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Series GSE189556 Query DataSets for GSE189556
Status Public on Jul 06, 2022
Title Transcriptomic impact of PrsA over-expression during fed-batch Bacillus subtilis alpha-amylase fermentation
Organism Bacillus subtilis subsp. subtilis str. 168
Experiment type Expression profiling by high throughput sequencing
Summary The production of alpha-amylase (AMY) enzyme in Bacillus subtilis at a high rate leads to accumulation of unfolded AMY, which causes secretion stress. The over-expression of the PrsA chaperon aids the enzyme folding and thus reduces stress. Stress pathways are complex and intertwined in regulation of a variety of cellular mechanism; for instance, PrsA over-expression leads to reduced cell growth. To capture an overview over the impacted mechanisms, we analyze the transcriptomic changes during fed-batch AMY fermentation between a PrsA over-expressing strain and a control in a time-series RNA-seq experiment (n=3, 6 timepoints). We found evidence of transcription in 542 previously un-annotated regions, of which 234 had significant changes in transcription levels (Overall FDR 0.01). The pairwise comparison of up-/downregulated genes and their over-representation in biological processes (FDR 0.01) suggest that the PrsA over-expression might alter ATP biosynthesis activity, amino acid metabolism, and cell wall stability. An additional investigation of the protein-protein association network highlights potential cell motility signaling. Overall, these highlighted mechanisms could potentially further reduce secretion stress or detrimental aspects of PrsA over-expression during AMY production.
 
Overall design RNA-seq study of fed-batch AMY fermentation over time compared between a PrsA over-expressing strain and a control
Web link https://rth.dk/resources/bsg/prsa
 
Contributor(s) Geissler AS, Poulsen LD, Doncheva NT, Anthon C, Seemann SE, González-Tortuero E, Breüner A, Jensen LJ, Hjort C, Vinther J, Gorodkin J
Citation(s) 35992681, 35780132
Submission date Nov 25, 2021
Last update date Aug 23, 2022
Contact name Christian Anthon
E-mail(s) anthon@rth.dk
Phone +4521510929
Organization name University of Copenhagen
Department Veterinary and Animal Sciences
Lab RTH
Street address Thorvaldsens Vej 57
City Frederiksberg C
ZIP/Postal code 1871
Country Denmark
 
Platforms (1)
GPL30999 DNBSEQ-G400 (Bacillus subtilis subsp. subtilis str. 168)
Samples (41)
GSM5703658 batch2-1_MIX1500_T1-1_prsA-je1zyn
GSM5703659 batch1-2a_MIX1501_T1-1_prsA-je1zyn
GSM5703660 batch1-2b_MIX1501_T1-1_prsA-je1zyn
Relations
BioProject PRJNA783567
SRA SRP347876

Download family Format
SOFT formatted family file(s) SOFTHelp
MINiML formatted family file(s) MINiMLHelp
Series Matrix File(s) TXTHelp

Supplementary file Size Download File type/resource
GSE189556_BSGatlas-v1.1.gff.gz 903.7 Kb (ftp)(http) GFF
GSE189556_je1zyn.fna.gz 1.2 Mb (ftp)(http) FNA
GSE189556_prsA-je1zyn.fna.gz 1.2 Mb (ftp)(http) FNA
GSE189556_putative-ncRNA.bed.gz 1.5 Kb (ftp)(http) BED
GSE189556_unannotated-regions.bed.gz 17.2 Kb (ftp)(http) BED
GSE189556_uniquely_mapping-raw_counts.tsv.gz 584.2 Kb (ftp)(http) TSV
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Raw data are available in SRA
Processed data are available on Series record

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