Hfq Globally Binds and Destabilizes sRNAs and mRNAs in Yersinia pestis

The RNA chaperone Hfq is a novel regulator of catalase expression and hydrogen peroxide-induced oxidative stress response in Listeria monocytogenes EGD-e

The RNA chaperone Hfq plays a pivotal role in many bacteria, acting as a regulator of gene expression and promoting interaction between mRNA-sRNA pairs in Gram-negative bacteria. However, in Gram-positive bacteria this protein is expendable for riboregulation, and the main function of Hfq remains elusive. This work unveils a novel function for Hfq in the oxidative stress response of the human pathogen Listeria monocytogenes, a Gram-positive bacterium responsible for the infectious disease listeriosis. Disruption of hfq gene (Δhfq) results in a hypersensitive phenotype towards hydrogen peroxide (H2O2), in which sub-inhibitory concentrations of this reactive oxygen species (ROS) severely impair growth and viability of L. monocytogenes EGD-e. A Δhfq-complemented strain does not show this phenotype. This Hfq-dependent regulation of oxidative stress seems specific for H2O2, as exposure to superoxides caused no differences. We demonstrate that Hfq has a dual regulatory role in the expression of catalase (kat), the key enzyme involved in H2O2 detoxification. Hfq influences kat transcription under non-stress conditions by modulating the levels of the transcriptional repressor PerR, and also acts post-transcriptionally by stabilizing kat mRNA under H2O2-induced stress. Indeed, enzymatic assays revealed reduced catalase activity in Δhfq cell extracts, a result unrelated to differences in cellular iron content. Bacterial infection triggers immune cells to produce massive amounts of ROS, like H2O2. We show that inactivation of Hfq increases susceptibility to macrophage killing, connecting Hfq with the stress resistance and virulence of L. monocytogenes EGD-e. Overall, these findings advance the understanding of Hfq function within Gram-positive bacteria, revealing for the first time that Hfq is a novel regulator of catalase expression. This paves the way for the study of yet unknown oxidative stress response pathways regulated by Hfq in other pathogens.

Rational Design of High-Efficiency Synthetic Small Regulatory RNAs and Their Application in Robust Genetic Circuit Performance Through Tight Control of Leaky Gene Expression

Synthetic sRNAs show promise as tools for targeted and programmable gene expression manipulation. However, the design of high-efficiency synthetic sRNAs is a challenging task that necessitates careful consideration of multiple factors. Therefore, this study aims to investigate rational design strategies that significantly and robustly enhance the efficiency of synthetic sRNAs. This is achieved by optimizing the following parameters: the sRNA scaffold, mRNA binding affinity, Hfq protein expression level, and mRNA secondary structure. By utilizing optimized synthetic sRNAs within a positive feedback circuit, we effectively addressed the issue of gene expression leakage─an enduring challenge in synthetic biology that undermines the reliability of genetic circuits in bacteria. Our designed synthetic sRNAs successfully prevented gene expression leakage, thus averting unintended circuit activation caused by initial expression noise, even in the absence of signal molecules. This result shows that high-efficiency synthetic sRNAs not only enable precise gene knockdown for metabolic engineering but also ensure the robust performance of synthetic circuits. The strategies developed here hold significant promise for broad applications across diverse biotechnological fields, establishing synthetic sRNAs as pivotal tools in advancing synthetic biology and gene regulation.

Molecular mechanism of enhanced ethanol tolerance associated with hfq overexpression in Zymomonas mobilis

Zymomonas mobilis is a promising microorganism for industrial bioethanol production. However, ethanol produced during fermentation is toxic to Z. mobilis and affects its growth and bioethanol production. Although several reports demonstrated that the RNA-binding protein Hfq in Z. mobilis contributes to the tolerance against multiple lignocellulosic hydrolysate inhibitors, the role of Hfq on ethanol tolerance has not been investigated. In this study, hfq in Z. mobilis was either deleted or overexpressed and their effects on cell growth and ethanol tolerance were examined. Our results demonstrated that hfq overexpression improved ethanol tolerance of Z. mobilis, which is probably due to energy saving by downregulating flagellar biosynthesis and heat stress response proteins, as well as reducing the reactive oxygen species induced by ethanol stress via upregulating the sulfate assimilation and cysteine biosynthesis. To explore proteins potentially interacted with Hfq, the TEV protease mediated Yeast Endoplasmic Reticulum Sequestration Screening system (YESS) was established in Z. mobilis. YESS results suggested that Hfq may modulate the cytoplasmic heat shock response by interacting with the heat shock proteins DnaK and DnaJ to deal with the ethanol inhibition. This study thus not only revealed the underlying mechanism of enhanced ethanol tolerance by hfq overexpression, but also provided an alternative approach to investigate protein-protein interactions in Z. mobilis.

Seneca Valley Virus Induces DHX30 Cleavage to Antagonize Its Antiviral Effects

Seneca Valley virus (SVV) is a new pathogen associated with porcine idiopathic vesicular disease (PIVD) in recent years. However, SVV-host interaction is still unclear. In this study, through LC-MS/MS analysis and coimmunoprecipitation analysis, DHX30 was identified as a 3C^pro-interacting protein. 3C^pro mediated the cleavage of DHX30 at a specific site, which depends on its protease activity. Further study showed that DHX30 was an intrinsic antiviral factor against SVV that was dependent on its helicase activity. DHX30 functioned as a viral-RNA binding protein that inhibited SVV replication at the early stage of viral infection. RIP-seq showed comparatively higher coverage depth at SVV 5'UTR, but the distribution across SVV RNA suggested that the interaction had low specificity. DHX30 expression strongly inhibited double-stranded RNA (dsRNA) production. Interestingly, DHX30 was determined to interact with 3D in an SVV RNA-dependent manner. Thus, DHX30 negatively regulated SVV propagation by blocking viral RNA synthesis, presumably by participating in the viral replication complex. IMPORTANCE DHX30, an RNA helicase, is identified as a 3C^pro-interacting protein regulating Seneca Valley virus (SVV) replication dependent on its helicase activity. DHX30 functioned as a viral-RNA binding protein that inhibited SVV replication at the early stage of virus infection. DHX30 expression strongly inhibited double-stranded RNA (dsRNA) production. In addition, 3C^pro abolished DHX30 antiviral effects by inducing DHX30 cleavage. Thus, DHX30 is an intrinsic antiviral factor that inhibits SVV replication.

Binding of the RNA Chaperone Hfq on Target mRNAs Promotes the Small RNA RyhB-Induced Degradation in Escherichia coli

Many RNA-RNA interactions depend on molecular chaperones to form and remain stable in living cells. A prime example is the RNA chaperone Hfq, which is a critical effector involved in regulatory interactions between small RNAs (sRNAs) and cognate target mRNAs in Enterobacteriaceae. While there is a great deal of in vitro biochemical evidence supporting the model that Hfq enhances rates or affinities of sRNA:mRNA interactions, there is little corroborating in vivo evidence. Here we used in vivo tools including reporter genes, co-purification assays, and super-resolution microscopy to analyze the role of Hfq in RyhB-mediated regulation, and we found that Hfq is often unnecessary for efficient RyhB:mRNA complex formation in vivo. Remarkably, our data suggest that a primary function of Hfq is to promote RyhB-induced cleavage of mRNA targets by RNase E. Moreover, our work indicates that Hfq plays a more limited role in dictating regulatory outcomes following sRNAs RybB and DsrA complex formation with specific target mRNAs. Our investigation helps evaluate the roles played by Hfq in some RNA-mediated regulation.

Metagenomic and metatranscriptomic profiling of Lactobacillus casei Zhang in the human gut

Little is known about the replication and dynamic transcription of probiotics during their “passenger” journey in the human GI tract, which has therefore limited the understanding of their probiotic mechanisms. Here, metagenomic and metatranscriptomic sequencing was used to expose the in vivo expression patterns of the probiotic Lactobacillus casei Zhang (LcZ), which was compared with its in vitro growth transcriptomes, as well as the dynamics of the indigenous microbiome response to probiotic consumption. Extraction of the strain-specific reads revealed that replication and transcripts from the ingested LcZ were increased, while those from the resident L. casei strains remained unchanged. Mapping of all sequencing reads to LcZ genome showed that gene expression in vitro and in vivo differed dramatically. Approximately 39% of mRNAs and 45% of sRNAs of LcZ well-expressed were repressed after ingestion into human gut. The expression of ABC transporter genes and amino acid metabolism genes was induced at day 14 of ingestion, and genes for sugar and SCFA metabolism were activated at day 28 of ingestion. Expression of rli28c sRNA with peaked expression during the in vitro stationary phase was also activated in the human gut; this sRNA repressed LcZ growth and lactic acid production in vitro. However, the response of the human gut microbiome to LcZ was limited and heterogeneous. These findings implicate the ingested probiotic has to change its transcription patterns to survive and adapt in the human gut, and the time-dependent activation patterns indicate highly dynamic cross-talk between the probiotic and human gut microbes.

Small RNAs as Fundamental Players in the Transference of Information During Bacterial Infectious Diseases

Communication shapes life on Earth. Transference of information has played a paramount role on the evolution of all living or extinct organisms since the appearance of life. Success or failure in this process will determine the prevalence or disappearance of a certain set of genes, the basis of Darwinian paradigm. Among different molecules used for transmission or reception of information, RNA plays a key role. For instance, the early precursors of life were information molecules based in primitive RNA forms. A growing field of research has focused on the contribution of small non-coding RNA forms due to its role on infectious diseases. These are short RNA species that carry out regulatory tasks in cis or trans. Small RNAs have shown their relevance in fine tuning the expression and activity of important regulators of essential genes for bacteria. Regulation of targets occurs through a plethora of mechanisms, including mRNA stabilization/destabilization, driving target mRNAs to degradation, or direct binding to regulatory proteins. Different studies have been conducted during the interplay of pathogenic bacteria with several hosts, including humans, animals, or plants. The sRNAs help the invader to quickly adapt to the change in environmental conditions when it enters in the host, or passes to a free state. The adaptation is achieved by direct targeting of the pathogen genes, or subversion of the host immune system. Pathogens trigger also an immune response in the host, which has been shown as well to be regulated by a wide range of sRNAs. This review focuses on the most recent host-pathogen interaction studies during bacterial infectious diseases, providing the perspective of the pathogen.

Potential regulation of small RNAs on bacterial function activities in pig farm wastewater treatment plants

Small RNAs (sRNAs) are key players in the regulation of bacterial gene expression. However, the distribution and regulatory functions of sRNA in pig farm wastewater treatment plants (WWTPs) remains unknown. In this study, the wastewaters in anoxic and oxic tanks of the WWTPs were collected. The profiles of the community structure, mRNA expression, and sRNA expression of bacteria in pig farm wastewater were investigated using transcriptome sequencing and qPCR. This study demonstrated that there was a higher abundance of sRNA in the pig farm WWTPs and 52 sRNAs were detected. The sRNAs were mainly present in Proteobacteria and Firmicutes, including the potential human pathogenic bacteria (HPB) (Escherichia, Shigella, Bordetella and Morganella), crop pathogen (Pectobacterium) and denitrifying bacteria (Zobellella). And the sRNAs were involved in the bacterial functional activities such as translation, transcription, drug resistance, membrane transport and amino acid metabolism. In addition, most sRNAs had a higher abundance in anoxic tanks which contained a higher abundance of the genes associated with infectious diseases and drug resistance than that in oxic tanks. The results presented here show that in pig farm WWTPs, sRNA played an important role in bacterial function activities, especially the infectious diseases, drug resistance and denitrification, which can provide a new point of penetration for improving the pig farm WWTPs.