Phage Ghost Attachment Induces Mutations in Bacteria
Ontology highlight
ABSTRACT:
ORGANISM(S): Escherichia coli K-12
SUBMITTER: Takehiko Kenzaka
PROVIDER: E-MTAB-2938 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:After the attachment of the lytic phage T4 to Escherichia coli cells, 1% E. coli cells showed an approximately 40-fold increase in mutant frequency. They were designated as mutator A global transcriptome analysis using microarrays was conducted to determine the difference between parental strain and mutators, and the host responce after adsorption of the phage and the ghost.
2018-11-29 | E-MTAB-5636 | biostudies-arrayexpress
Project description:We studied SOS mutator effect mediated by recA730 and changes in the dNTP pool. We found that established dNTP pool changes resulting from deficiencies in the ndk or dcd genes, had a strongly suppressive effect on the recA730 mutator effect. To investigate whether the observed reduction in SOS mutator effect is due to lowered expression of the entire SOS regulon, we performed microarray analysis of gene expression profiles in each of the single ndk, dcd, and recA730 strains, as well as the double recA730 ndk and recA730 dcd strains. Comparison of transcriptomes of the bacterium Escherichia coli six strains: wt, dcd, ndk, recA730, recA730 dcd and recA730 ndk. All strains were derivatives of the MC4100 strain, carrying a sulA366 allele (?(argF-lac)169 sulA366). dcd and ndk alleles used were dcd::kan and ndk::cam, respectively. Strains were compared in pairs: wt vs dcd, wt vs ndk, wt vs recA730, recA730 vs recA730 dcd and recA730 vs recA730 ndk. Two or three biological replicates for each strain were used. Each biological replicate had two technical replicates with dye swapping.
2015-03-31 | E-GEOD-62898 | biostudies-arrayexpress
Project description:Bacteria respond to osmotic stress by a substantial increase in the intracellular osmolality, adjusting their cell turgor for altered growth conditions. Using E. coli as a model organism we demonstrate here that bacterial responses to hyperosmotic stress specifically depend on the nature of osmoticum used. We show that increasing acute hyperosmotic NaCl stress above ~1.0 Os kg-1 causes a dose-dependent K+ leak from the cell, resulting in a substantial decrease in cytosolic K+ content and a concurrent accumulation of Na+ in the cell. At the same time, isotonic sucrose or mannitol treatment (non-ionic osmotica) results in a gradual increase of the net K+ uptake. Ion flux data is consistent with growth experiments showing that bacterial growth is impaired by NaCl at the concentration resulting in a switch from net K+ uptake to efflux. Microarray experiments reveal that about 40% of up-regulated genes shared no similarity in their responses to NaCl and sucrose treatment, further suggesting specificity of osmotic adjustment in E. coli to ionic- and non-ionic osmotica The observed differences are explained by the specificity of the stress-induced changes in the membrane potential of bacterial cells highlighting the importance of voltage-gated K+ transporters for bacterial adaptation to hyperosmotic stress. Experiment Overall Design: Two biological replicates per treatment with microarray analysis using the Affymetrix GeneChip E. coli Genome array. Treatments used included: Experiment Overall Design: Control - E. coli Frag1, grown to early stationary growth phase in a mineral salts medium with 0.1% glucose at 25 C Experiment Overall Design: Sucrose hyperosmotic treatment - 1.25 M sucrose added to control culture Experiment Overall Design: for 10 min. Experiment Overall Design: NaCl hyperosmotic treatment - 1.37 M NaCl added to control culture Experiment Overall Design: For microarray data comparisons the sucrose and NaCl hyperosmotic treatment data was compared to the no treatment control data separately. The sucrose to control and NaCL to control comparison data tables are linked below.
2008-10-21 | E-GEOD-12190 | biostudies-arrayexpress
Project description:We created a mutator protein. The mutator, was prepared by fusing a PmCDA1 (Petromyzon marinus Cytidine DeAminase) and E.coli RNA polymerase alpha subunit(EcoRNAP alpha). After 120 cycles, whole genome sequencing was performed on the wild type and evolved sample. After characterization of the mutation capacity of our mutator, we evolved a sucrose utilization strain and we sequenced Suc strain.
2021-05-03 | E-MTAB-10368 | biostudies-arrayexpress
Project description:Gene-expression measurements were made over a 24 h time course as fermentative steady state E. coli cells were subjected to a shift to TMAO respiration.
2014-12-13 | E-MTAB-2784 | biostudies-arrayexpress
Project description:Genomic Library Enrichment to determine the n-Butanol Tolerant related genes in E. coli. The samples involves a series of batch transfers to increasing concentrations of n-butanol and controls (always grew in absence of the solvent) Two technical replicas. Samples 1, 3, 5, and 7 are the serial transfers (samples 15, 13, 11, and 9 are their respective replicas). Samples 2, 4, 6 and 8 are the controls grown in absence of n-butanol (samples 16, 14, 12 and 10 are their respective replicas)
2012-09-19 | E-GEOD-26223 | biostudies-arrayexpress
Project description:There is increasing evidence to support a role for sigma factor 54 (RpoN) in the regulation of stress resistance factors and protein secretion systems important to bacterial transmission and pathogenesis. In enterohemorrhagic E. coli O157:H7, acid resistance and type III secretion are essential determinants of gastric passage and colonization. This study thus described the transcriptome of an rpoN null strain of E. coli O157:H7 (EcJR-8) to determine the influence of RpoN on virulence and stress resistance gene regulation, and further explored its contribution to glutamate-dependent acid resistance (GDAR). Inactivation of rpoN resulted in the growth phase-dependent, differential expression of 104 genes. This included type III secretion structural and regulatory genes encoded on the locus of enterocyte effacement (LEE), as well as GDAR genes gadA, gadBC and gadE. Upregulation of gad transcript levels in EcJR-8 during logarithmic growth correlated with increased GDAR and survival in a model stomach. Acid susceptibility was reconstituted in EcJR-8 complemented in trans with wild-type rpoN. Acid resistance in EcJR-8 was dependent on exogenous glutamate, gadE and rpoS, but was independent of hns. Results also suggest that GDAR may be controlled by RpoN at multiple regulatory levels. This study supports the hypothesis that RpoN is an important regulator of virulence and stress resistance factors in E. coli O157:H7, and is the first to examine the mechanism by which it represses GDAR. Hybridizations measured transcriptional differences between an rpoN null and wild-type (WT) strain of E. coli O157:H7 Sakai at logarithmic and transition phase. Image files (TIFF) of hybridized microarray slides were generated using an Axon 4000B scanner (Molecular Devices), and analyzed using GenePix Pro software (Molecular Devices, ver. 6.0). The resulting microarray intensity data was log2-transformed, and normalized using the LOWESS algorithm in MAANOVA ver. 0.98-8 (R ver. 2.2.1).
2009-08-08 | E-GEOD-17467 | biostudies-arrayexpress
Project description:Prokaryotic proteins must be deformylated before the removal of their first methionine. Peptide deformylase (PDF) is indispensable and guarantees this cotranslational mechanism. Recent genome sequencing and annotation studies highlighted over 2x104 putative peptide deformylase sequences. Furthermore, unpredicted modified bacterial PDF genes have been retrieved from many phages. Sequence comparisons with other known PDFs reveal that viral PDFs are devoid of the key ribosome-interacting C-terminal region. Little is known regarding these viral PDFs, including the capacity of the corresponding encoded proteins to ensure deformylase activity in vitro or in vivo. This investigation determines the activity of the recombinant Vp16 PDF in E. coli PDF defective cell to remove the N-formyl group at the protein N-terminus.
2017-09-25 | PXD006008 | Pride
Project description:The gene NMB0419 of Neisseria meningitidis strain MC58 encodes a putative tetratricopeptide repeats (TPR) containing protein, which was implicated in respiratory epithelial invasion. We have accordingly sought a role for NMB0419 in meningococcal adherence and invasion of human epithelial cells using Escherichia coli surrogates. In trans expression of NMB0419 promoted adherence of the E. coli strain to human epithelial cells, which showed a unique aggregative adherence pattern that was observed for pathogenic E. coli. This adherence was totally abolished by addition of D-mannose, suggesting that formation of type 1 pili on the surface of E. coli strain was solely responsible for the adherence and was facilitated by the expression of NMB0419. This was further supported by rigid pilus structures seen on the surface of NMB0419 expressing E. coli using electron microscopy. A survey of other meningococcal strains including serogroup A, B, C, W, X, Y and Z (n=3, 42, 10, 1, 1, 1, and 1, respectively) revealed that an NMB0419 homologue was present in all strains, however, encoded varying number of TPR domains from 1 to 7. E. coli with in trans expression of such a homologue (NMA2065) encoding single TPR domain also showed enhanced adherence to the level that was observed for the E. coli strain expressing NMB0419 encoding for 4 TPR domains. Nevertheless, in-frame deletion of the TPR-domain coding sequence from the expression plasmid construct reduced the E. coli adherence to the background level. Revisit of the NMB0419 mutant strain of meningococcus indicated that reduction in adherence was primarily responsible for the reduced epithelial invasion that was previously observed. Study of transcriptome profiles in E. coli using microarray showed that the most significantly up-regulated genes in NMB0419 expressing E. coli belonging to the fim operon encoding all necessary structure proteins and chaperons for type 1 pili, strongly suggesting a gene regulatory role for NMB0419. Although the mechanism yet to be explored, this is the first study to showed that TPR domains are involved in bacterial adherence and that a gene encoding single functional TPR domain produced the same phenotype as a homologue encoding multiple TPR domains did.
2010-11-27 | E-MEXP-2485 | biostudies-arrayexpress
Project description:A microarray study was performed to identify the Escherichia coli SlyA regulon. The wild-type (parental) Escherichia coli MG1655 strain was compared to an isogenic slyA deletion mutant, whilst a slyA-overexpression strain (in pET28a) was compared to an empty (pET28a) vector control. Continuous chemostat cultures were obtained (Evans medium pH 6.9, 0.2 h-1 dilution rate, 1 culture volume per hour air input, 400 rpm). Samples were eluted directly into RNAprotect, RNA purified and then hybridised in a reference-style format to micorarrays.
2017-01-25 | E-MTAB-5220 | biostudies-arrayexpress