lpp mutation on the transcriptomes of Y. pestis grown at 37 versus 26°C. While the absence of Lpp resulted mainly in the down-regulation of metabolic genes at 26°C, the Y. pestis CO92 lpp mutant cultured at 37°C exhibited profound alterations in stress response and virulence genes, compared to the WT bacterium. We further investigated one of the stress-related genes (htrA) down-regulated in the lpp mutant relative to WT Y. pestis, as HtrA was previously shown to be important for intracellular survival of Y. enterocolitica in macrophages. Indeed, complementation of the delta-lpp mutant with the htrA gene in trans restored intracellular survival of the Y. pestis lpp mutant. Our results support a role for Lpp in Y. pestis CO92 adapatation to the host environment, possibly via transcriptional activation of htrA.
2010-06-04 | GSE19840 | GEO
Project description:Gram negative bacteria are surrounded by the cell envelope, a structure comprised of an outer membrane (OM) and an inner membrane (IM). These two membranes delimit the periplasmic space, a compartment containing the peptidoglycan (PG), a giant polymer surrounding the cell and functioning as an extracytoplasmic skeleton. In the model organism Escherichia coli, covalently anchoring the OM to the peptidoglycan is crucial for envelope integrity. When attachment is prevented, the OM forms blebs and detaches from the cell body. Intriguingly, the only bacterial protein known to covalently attach the OM to the PG (the Braun lipoprotein or Lpp) is present in a small number of γ-proteobacteria, raising the question of OM-PG attachment in other species. Here, we show that in -proteobacteria Brucella abortus and Agrobacterium tumefaciens, the OM is attached to the peptidoglycan via the formation of covalent crosslinks between the N-terminus of integral OM proteins (OMPs; including porins) and peptide stems of peptidoglycan.
2020-10-20 | PXD019023 | Pride
Project description:Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope. Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane. The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized. The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity. During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs). To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin. Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses. We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses. The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested. Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis. Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB. We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics. We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination. This SuperSeries is composed of the following subset Series:; GSE10158: Expression of Escherichia coli treated with cefsulodin and mecillinam, alone and in combination; GSE10159: Expression of Escherichia coli treated with cefsulodin and mecillinam, alone at the minimum inhibitory concentration Experiment Overall Design: Refer to individual Series
2008-10-20 | E-GEOD-10160 | biostudies-arrayexpress
Project description:Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope. Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane. The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized. The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity. During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs). To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin. Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses. We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses. The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested. Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis. Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB. We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics. We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination. Keywords: Dose response, stress response
2008-07-15 | GSE10159 | GEO
Project description:Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope. Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane. The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized. The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity. During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs). To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin. Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses. We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses. The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested. Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis. Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB. We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics. We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination. Keywords: dose response, stress response
2008-07-15 | GSE10158 | GEO
Project description:Gram-negative bacteria possess stress responses to maintain the integrity of the cell envelope. Stress sensors monitor outer membrane permeability, envelope protein folding, and energization of the inner membrane. The systems used by Gram-negative bacteria to sense and combat stress resulting from disruption of the peptidoglycan layer are not well characterized. The peptidoglycan layer is a single molecule that completely surrounds the cell and ensures its structural integrity. During cell growth new peptidoglcyan subunits are incorporated into the peptidoglycan layer by a series of enzymes called the penicillin-binding proteins (PBPs). To explore how Gram-negative bacteria respond to peptidoglycan stress, global gene expression analysis was used to identify Escherichia coli stress responses activated following inhibition of specific PBPs by the β-lactam antibiotics mecillinam and cefsulodin. Inhibition of PBPs with different roles in peptidoglycan synthesis has different consequences for cell morphology and viability, suggesting that not all perturbations to the peptidoglycan layer generate equivalent stresses. We demonstrate that inhibition of different PBPs resulted in both shared and unique stress responses. The regulation of capsular synthesis (Rcs) phosphorelay was activated by inhibition of all of the PBPs tested. Furthermore, we show that activation of the Rcs phosphorelay increased survival in the presence of these antibiotics, independently of capsule synthesis. Both activation of the phosphorelay and survival required signal transduction via the outer membrane lipoprotein RcsF and the response regulator RcsB. We propose that the Rcs pathway responds to peptidoglycan damage and contributes to the intrinsic resistance of E. coli to β-lactam antibiotics. We used microarrays to identify changes in gene expression resulting from treatment of Escherichia coli with the β-lactam antibiotics cefsulodin, mecillinam, or the combination. This SuperSeries is composed of the SubSeries listed below.
2008-07-15 | GSE10160 | GEO
Project description:This study demonstrates that Lpp (Braun’s lipoprotein), and L, D-transpeptidases are required for AggR activation. We found that deletion lpp in EAEC resulted in the downregulation of more than 100 genes involved in transport, metabolism, and virulence. Among those genes, fourteen transcriptional factors, including AggR, were differentially expressed in 042Dlpp.
2025-04-30 | GSE282211 | GEO