Ontology highlight
ABSTRACT:
PROVIDER: PRJEB13402 | ENA |
REPOSITORIES: ENA
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Project description:Genome engineering offers the possibility to create completely novel cell factories with enhanced properties for biotechnological application. In recent years, the possibilities for genome engineering have been extensively explored in the Gram-positive bacterial cell factory Bacillus subtilis, where up to 42% of the genome, encoding dispensable functions has been removed. Such studies have shown that some strains with minimized genomes gained beneficial features, for instance in protein production. However, strains with the most minimal genomes also showed particular growth defects. This has focused our attention on strains with less extensive genome deletions that show close-to-wild-type growth properties, while retaining the acquired beneficial traits in secretory protein production of strains lacking larger genomic segments. A strain of the latter category is B. subtilis IIG-Bs27-47-24, here referred to as midiBacillus II, which lacks 30.95% of the parental genome. To date, it was unknown how the altered genomic configuration of midiBacillus II impacts on cell physiology at large, and protein secretion in particular. Therefore, the present study was aimed at bridging this knowledge gap through an in-depth proteomics analysis with special focus on protein secretion stress responses. Interestingly, the results show that the secretion stress response of midiBacillus II as elicited by high-level expression of a staphylococcal antigen is completely different from the secretion stress responses that occur in the parental strain 168. This implies that high-level protein secretion has different implications for wild-type and genome-engineered Bacillus strains, dictated by the altered genomic and proteomic configurations.
2021-11-25 | PXD021841 | Pride
Project description:AtxA, the master virulence regulator of Bacillus anthracis, regulates the expression of three toxins that are required for the pathogenicity of Bacillus anthracis. Recent transcriptome analyses also showed that AtxA affects a large number of genes on both chromosome and plasmid, suggesting its role as a global regulator. Its mechanism of gene regulation nor binding target in vivo was, however, not well understood. In this work, we conducted ChIP-seq for cataloging binding sites of AtxA in vivo and Cappable-seq for catalogging the transcription start sites on the B. anthracis genome. For detected regulons, single knockout strains were constructed and RNA-seq was conducted for each strain.
2021-06-28 | GSE167871 | GEO
Project description:Primary objectives: The primary objective is to investigate circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
Primary endpoints: circulating tumor DNA (ctDNA) via deep sequencing for mutation detection and by whole genome sequencing for copy number analyses before start (baseline) with regorafenib and at defined time points during administration of regorafenib for treatment efficacy in colorectal cancer patients in terms of overall survival (OS).
| 2533916 | ecrin-mdr-crc
Project description:To determine Sigma 54 (SigL) reglons in Bacillus thuringiensis HD73 strain, A sigLmutant, HD(ΔsigL::kan), was constructed with insertion of kanamycin resistance gene cassete. We have employed whole genome microarray expression profiling as a discovery platform to identify the difference of gene expression between mutant and wild-type strains.
2013-06-29 | GSE48410 | GEO
Project description:With these experiments we investigate the impact of the deletion of the ydcH gene on the transcriptomes of Bacillus subtilis strains ABS2005.
2017-11-06 | GSE104816 | GEO
Project description:To investigate which cellular functions may be perturbed along the branches of a synthetic evolutionary tree obtained by incremental deletions of large genomic regions, we subjected six Bacillus subtilis strains to transcriptome profiling. These six strains are : MS (~3.98 Mbp), which is already a genome-reduced derivative of the B. subtilis 168 (~4.22 Mbp) and the root of our evolutionary tree; MGP254 (~2.73 Mbp), the farthest genome-reduced strain; MGP234 (~2.81 Mbp), another terminal leaf in our tree; MGP181 (~2.87 Mb) and MGP192 (~2.85 Mbp), two intermediate strains in the ancestor lineage common to MGP254 and MGP234; and finally MGP229 (2.82 Mbp), an intermedidate strain between MGP192 and MGP254 (i.e. an ancestor of MGP254 but not MGP234). The vast majority of genes conserved in the six strains displayed no differential expression, showing the robustness of the cell transcriptional network against massive genome reduction. Among deregulated genes, more than half could be explained by loss of known functions and aberrant transcription at deletion boundaries. An unexpected common feature in genome-reduced strains was the upregulation of genes involved in cell responses to oxidative stresses.
2023-02-15 | GSE207089 | GEO