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Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.

ABSTRACT: Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.

PROVIDER: PRJNA853626 | ENA |

REPOSITORIES: ENA

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Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.

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

Transcriptome analysis of genome-reduced Bacillus subtilis strains

Project description:In this study two genome-reduced Bacillus subtilis strains lacking about 36% of dispensable genetic information were constructed using a markerless and scarless deletion method. In order to analyze the consequences of the deletions for the bacteria, a multi-omics characterization of the reference strain Δ6 (Westers et al., 2003; PMID 12949151) and the two deletion strains was carried out. Bacteria were cultivated in complex medium supplemented with glucose, and samples of the same cultures were subjected to metabolome, proteome, and transcriptome analyses.These revealed a massive re-organization of metabolism as well as substantial changes in the transcriptome and the proteome.

2016-11-30 | GSE82249 | GEO

An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

Project description:Neural crest cells (NCCs) are vertebrate stem cells that give rise to various cell types throughout the developing body in early life. Here, we utilized single-cell transcriptomic analyses to delineate NCC-derivatives along the posterior developing vertebrate, zebrafish, during the late embryonic to early larval stage, a period when NCCs are actively differentiating into distinct cellular lineages. We identified several major NCC/NCC-derived cell-types including mesenchyme, neural crest, neural, neuronal, glial, and pigment, from which we resolved over three dozen cellular subtypes. We dissected gene expression signatures of pigment progenitors delineating into chromatophore lineages, mesenchyme subtypes, and enteric NCCs transforming into enteric neurons. Global analysis of NCC derivatives revealed they were demarcated by combinatorial hox gene codes, with distinct profiles within neuronal cells. From these analyses, we present a comprehensive cell-type atlas that can be utilized as a valuable resource for further mechanistic and evolutionary investigations of NCC differentiation.

2021-02-16 | GSE152906 | GEO

An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

Project description:An atlas of neural crest lineages along the posterior developing zebrafish at single-cell resolution

| PRJNA640816 | ENA

Mycobacterium tuberculosis strain:Mtb lineages | isolate:Mtb lineages and sub-lineages

Project description:Mycobacterium tuberculosis strain:Mtb lineages | isolate:Mtb lineages and sub-lineages Genome sequencing and assembly

| PRJNA975069 | ENA

Zygotes segregate entire parental genomes in distinct blastomere lineages causing cleavage stage chimaerism and mixolpoidy

Project description:Chimaerism and mixoploidy define the presence of cell lineages with different parental genomes or different ploidy states in a single individual. Our knowledge on their mechanistic origin results from indirect observations, often when the cell lineages have been subject to rigorous selective pressure during development. Here, we applied haplarithmisis to infer the haplotypes and the copy number of parental genomes in 116 single blastomeres comprising entire preimplantation stage bovine embryos (n=23) following in vitro fertilization. Not only abnormal fertilizations leading to triploid zygotes, but also normally fertilized zygotes can spontaneously segregate entire parental genomes into different cell lineages during cleavage of the zygote. We coin the term “heterogoneic division” to indicate the events leading to non-canonical zygotic cytokinesis segregating the parental genomes into distinct lineages. Persistence of those cell lines during development is the likely cause of chimaerism and mixoploidy in mammals.

2016-03-11 | GSE76305 | GEO

Genetic, epigenetic and microbiome characterisation of earthworm species and lineages along a radiation exposure gradient at Chernobyl

Project description:Genetic, epigenetic and microbiome characterisation of earthworm species and lineages along a radiation exposure gradient at Chernobyl

| PRJEB33639 | ENA

Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis

Project description:Oviduct epithelial cells constitute two developmentally distinct lineages that are spatially separated along the distal-proximal axis

| PRJNA746566 | ENA

Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages

Project description:Draft genomes from diverse jellyfish (Cnidaria, Acraspeda) lineages: Calvadosia cruxmelitensis (Staurozoa) and Cassiopea xamachana (Scyphozoa)

| PRJEB23739 | ENA

Sigma B in Listeria monocytogenes strains from different lineages

Project description:Listeria monocytogenes strains classify into at least three distinct phylogenetic lineages. Correlations exist between lineage classification and source of bacterial isolation, e.g., human clinical and food isolates usually classify into either lineage I or II, however, human clinical isolates are over-represented in lineage I while food isolates are over-represented in lineage II. σB, a transcriptional regulator previously demonstrated to contribute to environmental stress response and virulence in L. monocytogenes lineage II strains, was hypothesized to provide differential capabilities for L. monocytogenes survival in various niches (e.g., food vs. human clinical). To determine if σB contributions to stress response and virulence differ across diverse L. monocytogenes strains, ΔsigB mutations were created in strains from lineages I, II, IIIA, and IIIB. Paired parent and ΔsigB mutant strains were tested for acid and oxidative stress survival, Caco-2 cell invasion efficiency, and virulence using the guinea pig listeriosis infection model. Parent and ΔsigB mutant strain transcriptomes were compared using whole-genome expression microarrays. σB contributed to virulence in each strain. However, while σB contributed significantly to acid and oxidative stress survival and Caco-2 cell invasion in lineage I, II, and IIIB strains, σB contributions were not significant for these phenotypes in the lineage IIIA strain. A core set of 63 genes was positively regulated by σB in all four strains; different total numbers of genes were positively regulated by σB in each strain. Our results suggest that σB universally contributes to L. monocytogenes virulence, but specific σB-regulated stress response phenotypes vary among strains.

2010-06-01 | E-GEOD-21427 | biostudies-arrayexpress

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