Global RNA recognition patterns of post-transcriptional regulators Hfq and CsrA revealed by UV crosslinking in vivo

The molecular roles of many RNA-binding proteins in bacterial post-transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP-seq) have begun to revolutionize the transcriptome-wide mapping of eukaryotic RNA-binding protein target sites. We have applied CLIP-seq to chart the target landscape of two major bacterial post-transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single-nucleotide resolution, we identify RNA preferences and structural constraints of Hfq and CsrA during their interactions with hundreds of cellular transcripts. This reveals 3'-located Rho-independent terminators as a universal motif involved in Hfq–RNA interactions. Additionally, Hfq preferentially binds 5' to sRNA-target sites in mRNAs, and 3' to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA-target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP-seq approach will bring new insights into post-transcriptional gene regulation by RNA-binding proteins in diverse bacterial species.
Source: EMBO Journal - Category: Molecular Biology Authors: Tags: Methods & Resources, Microbiology, Virology & Host Pathogen Interaction, RNA Biology Source Type: research

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Contributors : Cunkuan Shen ; Tariqul Islam ; Yoshimitsu Masuda ; Ken-ichi Honjoh ; Takahisa MiyamotoSeries Type : Expression profiling by arrayOrganism : Salmonella enterica subsp. enterica serovar Typhimurium ; Salmonella enterica subsp. enterica serovar Typhimurium str. LT2Salmonella Typhimurium is one of the major foodborne pathogens due to its biofilm formation on food contact surfaces. A polymer of positively charged lysine, ε-Polylysine has been demonstrated to inhibit biofilm formation of both Gram-positive and -negative bacteria. To elucidate the mechanism for inhibition of biofilm formation by ε-P...
Source: GEO: Gene Expression Omnibus - Category: Genetics & Stem Cells Tags: Expression profiling by array Salmonella enterica subsp. enterica serovar Typhimurium Salmonella enterica subsp. enterica serovar Typhimurium str. LT2 Source Type: research
Source: Infection and Drug Resistance - Category: Infectious Diseases Tags: Infection and Drug Resistance Source Type: research
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Source: Frontiers in Immunology - Category: Allergy & Immunology Source Type: research
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
Sutapa Rath, Shennaz Firdaus, Monalisa Mohanty, Rajeev Kumar Seth, Amit Kumar Satapathy, Bijayini BeheraIndian Journal of Nephrology 2019 29(6):434-435
Source: Indian Journal of Nephrology - Category: Urology & Nephrology Authors: Source Type: research
Publication date: Available online 12 November 2019Source: Veterinary MicrobiologyAuthor(s): Sahar Rostami, Jalil Mehrzad, Ramak Yahyaraeyat, Taghi Zahraei SalehiAbstractSalmonella enterica Subsp enterica serovar Typhimurium (S. Typhimurium, ST) is one of the most important serovars of the genus Salmonella in human and animals. Because of its intracellular tropism, monocytes/macrophages are pivotal in killing of Salmonella serovars; they are also responsible for transporting of ST to extra-intestinal organs. To investigate the effect of the ST on the functions of avian innate immune cells, almost homogeneous enriched monoc...
Source: Veterinary Microbiology - Category: Veterinary Research Source Type: research
Abstract Escherichia coli O157:H7 and Salmonella enterica are foodborne pathogens with major public health concern in the U.S. These pathogens utilize several virulence factors to initiate infections in humans. The antimicrobial effect of seven glucosinolate hydrolysis compounds against Salmonella and E. coli O157:H7 was investigated by the disc diffusion assay. Among the tested compounds, benzyl isothiocyanate (BIT), which exerted the highest antimicrobial activity, was evaluated for its anti-virulence properties against these pathogens. The effect of BIT on motility of Salmonella and E. coli O157:H7 and Shiga to...
Source: Food Microbiology - Category: Food Science Authors: Tags: Food Microbiol Source Type: research
C, Pérez-Rodríguez F Abstract This work aimed to study the effect of the combination of Sodium hypochlorite, the most used disinfectant by the vegetable industry, with a natural antimicrobial, benzyl-isothiocyanate (BITC), considering cutting surface and contact time, on the reduction of Salmonella in fresh-cut produce in washing operations under typical industrial conditions. Overall, the combinations of disinfectant and process parameters resulted in a mean reduction of Salmonella of 2.5 log CFU/g. According to statistical analysis, free chlorine and BITC concentrations, contact time and cut size ...
Source: Food Microbiology - Category: Food Science Authors: Tags: Food Microbiol Source Type: research
The objectives of the current study were to investigate: i) the effectiveness of 10 plant essential oil extracts on the viability of Salmonella spp. using disc diffusion ii) the antimicrobial activity of the most effective oils against Salmonella spp. in commercial or 10% w/v hydrated tahini (tahini-based product model) stored at 37, 25 and 10 °C for 28 d and iii) the effect of the addition of essential oil extracts on the sensory acceptability of tahini and hydrated tahini. Among the tested essential oils, thyme (TO) and cinnamon oil (CO) showed the highest antimicrobial activity against tested Salmonella spp. at ...
Source: Food Microbiology - Category: Food Science Authors: Tags: Food Microbiol Source Type: research
Pickled ready-to-eat meat (PRTEM) is a meat product that is treated with various seasonings and then cooked. PRTEM is a popular food consumed mostly in China and some Asian countries. Since this food is considered ‘ready to eat’, once it is contaminated by foodborne pathogens such as Salmonella, the prospect for significant morbidity, mortality, and immeasurable economic losses can occur. Here we investigated the prevalence and concentration of Salmonella in 107 PRTEM samples collected from Shaanxi, China during 2015–2016. Furthermore, we analyzed the serotype, antibiotic susceptibility, and presence of a...
Source: Frontiers in Microbiology - Category: Microbiology Source Type: research
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