Metabolomics,Unknown,Transcriptomics,Genomics,Proteomics

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Genomic Response of Escherichia coli during coexpression of a bacteriocin release protein

ABSTRACT: 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.

ORGANISM(S): Escherichia coli

SUBMITTER: Benjamin Sommer

PROVIDER: E-GEOD-16946 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Project description:The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specific cell wall components and attenuation both ex vivo and in vivo. Using antibodies against the native protein in ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds to at least 35 loci on the M. tuberculosis genome. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. Integration of ChIP-seq results with high-resolution transcriptomic analysis (RNA-seq) revealed that PhoP controls 30 genes directly, whilst regulatory cascades are responsible for signal amplification and downstream effects. The most prominent site of PhoP regulation was located in the intergenic region between rv2395 and PE_PGRS41, where the mcr7 gene codes for a small non-coding RNA (ncRNA). Northern blot experiments confirmed the absence of Mcr7 in the M. tuberculosis phoP mutant as well as low-level expression of the ncRNA in M. tuberculosis complex members other than M. tuberculosis. By means of genetic and proteomic analyses we demonstrated that Mcr7 modulates translation of the tatC mRNA thereby impacting the activity of the Twin Arginine Translocation (Tat) protein secretion apparatus. As a result, secretion of the immunodominant Ag85 complex and the beta-lactamase BlaC is affected, among others. Mcr7, the first ncRNA of M. tuberculosis whose function has been established, therefore represents a missing link between the PhoPR two-component system and the downstream functions necessary for successful infection of the host. ChiP-Seq: M. tuberculosis H37Rv (GC1237) cultures grown in vitro to exponential phase. Two wild type samples plus one isogenic phoP mutant as control

Project description:The PhoPR two-component system is essential for virulence in Mycobacterium tuberculosis where it controls expression of approximately 2% of the genes, including those for the ESX-1 secretion apparatus, a major virulence determinant. Mutations in phoP lead to compromised production of pathogen-specific cell wall components and attenuation both ex vivo and in vivo. Using antibodies against the native protein in ChIP-seq experiments (chromatin immunoprecipitation followed by high-throughput sequencing) we demonstrated that PhoP binds to at least 35 loci on the M. tuberculosis genome. The PhoP regulon comprises several transcriptional regulators as well as genes for polyketide synthases and PE/PPE proteins. Integration of ChIP-seq results with high-resolution transcriptomic analysis (RNA-seq) revealed that PhoP controls 30 genes directly, whilst regulatory cascades are responsible for signal amplification and downstream effects. The most prominent site of PhoP regulation was located in the intergenic region between rv2395 and PE_PGRS41, where the mcr7 gene codes for a small non-coding RNA (ncRNA). Northern blot experiments confirmed the absence of Mcr7 in the M. tuberculosis phoP mutant as well as low-level expression of the ncRNA in M. tuberculosis complex members other than M. tuberculosis. By means of genetic and proteomic analyses we demonstrated that Mcr7 modulates translation of the tatC mRNA thereby impacting the activity of the Twin Arginine Translocation (Tat) protein secretion apparatus. As a result, secretion of the immunodominant Ag85 complex and the beta-lactamase BlaC is affected, among others. Mcr7, the first ncRNA of M. tuberculosis whose function has been established, therefore represents a missing link between the PhoPR two-component system and the downstream functions necessary for successful infection of the host. RNA-Seq: M. tuberculosis H37Rv (GC1237) cultures grown in vitro to exponential phase. One wild type sample plus one isogenic phoP mutant sample

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Genomic Response of Escherichia coli during coexpression of a bacteriocin release protein

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