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Series GSE155764 Query DataSets for GSE155764
Status Public on Mar 19, 2021
Title Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics
Organism Salmonella enterica subsp. enterica serovar Typhimurium
Experiment type Expression profiling by high throughput sequencing
Summary Antisense peptide nucleic acids (PNAs) inhibiting mRNAs of essential genes provide a straight-forward way to repurpose our knowledge of bacterial regulatory RNAs for development of programmable species-specific antibiotics. While there is ample proof of PNA efficacy, their target selectivity and impact on bacterial physiology are poorly understood. Moreover, while antibacterial PNAs are typically designed to block mRNA translation, effects on target mRNA levels are not well-investigated. Here, we pioneer the use of global RNA-seq analysis to decipher PNA activity in a transcriptome-wide manner. We find that PNA-based antisense oligomer conjugates robustly decrease mRNA levels of the widely-used target gene, acpP, in Salmonella enterica, with limited off-target effects. Systematic analysis of several different PNA-carrier peptides attached not only shows different bactericidal efficiency, but also activation of stress pathways. In particular, KFF-, RXR- and Tat-PNA conjugates especially induce the PhoP/Q response, whereas the latter two additionally trigger several distinct pathways. We show that constitutive activation of the PhoP/Q response can lead to Tat-PNA resistance, illustrating the utility of RNA-seq for understanding PNA antibacterial activity. In sum, our study establishes an experimental framework for the design and assessment of PNA antimicrobials in the long-term quest to use these for precision editing of microbiota.

 
Overall design Transcriptome profile of Salmonella enterica in response to three different carrier peptide-PNA conjugates with three replicates per sample. Total of 30 samples (3 carrier peptides*3 conditions*3 replicates + 3 Water controls).

 
Contributor(s) Popella L, Jung J, Barquist L, Vogel J, Popova K, Durica-Mitić S
Citation(s)
  • Popella L, Jung J, Popova K, Ðurica-Mitić S et al. Global RNA profiles show target selectivity and physiological effects of peptide-delivered antisense antibiotics. Nucleic Acids Res 2021 May 7;49(8):4705-4724. PMID: 33849070
Submission date Aug 05, 2020
Last update date May 20, 2021
Contact name Jakob Jeremias Jung
E-mail(s) jakobjung@tutanota.com
Organization name University of Würzburg
Department Institute of Molecular Infection Biology (IMIB)
Lab Vogel lab
Street address Josef-Schneider-Str. 2/Bau D15
City Würzburg
State/province Bayern
ZIP/Postal code 97080
Country Germany
 
Platforms (1)
GPL21220 Illumina NextSeq 500 (Salmonella enterica subsp. enterica serovar Typhimurium)
Samples (30)
GSM4979302 Water control R1
GSM4979303 KFF-acpP R1
GSM4979304 KFF-acpP-scrambled R1
Relations
BioProject PRJNA655500
SRA SRP276137

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
GSE155764_read_counts.xlsx 788.1 Kb (ftp)(http) XLSX
SRA Run SelectorHelp
Raw data are available in SRA
Processed data are available on Series record

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