Escherichia coli
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA117305 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Secretion of recombinant proteins to the culture medium after transport to the periplasm of gram-negative bacteria often facilitates downstream-processing. It could lead to more biological active and correct folded proteins and low contamination with host proteins, thereby reducing the costs of the production process. However, Escherichia coli K12 secrets only little amount and few substrates naturally. This is one of the major drawbacks for the applicability of this strain in the biotechnology industry, when large amounts of biological active proteins are desirable. Therefore, different attempts were made to enhance the level of secreted proteins. Coexpression of bacteriocin release proteins makes the outer membrane permeable for proteins. A detailed insight into the complex underlying regulatory mechanism and metabolic changes when such release proteins are expressed could be very useful for successful optimisation strategies. The identification of potential optimisation targets can be achieved by DNA-microarray-technology, as proven in many cases before. In this work DNA-microarrays were used for the identification of differentially expressed genes of an inducible E.coli secretion strain expressing reporter proteins bacterial alkaline phosphatase, PhoA and beta-lactamase, Bla and their release to the culture medium by coexpression of the BRP of CloDF13. Based on the data of whole genome experiments and on the different databases genes which are regulated after induction of BRP expression are identified and discussed. BRP activity was found to cause a substantial cellular response and considerable changes in global gene expression. Additionally, performed cluster-analysis using k-means algorithm identified clusters containing promising candidates for new optimisation strategies aiming for an enhanced protein secretion. time series of BRP Induction, every sample was labeled with Cy3 and Cy5 (Dye Swap) to compensate dye-specific effects.
2009-08-01 | E-GEOD-16946 | biostudies-arrayexpress
Project description:Secretion of recombinant proteins to the culture medium after transport to the periplasm of gram-negative bacteria often facilitates downstream-processing. It could lead to more biological active and correct folded proteins and low contamination with host proteins, thereby reducing the costs of the production process. However, Escherichia coli K12 secrets only little amount and few substrates naturally. This is one of the major drawbacks for the applicability of this strain in the biotechnology industry, when large amounts of biological active proteins are desirable. Therefore, different attempts were made to enhance the level of secreted proteins. Coexpression of bacteriocin release proteins makes the outer membrane permeable for proteins. A detailed insight into the complex underlying regulatory mechanism and metabolic changes when such release proteins are expressed could be very useful for successful optimisation strategies. The identification of potential optimisation targets can be achieved by DNA-microarray-technology, as proven in many cases before. In this work DNA-microarrays were used for the identification of differentially expressed genes of an inducible E.coli secretion strain expressing reporter proteins bacterial alkaline phosphatase, PhoA and beta-lactamase, Bla and their release to the culture medium by coexpression of the BRP of CloDF13. Based on the data of whole genome experiments and on the different databases genes which are regulated after induction of BRP expression are identified and discussed. BRP activity was found to cause a substantial cellular response and considerable changes in global gene expression. Additionally, performed cluster-analysis using k-means algorithm identified clusters containing promising candidates for new optimisation strategies aiming for an enhanced protein secretion.
2009-08-01 | GSE16946 | GEO
Project description:The purpose of this study is to determine whether the presence of pathogenic Escherichia coli in colon is associated with psychiatric disorders.
| 2230352 | ecrin-mdr-crc
Project description:Despite the characterization of many aetiologic genetic changes. The specific causative factors in the development of sporadic colorectal cancer remain unclear. This study was performed to detect the possible role of Enteropathogenic Escherichia coli (EPEC) in developing colorectal carcinoma.
| 2184564 | ecrin-mdr-crc
Project description:We report the effect of oxygenation state in lactose grown escherichia coli producing recombinant proteins. To shed more light on the mechanistic correlation between the uptake of lactose and dissolved oxygen, a comprehensive study has been undertaken with the E. coli BL21 (DE3) strain. Differences in consumption pattern of lactose, metabolites, biomass and product formation due to aerobiosis have been investigated. Transcriptomic profiling of metabolic changes due to aerobic process and microaerobic process during protein formation phase has been studied and the results provide a deeper understanding of protein production in E. coli BL21 (DE3) strains with lactose based promoter expression systems.This study also provides a scientific understanding of escherichia coli metabolism upon oxygen fluctuations.
2020-05-18 | GSE135698 | GEO
Project description:Escherichia coli release Extracellular Vesicles (EVs) which carry diverse molecular cargo. Pathogenic E.coli EVs contain virulence factors which assist during infection in the host in different mechanisms.The RNA cargo of E.coli EVs has not been assessed in their effect in the host. We used microarray data to asses and compare the global response of bladder cells to EV-RNA from pathogenic E.coli (Uropathogenic UPEC 536) and non-pathogenic E. coli (probiotic Nissle 1917)
2020-07-08 | GSE148711 | GEO
Project description:Gene expression from Escherichia coli.
2013-07-12 | GSE48776 | GEO
Project description:Escherichia coli (E. coli) amine oxidase (ECAO) encoded by tynA gene has been one of the model enzymes to study the mechanism of oxidative deamination of amines to the corresponding aldehydes by amine oxidases. The biological roles of ECAO have been less addressed. Therefore we have constructed a gene deletion Escherichia coli K-12 strain, E. coli tynA-, and used the microarray technique to address its function by comparing the total RNA gene expression to the one of the wt. Our results suggest that tynA is a reserve gene for stringent environmental conditions and its gene product ECAO a growth advantage compared to other bacteria due to H2O2 production.
2015-09-30 | GSE65385 | GEO
Project description:The transcriptional changes in Escherichia coli upon induction of the SOS response are investigated by utilizing custom designed oligonucleotide microarrays. Keywords: Gene expression during the SOS response in Escherichia coli
2009-08-18 | GSE13829 | GEO
Project description:The intention of this study is to analyse the effect of antibiotics on the gene expression of Escherichia coli. Shaking-flask cultivations of Escherichia coli K12GFP-UTL2 were carried out with a medium containing nalidixic acid. Cultures with antibiotic-free medium, which were run in an identical way, served as reference. Samples were taken at different times during the cultivations, the RNA was isolated and hybridised on whole genome yeast microarrays. Keywords: Influence of toxins on gene expression in E. coli
2008-07-20 | GSE8674 | GEO