Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

Tree, Jai J.; Granneman, Sander; McAteer, Sean P.; Tollervey, David; Gally, David L.

doi:10.1016/j.molcel.2014.05.006

Cited by 213 publications

(330 citation statements)

References 48 publications

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“…However, it was recently proposed that there is a continuum of possible interactions of Hfq with different RNA sequences . Consistently, it was also reported that Hfq binding sites in E. coli transcriptome often contained mismatches in ARN repeats (Tree et al 2014). The dependence of RybB, SdsR, and MicC binding on the proximal face of Hfq (Table 1) is typical for Class I sRNAs (Zhang et al 2013;Schu et al 2015).…”

supporting

confidence: 62%

“…These noncoding RNAs recognize complementary sequences in their target mRNAs, and induce the activation or repression of translation (Waters and Storz 2009;Updegrove et al 2015). This regulation is important for the adaptation of enterobacteria to changing environmental conditions (De Lay and Gottesman 2012), maintenance of cellular homeostasis (Papenfort et al 2013), and virulence of pathogenic species Tree et al 2014). Hfq is an Sm-like protein, which has a shape of a homohexameric ring (Moller et al 2002;Zhang et al 2002).…”

Section: Introductionmentioning

confidence: 99%

“…Recent Hfq profiling data in a pathogenic E. coli strain showed that almost 40% of recovered reads mapped to the coding regions (Tree et al 2014), which suggested that the coding sequence could be an important target of Hfq-dependent regulation. Indeed, although the majority of sRNAs target the 5 ′ -untranslated regions, several Salmonella and E. coli sRNAs bind within the coding sequence of mRNAs (Bouvier et al 2008;Pfeiffer et al 2009;Gutierrez et al 2013;Papenfort et al 2013;Guo et al 2014;Bobrovskyy and Vanderpool 2016).…”

Section: Introductionmentioning

confidence: 99%

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Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Wróblewska

Olejniczak

2016

RNA

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The bacterial protein Hfq participates in the regulation of translation by small noncoding RNAs (sRNAs). Several mechanisms have been proposed to explain the role of Hfq in the regulation by sRNAs binding to the 5 ′ -untranslated mRNA regions. However, it remains unknown how Hfq affects those sRNAs that target the coding sequence. Here, the contribution of Hfq to the annealing of three sRNAs, RybB, SdsR, and MicC, to the coding sequence of Salmonella ompD mRNA was investigated. Hfq bound to ompD mRNA with tight, subnanomolar affinity. Moreover, Hfq strongly accelerated the rates of annealing of RybB and MicC sRNAs to this mRNA, and it also had a small effect on the annealing of SdsR. The experiments using truncated RNAs revealed that the contributions of Hfq to the annealing of each sRNA were individually adjusted depending on the structures of interacting RNAs. In agreement with that, the mRNA structure probing revealed different structural contexts of each sRNA binding site. Additionally, the annealing of RybB and MicC sRNAs induced specific conformational changes in ompD mRNA consistent with local unfolding of mRNA secondary structure. Finally, the mutation analysis showed that the long AU-rich sequence in the 5 ′ -untranslated mRNA region served as an Hfq binding site essential for the annealing of sRNAs to the coding sequence. Overall, the data showed that the functional specificity of Hfq in the annealing of each sRNA to the ompD mRNA coding sequence was determined by the sequence and structure of the interacting RNAs.

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supporting

confidence: 62%

Section: Introductionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

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Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Wróblewska

Olejniczak

2016

RNA

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“…Although oop RNA is the only polyadenylated short regulatory transcript specifically affecting lambdoid phage development reported to date (Wró bel et al, 1998), results from a recent study suggest that phageencoded sRNAs may be significantly more abundant. Namely, global genomic analysis indicated that one of the prophages present in EHEC encodes 55 potential candidates for such RNA species (Tree et al, 2014).…”

Section: Discussionmentioning

confidence: 99%

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Nowicki

Bloch

Nejman-Faleńczyk

et al. 2015

Journal of General Virology

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In Escherichia coli, the major poly(A) polymerase (PAP I) is encoded by the pcnB gene. In this report, a significant impairment of lysogenization by Shiga toxin-converting (Stx) bacteriophages (W24 B , 933W, P22, P27 and P32) is demonstrated in host cells with a mutant pcnB gene. Moreover, lytic development of these phages after both infection and prophage induction was significantly less efficient in the pcnB mutant than in the WT host. The increase in DNA accumulation of the Stx phages was lower under conditions of defective RNA polyadenylation. Although shortly after prophage induction, the levels of mRNAs of most phage-borne early genes were higher in the pcnB mutant, at subsequent phases of the lytic development, a drastically decreased abundance of certain mRNAs, including those derived from the N, O and Q genes, was observed in PAP I-deficient cells. All of these effects observed in the pcnB cells were significantly more strongly pronounced in the Stx phages than in bacteriophage l. Abundance of mRNA derived from the pcnB gene was drastically increased shortly (20 min) after prophage induction by mitomycin C and decreased after the next 20 min, while no such changes were observed in non-lysogenic cells treated with this antibiotic. This prophage induction-dependent transient increase in pcnB transcript may explain the polyadenylation-driven regulation of phage gene expression.

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“…On the other hand, stx phage lysogeny has a direct effect on the global expression of bacterial genes; moreover, an increase in acid tolerance and motility has been reported when bacteria were lysogenized (Su et al, 2010). Tree et al (2014) found that stx 2 bacteriophages encoded an anti-small RNA that can regulate bacterial mRNA translation. Phages can also regulate different steps of STEC interaction with the intestinal epithelium, providing a selective advantage to STEC strains for colonization and persistence.…”

Section: Induction Of Stx Phagesmentioning

confidence: 99%

Shiga toxins and stx phages: highly diverse entities

2015

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Shiga toxins are the main virulence factors of a group of Escherichia coli strains [Shiga toxinproducing E. coli (STEC)] that cause severe human diseases, such as haemorrhagic colitis and haemolytic-uraemic syndrome. The Shiga toxin family comprises several toxin subtypes, which have been differentially related to clinical manifestations. In addition, the phages that carry the Shiga toxin genes (stx phages) are also diverse. These phages play an important role not only in the dissemination of Shiga toxin genes and the emergence of new STEC strains, but also in the regulation of Shiga toxin production. Consequently, differences in stx phages may affect the dissemination of stx genes as well as the virulence of STEC strains. In addition to presenting an overview of Shiga toxins and stx phages, in this review we highlight current knowledge about the diversity of stx phages, with emphasis on its impact on STEC virulence. We consider that this diversity should be taken into account when developing STEC infection treatments and diagnostic approaches, and when conducting STEC control in reservoirs.

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Identification of Bacteriophage-Encoded Anti-sRNAs in Pathogenic Escherichia coli

Cited by 213 publications

References 48 publications

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Hfq assists small RNAs in binding to the coding sequence of ompD mRNA and in rearranging its structure

Defects in RNA polyadenylation impair both lysogenization by and lytic development of Shiga toxin-converting bacteriophages

Shiga toxins and stx phages: highly diverse entities

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