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Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

ABSTRACT: Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa.

ORGANISM(S): Bacillus subtilis subsp. subtilis str. 168

PROVIDER: GSE50653 | GEO | 2014/03/14

SECONDARY ACCESSION(S): PRJNA218207

REPOSITORIES: GEO

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Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

Project description:Comparing the transcriptional responses of Bacillus subtilis strains WN624 and WN1106 at 5 kPa and 101 kPa. WN1106 is a 5 kPa-evolved strain with increased fitness compared to ancestor-WN624 strain at 5 kPa. This experiment probed the difference in response when the strains are grown at 5 kPa. Two-condition experiment, 5 kPa vs. 101 kPa, for both strains. And two component condition of WN1106 compared to WN624 at either 5 kPa or 101 kPa. 4 pressure comparisons.

2014-03-14 | E-GEOD-50653 | biostudies-arrayexpress

Bacillus subtilis subsp. subtilis str. 168

Project description:Bacillus subtilis strains at low-pressure: 5 kPa versus 101 kPa growth

| PRJNA218207 | ENA

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.

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Trancriptional profiling of Bacillus subtilis BsB1 and NCIB3610 rho-deletion mutant

Project description:With these experiments we investigate the impact of the deletion of the gene encoding transcription termination Rho on the transcriptomes of two different Bacillus subtilis strains, BsB1 and NCIB3610. The results confirm massive increase of antisense transcription initially observed with tiling arrays in B. subtilis strain 1012 (Nicolas et al. 2012; PMID:22383849; GSE27303).

2017-07-10 | GSE94303 | GEO

Comparison of the transcription profile of B. subtilis clpX strain with B. subtilis clpX spx strain, reporting on Spx activity

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Membrane protein overproduction stress in Bacillus subtilis

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2021-12-09 | GSE190460 | GEO

Analysis of mRNA decay intermediates in Bacillus subtilis 3' exoribonuclease and RNA helicase mutant strains

Project description:The Bacillus subtilis genome encodes four 3’ exoribonucleases: polynucleotide phosphorylase (PNPase), RNase R, RNase PH, and YhaM. Previous work showed that PNPase, encoded by the pnpA gene, is the major 3’ exonuclease involved in mRNA turnover; in a pnpA deletion strain, numerous mRNA decay intermediates accumulate. Whether B. subtilis mRNA decay occurs in the context of a degradosome complex is controversial. In this study, global mapping of mRNA decay intermediate 3’ ends within coding sequences was performed in strains that were either deleted for, or had an inactivating point mutation in, the pnpA gene. The pattern of 3’ end accumulation in these strains was highly similar, suggesting that mRNA decay was not occurring in the context of a degradosome, whose structure would be affected by the absence of PNPase. A comparison with mapped 3’ ends in a strain lacking CshA, the major RNA helicase, indicated that different mRNAs may require both PNPase and CshA for efficient decay. RNA-seq analysis of strains lacking RNase R suggested that this enzyme did not play a major role in mRNA turnover in the wild-type strain. Strains were constructed that contained only one of the four known 3’ exoribonucleases. When RNase R was the only 3’ exonuclease present, it was able to degrade a model mRNA efficiently, showing processive decay even through a strong stem-loop structure that inhibits PNPase processivity. Strains containing only RNase PH or only YhaM were also insensitive to this RNA secondary structure, suggesting the existence of another, as-yet unidentified, 3’ exoribonuclease.

2022-01-03 | GSE192670 | GEO

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