Sofia Bergman: Identification and functional characterization of RNA-binding proteins in Salmonella

Abstract

Bacteria live in an ever-changing environment, and thus require adequate gene expression changes to survive and adapt in variable conditions. Regulation of gene expression occurs at several levels. The work presented in this thesis concerns post-transcriptional regulation, i.e. regulation that acts on the transcribed mRNA. The main players at this level of regulation are regulatory small RNAs and RNA-binding proteins (RBPs), which affect mRNA translation and degradation rates. 

This work has mainly focused on characterizing the globally acting RBP ProQ in Salmonella enterica serovar Typhimurium (S.Tm). ProQ interacts with hundreds of RNA transcripts and is important for many phenotypical traits such as motility, virulence and persister cell formation. In paper I, we identify the interactome of ProQ in infection-like conditions that mimic the Salmonella-containing vacuole (SCV) of eukaryotic host cells. We also highlight ProQ’s relevance for proper expression of the virulence genes connected to survival and proliferation within the SCV, by post-transcriptionally affecting expression of the important regulator PhoP. In paper II, we demonstrate that ProQ promotes biofilm formation in S.Tm, and present a new molecular mechanism of ProQ’s interaction with intrinsic terminators. Upon binding, ProQ hinders poly(A) polymerase I-dependent polyadenylation and thereby protects against 3’end-dependent degradation. In paper III, we implement our RNA interactome capture method in S.Tm, and thereby expand the RNA-binding proteome. Among the identified RBPs we discovered virulence-associated proteins previously not connected to RNA binding activities.

In conclusion, the work in this thesis shows new aspects concerning the function of ProQ, highlights the physiological relevance of this protein, and generally expands the RNA-binding proteome of S.Tm. Importantly, the findings presented here point to new scientific questions that will help drive future research in the area of post-transcriptional gene regulation.