Impact of Hfq on the Bacillus subtilis transcriptome

Hermann Hämmerle; Fabian Amman; Branislav Večerek; Jörg Stülke; Ivo Hofacker; Udo Bläsi

doi:10.1371/journal.pone.0098661

Impact of Hfq on the Bacillus subtilis transcriptome

PLoS One. 2014 Jun 16;9(6):e98661. doi: 10.1371/journal.pone.0098661. eCollection 2014.

Authors

Hermann Hämmerle¹, Fabian Amman², Branislav Večerek¹, Jörg Stülke³, Ivo Hofacker², Udo Bläsi¹

Affiliations

¹ Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Centre of Molecular Biology, University of Vienna, Vienna, Austria.
² Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.
³ Department of General Microbiology, Institute of Microbiology and Genetics, Georg-August University Göttingen, Göttingen, Germany.

Abstract

The RNA chaperone Hfq acts as a central player in post-transcriptional gene regulation in several Gram-negative Bacteria, whereas comparatively little is known about its role in Gram-positive Bacteria. Here, we studied the function of Hfq in Bacillus subtilis, and show that it confers a survival advantage. A comparative transcriptome analysis revealed mRNAs with a differential abundance that are governed by the ResD-ResE system required for aerobic and anaerobic respiration. Expression of resD was found to be up-regulated in the hfq- strain. Furthermore, several genes of the GerE and ComK regulons were de-regulated in the hfq- background. Surprisingly, only six out of >100 known and predicted small RNAs (sRNAs) showed altered abundance in the absence of Hfq. Moreover, Hfq positively affected the transcript abundance of genes encoding type I toxin-antitoxin systems. Taken the moderate effect on sRNA levels and mRNAs together, it seems rather unlikely that Hfq plays a central role in RNA transactions in Bacillus subtilis.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Aerobiosis
Bacillus subtilis / genetics
Bacillus subtilis / growth & development*
Bacillus subtilis / metabolism
Bacterial Proteins / genetics
Bacterial Proteins / metabolism*
DNA-Binding Proteins / genetics
Gene Expression Profiling / methods*
Gene Expression Regulation, Bacterial*
Host Factor 1 Protein / genetics
Host Factor 1 Protein / metabolism*
RNA, Bacterial / analysis*
RNA, Messenger / analysis
RNA, Small Nuclear / analysis
Regulon
Stress, Physiological
Transcription Factors / genetics

Substances

Bacterial Proteins
DNA-Binding Proteins
Host Factor 1 Protein
RNA, Bacterial
RNA, Messenger
RNA, Small Nuclear
ResD protein, Bacillus subtilis
Transcription Factors

Grants and funding

The work was supported by the Austrian Science Fund (www.fwf.ac.at/en) through the Special Research Program RNA-REG F43, subproject AF4311 (UB), and the doctoral program RNA-Biology W-1207 (HH). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.