The RNA chaperone Hfq is mostly known to help small regulatory RNAs (sRNAs) interact with target mRNAs to block initiating ribosomes. In this model, whereas the sRNA is directly competing with ...initiating 30S ribosomal subunits, Hfq plays only an indirect role, allowing optimal sRNA-mRNA pairing. Here we report that Hfq is recruited by a sRNA, Spot42, to bind to a precise AU-rich region in the vicinity of the translation initiation region (TIR) of sdhC mRNA and competes directly with 30S ribosomal subunits. We show that the sRNA Spot42 binds sdhC too far upstream of the TIR to directly repress translation initiation in vitro and in vivo. Contrary to the canonical model of sRNA regulation, this suggests a new mechanism where Hfq is directly involved in the translational repression of the target mRNA and where the sRNA acts only as a recruitment factor.
During infection, bacterial pathogens successfully sense, respond and adapt to a myriad of harsh environments presented by the mammalian host. This exquisite level of adaptation requires a robust ...modulation of their physiological and metabolic features. Additionally, virulence determinants, which include host invasion, colonization and survival despite the host's immune responses and antimicrobial therapy, must be optimally orchestrated by the pathogen at all times during infection. This can only be achieved by tight coordination of gene expression. A large body of evidence implicate the prolific roles played by bacterial regulatory RNAs in mediating gene expression both at the transcriptional and post-transcriptional levels. This review describes mechanistic and regulatory aspects of bacterial regulatory RNAs and highlights how these molecules increase virulence efficiency in human pathogens. As illustrative examples,
, the uropathogenic strain of
, and
have been selected.
Recent advances in prokaryote genetics have highlighted the important and complex roles of small regulatory RNAs (sRNAs). Although blocking mRNA translation is often the main function of sRNAs, these ...molecules can also induce the degradation of target mRNAs using a mechanism that drastically differs from eukaryotic RNA interference (RNAi). Whereas RNAi relies on RNase III-like machinery that is specific to double-strand RNAs, sRNA-mediated mRNA degradation in Escherichia coli and Samonella typhimurium depends on RNase E, a single-strand specific endoribonuclease. Surprisingly, the latest descriptions of sRNA-mediated mRNA degradation in various bacteria suggest a variety of previously unsuspected mechanisms. In this review, we focus on recently characterized mechanisms in which sRNAs can bind to target mRNAs to induce decay. These new mechanisms illustrate how sRNAs and mRNA structures, including riboswitches, act cooperatively with protein partners to initiate the decay of mRNAs. This article is part of a Special Issue entitled: RNA Decay mechanisms.
•Many small RNAs regulate translation initiation in prokaryotes.•Small RNAs interact with the RNA chaperone Hfq for stability and function.•Some small RNAs also initiate mRNA decay through RNAse E recruitment.•New mechanisms including Rho termination factor and riboswitches are discussed.
The first report of
trans
-acting RNA-based regulation in bacterial cells dates back to 1984. Subsequent studies in diverse bacteria unraveled shared properties of
trans
-acting small regulatory ...RNAs, forming a clear definition of these molecules. These shared characteristics have been used extensively to identify new small RNAs (sRNAs) and their interactomes. Recently however, emerging technologies able to resolve RNA-RNA interactions have identified new types of regulatory RNAs. In this review, we present a broader definition of
trans
-acting sRNA regulators and discuss their newly discovered intrinsic characteristics.
During ribosomal and transfer RNA maturation, external transcribed spacer (ETS) and internal transcribed spacer (ITS) sequences are excised and, as non-functional by-products, are rapidly degraded. ...However, we report that the 3’ETS of the glyW-cysT-leuZ polycistronic tRNA precursor is highly and specifically enriched by co-purification with at least two different small regulatory RNAs (sRNAs), RyhB and RybB. Both sRNAs are shown to base pair with the same region in the 3’ETS of leuZ (3’ETSleuZ). Disrupting the pairing by mutating 3’ETSleuZ strongly increased the activity of sRNAs, even under non-inducing conditions. Our results indicate that 3’ETSleuZ prevents sRNA-dependent remodeling of tricarboxylic acid (TCA) cycle fluxes and decreases antibiotic sensitivity when sRNAs are transcriptionally repressed. This suggests that 3’ETSleuZ functions as a sponge to absorb transcriptional noise from repressed sRNAs. Additional data showing RybB and MicF sRNAs are co-purified with ITSmetZ-metW and ITSmetW-metV strongly suggests a wide distribution of this phenomenon.
Summary
GcvB small RNA is described as post‐transcriptional regulator of 1–2% of all mRNAs in Escherichia coli and Salmonella Typhimurium. At least 24 GcvB:mRNA interactions have been validated in ...vivo, establishing the largest characterized sRNA targetome. By performing MS2‐affinity purification coupled with RNA sequencing (MAPS) technology, we identified seven additional mRNAs negatively regulated by GcvB in E. coli. Contrary to the vast majority of previously known targets, which pair to the well‐conserved GcvB R1 region, we validated four mRNAs targeted by GcvB R3 region. This indicates that base‐pairing through R3 seed sequence seems relatively common. We also noticed unusual GcvB pairing sites in the coding sequence of two target mRNAs. One of these target mRNAs has a pairing site displaying a unique ACA motif, suggesting that GcvB could hijack a translational enhancer element. The second target mRNA is likely regulated via an active RNase E‐mediated mRNA degradation mechanism. Remarkably, we confirmed the importance of the sRNA sponge SroC in the fine‐tuning control of GcvB activity in function of growth conditions such as growth phase and nutrient availability.
GcvB sRNA negatively regulates at least 31 target mRNAs mostly involved in amino acid metabolism in Escherichia coli and Salmonella Typhimurium. Two main regions of GcvB, referred to as R1 and R3, are required to base‐pair with described target mRNAs. Remarkably, SroC, a GcvB sRNA sponge, is of prime importance to release GcvB‐dependent repression in stationary phase of growth and in minimal medium.
Most polycistronic genes are expressed in a single transcript, in which each cistron produces a fixed amount of protein. In this report, we show the first example of differential degradation of a ...polycistronic gene induced by a small regulatory RNA (sRNA). Our data show that the iron‐responsive sRNA, RyhB, binds to the second cistron of the polycistronic mRNA, iscRSUA, which encodes the necessary machinery for biosynthesis of Fe–S clusters, and promotes the cleavage of the downstream iscSUA transcript. This cleavage gives rise to the remaining 5′‐section of the transcript encoding IscR, a transcriptional regulator responsible for activation and repression of several genes depending on the cellular Fe–S level. Our data indicate that the iscR transcript is stable and that translation is active. The stability of the iscR transcript depends on a 111‐nucleotide long non‐translated RNA section located between iscR and iscS, which forms a strong repetitive extragenic palindromic secondary structure and may protect against ribonucleases degradation. This novel regulation shows how sRNAs and mRNA structures can work together to modulate the transcriptional response to a specific stress.
Traffic of molecules across the bacterial membrane mainly relies on porins and transporters, whose expression must adapt to environmental conditions. To ensure bacterial fitness, synthesis and ...assembly of functional porins and transporters are regulated through a plethora of mechanisms. Among them, small regulatory RNAs (sRNAs) are known to be powerful post-transcriptional regulators. In Escherichia coli, the MicF sRNA is known to regulate only four targets, a very narrow targetome for a sRNA responding to various stresses, such as membrane stress, osmotic shock, or thermal shock. Using an in vivo pull-down assay combined with high-throughput RNA sequencing, we sought to identify new targets of MicF to better understand its role in the maintenance of cellular homoeostasis. Here, we report the first positively regulated target of MicF, the oppA mRNA. The OppA protein is the periplasmic component of the Opp ATP-binding cassette (ABC) oligopeptide transporter and regulates the import of short peptides, some of them bactericides. Mechanistic studies suggest that oppA translation is activated by MicF through a mechanism of action involving facilitated access to a translation-enhancing region in oppA 5ʹUTR. Intriguingly, MicF activation of oppA translation depends on cross-regulation by negative trans-acting effectors, the GcvB sRNA and the RNA chaperone protein Hfq.
Colorectal cancer (CRC) is one of the prevailing causes of cancer mortality in the world. A common screening test for CRC is based on the human hemoglobin immunochemical based fecal occult blood test ...(iFOBT), which consists in the detection of blood in the patient's stool. In addition to iFOBT, recent studies support the use of the gut microbiome as a biomarker for CRC prediction. However, these studies did not take into account the effect of blood itself on the microbiome composition, independently of CRC. Therefore, we investigated the microbiome of patients undergoing the iFOBT screening in order to determine the effect of blood alone. Our cohort consisted of patients who had no blood in their stools (n = 265) or did have blood but no underlying precancerous or cancerous lesions (n = 235). We also identified bacterial taxa specifically associated with the presence of blood in stools.
We observed significant differences in the intestinal bacterial composition that could be solely caused by the presence of blood in stools. More precisely, we identified 12 bacterial species showing significant differences in abundance between both our study groups. These species, Bacteroides uniformis, Collinsella aerofaciens, Eggerthella lenta and Clostridium symbiosum demonstrated increased abundance in the presence of blood. In contrast, the species Prevotella copri, Coprococcus eutactus and catus, Faecalibacterium prausnitzii, Roseburia faecis, Blautia obeum, Gemmiger formicilis and Clostridium celatum showed decreased abundance in patients with blood in their stools. Notably, we found multiple taxa that were reported in previous studies linking microbiome composition and diseases.
We show that, in the absence of disease, blood in the stools has a major influence on the composition of the microbiome. Our data suggest that blood itself should be taken into consideration when investigating the microbiome signatures of intestinal diseases.
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