The expanding targetome of small RNAs in Salmonella Typhimurium

Ryan, Daniel; Mukherjee, Mohana; Suar, Mrutyunjay

doi:10.1016/j.biochi.2017.03.005

Cited by 13 publications

(7 citation statements)

References 93 publications

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“…Then any additional targets with the same predicted target site found by ≥2 algorithms are ranked next (4). This is followed by targets that were only predicted by a single algorithm, in the following order: CopraRNA (5), TargetRNA, sTarPicker (6), and IntaRNA (7). Using the results filters, a user can narrow or widen their searches, for example, by limiting the predictions made by single algorithms or by applying secondary filters on binding site regions.…”

Section: Resultsmentioning

confidence: 99%

“…In recent years it has become evident that sRNAs are ubiquitous and play an important role in mediating and regulating many basic cellular processes and stress responses. Hundreds of small RNAs have been identified in numerous bacterial species such as Bacillus subtilis (5), Listeria monocytogenes (6), and Salmonella enterica (7, 8). With the advancement of current technologies, the number of sRNAs identified in diverse organisms will surely increase.…”

Section: Introductionmentioning

confidence: 99%

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sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs

King

Vanderpool²,

Degnan³

2018

Preprint

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Small RNAs (sRNAs) post-transcriptionally regulate mRNA targets, typically under conditions of environmental stress. Although hundreds of sRNAs have been discovered in diverse bacterial genomes, most sRNAs remain uncharacterized, even in model organisms. Identification of mRNA targets directly regulated by sRNAs is rate-limiting for sRNA functional characterization. To address this, we developed a computational pipeline that we named SPOT for sRNA-targetPredictionOrganizingTool. SPOT incorporates existing computational tools to search for sRNA binding sites, allows filtering based on experimental data, and organizes the results into a standardized report. SPOT sensitivity (Correctly Predicted Targets/Total Known Targets) was equal to or exceeded any individual method when used on 12 characterized sRNAs. Using SPOT, we generated a set of target predictions for the sRNA RydC, which was previously shown to positively regulatecfamRNA, encoding cyclopropane fatty acid synthase. SPOT identifiedcfaalong with additional putative mRNA targets, which we then tested experimentally. Our results demonstrated that in addition tocfamRNA, RydC also regulatestrpEandpheAmRNAs, which encode aromatic amino acid biosynthesis enzymes. Our results suggest that SPOT can facilitate elucidation of sRNA target regulons to expand our understanding of the many regulatory roles played by bacterial sRNAs.IMPORTANCESmall RNAs (sRNAs) regulate gene expression in diverse bacteria by interacting with mRNAs to change their structure, stability or translation. Hundreds of sRNAs have been identified in bacteria, but characterization of their regulatory functions is limited by difficulty with sensitive and accurate identification of mRNA targets. Thus, new robust methods of bacterial sRNA target identification are in demand. Here, we describe ourSmall RNA-targetPredictionOrganizingTool, which streamlines the process of sRNA target prediction by providing a single pipeline that combines available computational prediction tools with customizable results filtering based on experimental data. SPOT allows the user to rapidly produce a prioritized list of predicted sRNA-target mRNA interactions that serves as a basis for further experimental characterization. This tool will facilitate elucidation of sRNA regulons in bacteria, allowing new discoveries regarding the roles of sRNAs in bacterial stress responses and metabolic regulation.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs

King

Vanderpool²,

Degnan³

2018

Preprint

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“…In recent years, approximately 280 sRNAs were predicted in STM [24]. Existing studies have found that sRNAs can bind to target mRNAs through incomplete base pairing and play important regulatory roles in STM at post-transcriptional level, which is closely involved in the environmental adaptation, metabolic responses and pathogenicity of STM [25,26]. In STM-infected mouse macrophages, Shabarinath et al found that there were 73 sRNAs significantly up-regulated, among which the STnc1280 gene transcript increased by 1.62-fold [15].…”

Section: Discussionmentioning

confidence: 99%

STnc1280, a trans-coding sRNA is involved in virulence modulation via targeting gldA mRNA in Salmonella Typhimurium

Ning,

Li,

Wang

et al. 2024

Journal of Medical Microbiology

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Introduction. Salmonella Typhimurium (STM) is a food-borne Gram-negative bacterium, which can infect humans and a wide range of livestock and poultry, causing a variety of diseases such as septicaemia, enteritis and abortion. Hypothesis/Gap Statement. We will decipher the impacts of sRNA STnc1280 on STM virulence and provide a theoretical basis to reveal the regulatory role and molecular mechanism of STnc1280. Aim. The main objective of this study was to clarify whether sRNA STnc1280 exerts regulatory roles on STM pathogenicity. Methodology. The STnc1280 gene was amplified and its molecular characteristics were analysed in this study. Then, STnc1280 gene deletion strain (STM-ΔSTnc1280) and the complementary strain (ΔSTnc1280/STnc1280) were constructed by λ-Red homologous recombination method, respectively, to analyse of adhesion and invasive ability and pathogenicity of different strains. Subsequently, the potential target gene regulated by STnc1280 was predicted using target RNA2 software, followed by the verification of the interaction between STnc1280 and target mRNA using the dual plasmid reporter system (DPRS). Furthermore, the mRNA and protein level of target gene was determined using qRT-PCR and Western blot, respectively. Results. The results revealed that the cell adhesion and invasive ability and pathogenicity of STM-ΔSTnc1280 were significantly reduced compared to STM-SL1344 strain, indicating that the deficiency of STnc1280 gene significantly influenced STM pathogenicity. The DPRS results showed that STnc1280 can interact with the mRNA of target gene gldA, thus suppressing the expression of lacZ gene. Furthermore, the level of gldA mRNA was not influenced in STM-ΔSTnc1280, but the expression of GldA protein decreased significantly. Conclusion. Combining the bioinformatic analysis, these findings suggested that STnc1280 may bind to the SD sequence of gldA mRNA, hindering the binding of ribosomes to gldA mRNA, thereby inhibiting the expression of GldA protein to modulate the virulence of STM.

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“…ArcZ, adrA, and csgD are genes involved in Salmonella biofilm formation and have been recognized as key regulators for biofilm formation [ 49 ]. ArcZ can regulate biofilm phenotypes in Salmonella [ 43 ].…”

Section: Discussionmentioning

confidence: 99%

Propionate and Butyrate Inhibit Biofilm Formation of Salmonella Typhimurium Grown in Laboratory Media and Food Models

Liu

Zhu

Qin

et al. 2022

Foods

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Salmonella is among the most frequently isolated foodborne pathogens, and biofilm formed by Salmonella poses a potential threat to food safety. Short-chain fatty acids (SCFAs), especially propionate and butyrate, have been demonstrated to exhibit a beneficial effect on promoting intestinal health and regulating the host immune system, but their anti-biofilm property has not been well studied. This study aims to investigate the effects of propionate or butyrate on the biofilm formation and certain virulence traits of Salmonella. We investigated the effect of propionate or butyrate on the biofilm formation of Salmonella enterica serovar Typhimurium (S. Typhimurium) SL1344 grown in LB broth or food models (milk or chicken juice) by crystal violet staining methods. Biofilm formation was significantly reduced in LB broth and food models and the reduction was visualized using a scanning electron microscope (SEM). Biofilm metabolic activity was attenuated in the presence of propionate or butyrate. Meanwhile, both SCFAs decreased AI-2 quorum sensing based on reporter strain assay. Butyrate, not propionate, could effectively reduce bacterial motility. Bacterial adhesion to and invasion of Caco-2 cells were also significantly inhibited in the presence of both SCFAs. Finally, two SCFAs downregulated virulence genes related to biofilm formation and invasion through real-time polymerase chain reaction (RT-PCR). These findings demonstrate the potential application of SCFAs in the mitigation of Salmonella biofilm in food systems, but future research mimicking food environments encountered during the food chain is necessitated.

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The expanding targetome of small RNAs in Salmonella Typhimurium

Cited by 13 publications

References 93 publications

sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs

sRNA-target Prediction Organizing Tool (SPOT) integrates computational and experimental data to facilitate functional characterization of bacterial small RNAs

STnc1280, a trans-coding sRNA is involved in virulence modulation via targeting gldA mRNA in Salmonella Typhimurium

Propionate and Butyrate Inhibit Biofilm Formation of Salmonella Typhimurium Grown in Laboratory Media and Food Models

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