Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli

Raad, Nicole; Luidalepp, Hannes; Fasnacht, Michel; Polacek, Norbert (2021). Transcriptome-Wide Analysis of Stationary Phase Small ncRNAs in E. coli. International journal of molecular sciences, 22(4), p. 1703. MDPI 10.3390/ijms22041703

ijms-22-01703.pdf - Published Version
Available under License Creative Commons: Attribution (CC-BY).

Download (718kB) | Preview

Almost two-thirds of the microbiome’s biomass has been predicted to be in a non-proliferating, and thus dormant, growth state. It is assumed that dormancy goes hand in hand with global downregulation of gene expression. However, it remains largely unknown how bacteria manage to establish this resting phenotype at the molecular level. Recently small non-protein-coding RNAs (sRNAs or ncRNAs) have been suggested to be involved in establishing the non-proliferating state in bacteria. Here, we have deep sequenced the small transcriptome of Escherichia coli in the exponential and stationary phases and analyzed the resulting reads by a novel biocomputational pipeline STARPA (Stable RNA Processing Product Analyzer). Our analysis reveals over 12,000 small transcripts enriched during both growth stages. Differential expression analysis reveals distinct sRNAs enriched in the stationary phase that originate from various genomic regions, including transfer RNA (tRNA) fragments. Furthermore, expression profiling by Northern blot and RT-qPCR analyses confirms the growth phase-dependent expression of several enriched sRNAs. Our study adds to the existing repertoire of bacterial sRNAs and suggests a role for some of these small molecules in establishing and maintaining stationary phase as well as the bacterial stress response. Functional characterization of these detected sRNAs has the potential of unraveling novel regulatory networks central for stationary phase biology.

Item Type:

Journal Article (Original Article)


08 Faculty of Science > Department of Chemistry, Biochemistry and Pharmaceutical Sciences (DCBP)

Graduate School:

Graduate School for Cellular and Biomedical Sciences (GCB)

UniBE Contributor:

Raad, Nicole, Luidalepp, Hannes, Fasnacht, Michel, Polacek, Norbert


500 Science > 570 Life sciences; biology
500 Science > 540 Chemistry








Christina Schüpbach

Date Deposited:

12 Feb 2021 14:43

Last Modified:

29 Apr 2024 08:02

Publisher DOI:


PubMed ID:





Actions (login required)

Edit item Edit item
Provide Feedback