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Series GSE173540 Query DataSets for GSE173540
Status Public on Apr 30, 2021
Title Analyses of competent and non‐competent subpopulations of Bacillus subtilis reveal yhfW, yhxC and ncRNAs as novel players in competence
Organism Bacillus subtilis
Experiment type Expression profiling by high throughput sequencing
Summary Upon competence‐inducing nutrient‐limited conditions, only part of the Bacillus subtilis population becomes competent. Here, we separated the two subpopulations by fluorescence‐assisted cell sorting (FACS). Using RNA‐seq, we confirmed the previously described ComK regulon. We also found for the first time significantly downregulated genes in the competent subpopulation. The downregulated genes are not under direct control by ComK but have higher levels of corresponding antisense RNAs in the competent subpopulation. During competence, cell division and replication are halted. By investigating the proteome during competence, we found higher levels of the regulators of cell division, MinD and Noc. The exonucleases SbcC and SbcD were also primarily regulated at the post‐transcriptional level. In the competent subpopulation, yhfW was newly identified as being highly upregulated. Its absence reduces the expression of comG, and has a modest, but statistically significant effect on the expression of comK. Although expression of yhfW is higher in the competent subpopulation, no ComK‐binding site is present in its promoter region. Mutants of yhfW have a small but significant defect in transformation. Metabolomic analyses revealed significant reductions in tricarboxylic acid (TCA) cycle metabolites and several amino acids in a ΔyhfW mutant. RNA‐seq analysis of ΔyhfW revealed higher expression of the NAD synthesis genes nadA, nadB and nadC.
 
Overall design 6 samples 2 replicates
 
Contributor(s) Boonstra M, Schaffer M, Sousa J, Morawska L, Holsappel S, Hildebrandt P, Sappa PK, Rath H, de Jong A, Lalk M, Mäder U, Völker U, Kuipers OP
Citation(s) 32249531
Submission date Apr 29, 2021
Last update date May 02, 2021
Contact name Anne de Jong
E-mail(s) anne.de.jong@rug.nl
Phone +31 50 363 2047
Organization name university of Groningen
Department Molecular Genetics
Street address Nijenborgh 7
City Groningen
ZIP/Postal code 9747 AG
Country Netherlands
 
Platforms (1)
GPL23851 Ion Torrent Proton (Bacillus subtilis)
Samples (12)
GSM5269455 BR1_T1_minus
GSM5269456 BR1_T1_plus
GSM5269457 BR1_T2_minus
Relations
BioProject PRJNA726040
SRA SRP316855

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Supplementary file Size Download File type/resource
GSE173540_RAW.tar 1.6 Mb (http)(custom) TAR (of RPKM)
SRA Run SelectorHelp
Raw data are available in SRA
Processed data provided as supplementary file

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