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  • 1
    In: EMBO Journal, 03 July 2013, Vol.32(13), pp.1802-1804
    Description: CRISPR systems not only defend bacteria from foreign DNA but also contribute to pathogenicity, by regulating endogenous gene expression to evade host innate immune responses.
    Keywords: Animals–Immunology ; Female–Pathogenicity ; Gammaproteobacteria–Immunology ; Gammaproteobacteria–Immunology ; Immune Evasion–Immunology ; Immunity, Innate–Immunology ; Germany ; Prokaryotes ; Gene Expression ; Eukaryotes ; Bacteria ; Molecular Biology;
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 2
    In: EMBO Journal, 02 July 2018, Vol.37(13), pp.n/a-n/a
    Description: Long non‐coding s (lncs) play important roles in many cellular pathways, but their contribution to the defense of eukaryotic cells against pathogens remains poorly understood. A new study from Imamura in reports that infection in human cells impacts nuclear decay, which in turn drives the accumulation of otherwise unstable nuclear lncs, some of which may have protective effects against this common bacterial pathogen. These unexpected findings demand more efforts to fully decrypt the molecular functions of lncs in innate and adaptive immunity. infection impairs the nuclear RNA decay machinery in human cells, increasing the abundance of long non‐coding RNAs with a role in innate immunity.
    Keywords: Pathogens ; Immunity ; Infections ; Pathogens ; Molecular Chains ; Salmonella ; Bacterial Infections ; Pathogens ; Ribonucleic Acid–RNA ; Ribonucleic Acid–RNA ; Adaptive Immunity;
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 3
    In: EMBO Journal, 03 June 2015, Vol.34(11), pp.1478-1492
    Description: There is an expanding list of examples by which one can posttranscriptionally influence the expression of others. This can involve sponges that sequester regulatory s of s in the same regulon, but the underlying molecular mechanism of such cross talk remains little understood. Here, we report sponge‐mediated cross talk in the posttranscriptional network of GcvB, a conserved Hfq‐dependent small with one of the largest regulons known in bacteria. We show that decay from the locus encoding an amino acid transporter generates a stable fragment (SroC) that base‐pairs with GcvB. This interaction triggers the degradation of GcvB by ase E, alleviating the GcvB‐mediated repression of other amino acid‐related transport and metabolic genes. Intriguingly, since the itself is a target of GcvB, the SroC sponge seems to enable both an internal feed‐forward loop to activate its parental in and activation of many ‐encoded s in the same pathway. Disabling this cross talk affects bacterial growth when peptides are the sole carbon and nitrogen sources. Decay of the bacterial GcvB , which keeps it from regulating its targets, is triggered by a 3′‐‐derived fragment from a target . This ability of s to compete for regulatory interaction presents a new mode of cross talk in bacteria. . Decay of the bacterial GcvB s, which keeps it from regulating its m targets, is triggered by a 3′‐‐derived fragment from a target m. This ability of ms to compete for regulatory interaction presents a new mode of cross talk in bacteria.
    Keywords: G Cv B ; H Fq ; Noncoding Rna ; Rn Ase E ; S Ro C
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 4
    In: EMBO Journal, 01 February 2017, Vol.36(3), pp.245-247
    Description: While bacteria were long thought to rely primarily on transcriptional control, it is now well established that they also use numerous small s to regulate translation and stability. There has recently been a surge in studies, including one by Waters ([Waters SA, 2017]) in this issue of , that have used clever variations of the ‐seq technique to comprehensively map small –target networks. Several recent studies have used clever variations of RNA‐seq techniques to comprehensively map small RNA–target networks involved in controlling bacterial gene expression.
    Keywords: Biology ; Chemistry;
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 5
    In: EMBO Journal, 17 October 2012, Vol.31(20), pp.4005-4019
    Description: The small RNAs associated with the protein Hfq constitute one of the largest classes of post‐transcriptional regulators known to date. Most previously investigated members of this class are encoded by conserved free‐standing genes. Here, deep sequencing of Hfq‐bound transcripts from multiple stages of growth of revealed a plethora of new small RNA species from within mRNA loci, including DapZ, which overlaps with the 3′ region of the biosynthetic gene, . Synthesis of the DapZ small RNA is independent of DapB protein synthesis, and is controlled by HilD, the master regulator of invasion genes. DapZ carries a short G/U‐rich domain similar to that of the globally acting GcvB small RNA, and uses GcvB‐like seed pairing to repress translation of the major ABC transporters, DppA and OppA. This exemplifies double functional output from an mRNA locus by the production of both a protein and an Hfq‐dependent ‐acting RNA. Our atlas of Hfq targets suggests that the 3′ regions of mRNA genes constitute a rich reservoir that provides the Hfq network with new regulatory small RNAs. Deep sequencing of Hfq‐binding RNAs isolated from at different growth stages reveals that the 3′ UTR of bacterial mRNAs are a rich source of regulatory small RNAs which modulate gene expression in trans.
    Keywords: Abc Transporter ; Dapz ; Gcvb ; Hfq ; 3′ Utr
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 6
    In: EMBO Journal, 13 April 2017, Vol.36(8), pp.1029-1045
    Description: Research into post‐transcriptional control of mRNAs by small noncoding RNAs (sRNAs) in the model bacteria and has mainly focused on sRNAs that associate with the RNA chaperone Hfq. However, the recent discovery of the protein ProQ as a common binding partner that stabilizes a distinct large class of structured sRNAs suggests that additional RNA regulons exist in these organisms. The cellular functions and molecular mechanisms of these new ProQ‐dependent sRNAs are largely unknown. Here, we report in Typhimurium the mode‐of‐action of RaiZ, a ProQ‐dependent sRNA that is made from the 3′ end of the mRNA encoding ribosome‐inactivating protein RaiA. We show that RaiZ is a base‐pairing sRNA that represses in the mRNA of histone‐like protein HU‐α. RaiZ forms an RNA duplex with the ribosome‐binding site of mRNA, facilitated by ProQ, to prevent 30S ribosome loading and protein synthesis of HU‐α. Similarities and differences between ProQ‐ and Hfq‐mediated regulation will be discussed. The enterobacterial sRNA RaiZ functions independent of the Hfq RNA chaperone via the recently identified general RNA‐binding protein ProQ. ProQ acts in a dual manner, stabilizing the sRNA and facilitating translational repression of the nucleid protein HU‐α. RaiZ is a small RNA produced by RNase E‐mediated cleavage of the raiA mRNA. RaiZ strongly binds RNA chaperone ProQ, leading to RaiZ stabilization. RaiZ represses translation of the hupA mRNA by base pairing with its ribosome‐binding site. ProQ and RaiZ jointly prevent initiating ribosomes from loading on hupA mRNA. The global RNA‐binding protein ProQ stabilizes bacterial small RNA RaiZ and facilitates translational repression of its target mRNA, thus exemplifying an Hfq‐independent RNA regulon.
    Keywords: Hu‐Α ; Proq ; Raiz ; Small Rna ; Translation Inhibition
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 7
    In: EMBO Journal, 13 November 2013, Vol.32(22), pp.2963-2979
    Description: Small RNAs use a diversity of well‐characterized mechanisms to repress mRNAs, but how they activate gene expression at the mRNA level remains not well understood. The predominant activation mechanism of Hfq‐associated small RNAs has been translational control whereby base pairing with the target prevents the formation of an intrinsic inhibitory structure in the mRNA and promotes translation initiation. Here, we report a translation‐independent mechanism whereby the small RNA RydC selectively activates the longer of two isoforms of mRNA (encoding cyclopropane fatty acid synthase) in . Target activation is achieved through seed pairing of the pseudoknot‐exposed, conserved 5′ end of RydC to an upstream region of the mRNA. The seed pairing stabilizes the messenger, likely by interfering directly with RNase E‐mediated decay in the 5′ untranslated region. Intriguingly, this mechanism is generic such that the activation is equally achieved by seed pairing of unrelated small RNAs, suggesting that this mechanism may be utilized in the design of RNA‐controlled synthetic circuits. Physiologically, RydC is the first small RNA known to regulate membrane stability. The small RNA RydC stabilizes target mRNAs in a translation‐independent manner through base pairing to the 5′UTR, blocking RNase E access. Cyclopropane fatty acid synthase is a target for RydC, providing the first link between sRNA regulation and membrane biosynthesis in bacteria.
    Keywords: Fatty Acid Synthesis ; Hfq ; Mrna Activation ; Noncoding Rna ; Small Rna
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 8
    In: EMBO Journal, 18 May 2011, Vol.30(10), pp.1977-1989
    Description: MicroRNAs have well‐established roles in eukaryotic host responses to viruses and extracellular bacterial pathogens. In contrast, microRNA responses to invasive bacteria have remained unknown. Here, we report cell type‐dependent microRNA regulations upon infection of mammalian cells with the enteroinvasive pathogen, Typhimurium. Murine macrophages strongly upregulate NF‐κB associated microRNAs; strikingly, these regulations which are induced by bacterial lipopolysaccharide (LPS) occur and persist regardless of successful host invasion and/or replication, or whether an inflammatory response is mounted, suggesting that microRNAs belong to the first line of anti‐bacterial defence. However, a suppression of the global immune regulator miR‐155 in endotoxin‐tolerant macrophages revealed that microRNA responses also depend on the status of infected cells. This study identifies the family as the common denominator of ‐regulated microRNAs in macrophages and epithelial cells, and suggests that repression of relieves cytokine IL‐6 and IL‐10 mRNAs from negative post‐transcriptional control. Our results establish a paradigm of microRNA‐mediated feed‐forward activation of inflammatory factors when mammalian cells are targeted by bacterial pathogens. This study describes the global mammalian micoRNA response to infection and the role of miRNAs in regulating the post‐transcriptional control of inflammatory cytokines.
    Keywords: Il‐10 ; Let‐7 ; Mir‐155 ; Mirna ; Salmonella
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 9
    In: EMBO Journal, 03 December 2018, Vol.37(23), pp.n/a-n/a
    Description: While mucosal inflammation is a major source of stress during enteropathogen infection, it remains to be fully elucidated how the host benefits from this environment to clear the pathogen. Here, we show that host stress induced by different stimuli mimicking inflammatory conditions strongly reduces the binding of to epithelial cells. Mechanistically, stress activates acid sphingomyelinase leading to host membrane remodeling. Consequently, knockdown or pharmacological inhibition of the acid sphingomyelinase blunts the stress‐dependent inhibition of binding to host cells. Interestingly, stress caused by intracellular replication also results in remodeling of the host cell membrane, and , which precludes re‐infection by this and other non‐motile pathogens. In contrast, Typhimurium overcomes the shortage of permissive entry sites by gathering effectively at the remaining platforms through its flagellar motility. Overall, our findings reveal host membrane remodeling as a novel stress‐responsive cell‐autonomous defense mechanism that protects epithelial cells from infection by non‐motile bacterial pathogens. Stress‐induced host membrane remodeling constitutes a novel cell‐autonomous defensive mechanism that protects epithelial cells from infection by and other non‐motile bacterial pathogens. Host oxidative stress strongly reduces S. flexneri binding to epithelial cells. Stress leads to host membrane remodeling, via activation of the acid sphingomyelinase by the MAPK p38 pathway, resulting in the formation of ceramide domains. Intracellular Shigella replication induces remodeling of the host cell membrane, in vitro and in vivo. Stress‐induced host membrane remodeling precludes re‐infection by non‐motile pathogens; motile pathogens are able to overcome this barrier through flagellar motility. Host membrane remodeling is a cell‐autonomous defense mechanism that protects epithelial cells from infection by .
    Keywords: Acid Sphingomyelinase ; Host Stress Response ; Membrane Remodeling ; Salmonella ; Shigella
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 10
    In: EMBO Journal, 02 May 2016, Vol.35(9), pp.991-1011
    Description: The molecular roles of many ‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining crosslinking with deep sequencing (‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic ‐binding protein target sites. We have applied ‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify 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– interactions. Additionally, Hfq preferentially binds 5′ to ‐target sites in s, and 3′ to seed sequences in s, reflecting a simple logic in how Hfq facilitates – interactions. Importantly, global knowledge of Hfq sites significantly improves ‐target predictions. CsrA binds sequences in apical loops and targets many virulence s. Overall, our generic ‐seq approach will bring new insights into post‐transcriptional gene regulation by ‐binding proteins in diverse bacterial species. A new pipeline for ‐seq in maps global –protein interactions and offers a tool for improved understanding of post‐transcriptional control in bacteria. Transcriptome‐wide mapping of Hfq and CsrA target sites by CLIP‐seq. Rho‐independent terminators comprise a general Hfq‐binding motif. Hfq binds 5′ to sRNA‐binding sites in mRNA targets and 3′ to seed sequences in cognate the sRNAs. CsrA preferentially recognizes AUGGA sequences present in loops of hairpin structures. CsrA binds and regulates many mRNAs encoding virulence factors. A new pipeline for CLIP‐seq in maps global RNA–protein interactions and offers a tool for improved understanding of post‐transcriptional control in bacteria.
    Keywords: Clip ; Csra ; Hfq ; Non‐Coding Rna ; Peak Calling ; Post‐Transcriptional Control ; Small Rna ; Terminator ; Translation
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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