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Series GSE207089 Query DataSets for GSE207089
Status Public on Feb 15, 2023
Title Transcriptional profiling along lineages of Bacillus subtilis strains with increasingly reduced genomes.
Organism Bacillus subtilis subsp. subtilis str. 168
Experiment type Expression profiling by genome tiling array
Summary 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.
Overall design The transcriptome of each strain was assessed by separate hybridization of two RNA samples extracted from two independent cultures (biological duplicates).
Contributor(s) Tanaka K, Dervyn E, Jules M, Noirot P, Guérin C, Nicolas P
Citation(s) 36919610
Submission date Jun 28, 2022
Last update date May 03, 2023
Contact name Pierre Nicolas
Phone +33-1-3465-2894
Organization name INRAE - Université Paris-Saclay
Street address INRAE - Domaine de Vilvert
City Jouy-en-Josas
ZIP/Postal code F-78350
Country France
Platforms (1)
GPL15150 BaSysBio Bacillus subtilis T2 385K array [gene-level]
Samples (12)
GSM6278362 MS_NMS_rep1
GSM6278363 MS_NMS_rep2
GSM6278364 MGP181_NMS_rep1
BioProject PRJNA853626

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Supplementary file Size Download File type/resource
GSE207089_RAW.tar 119.5 Mb (http)(custom) TAR (of PAIR)
Processed data included within Sample table

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