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Véronique Arluison - One of the best experts on this subject based on the ideXlab platform.
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Crucial Role of the C-Terminal Domain of Hfq Protein in Genomic Instability
Microorganisms, 2020Co-Authors: Virali J. Parekh, Frank Wien, Wilfried Grange, Thomas A. De Long, Véronique Arluison, Richard R. SindenAbstract:G-rich DNA repeats that can form G-quadruplex structures are prevalent in bacterial genomes and are frequently associated with regulatory regions of genes involved in virulence, antigenic variation, and antibiotic resistance. These sequences are also inherently mutagenic and can lead to changes affecting cell survival and adaptation. Transcription of the G-quadruplex-forming repeat (G3T)n in E. coli, when mRNA comprised the G-rich strand, promotes G-quadruplex formation in DNA and increases rates of deletion of G-quadruplex-forming sequences. The genomic instability of G-quadruplex repeats may be a source of genetic variability that can influence alterations and evolution of bacteria. The DNA chaperone Hfq is involved in the genetic instability of these G-quadruplex sequences. Inactivation of the Hfq gene decreases the genetic instability of G-quadruplex, demonstrating that the genomic instability of this regulatory element can be influenced by the E. coli highly pleiotropic Hfq Protein, which is involved in small noncoding RNA regulation pathways, and DNA organization and packaging. We have shown previously that the Protein binds to and stabilizes these sequences, increasing rates of their genomic instability. Here, we extend this analysis to characterize the role of the C-terminal domain of Hfq Protein in interaction with G-quadruplex structures. This allows to better understand the function of this specific region of the Hfq Protein in genomic instability.
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In Situ Characterization of Hfq Bacterial Amyloid: A Fourier-Transform Infrared Spectroscopy Study.
Pathogens (Basel Switzerland), 2019Co-Authors: David Partouche, Frank Wien, Valeria Militello, Andrea Gómez-zavaglia, Christophe Sandt, Véronique ArluisonAbstract:Hfq is a bacterial Protein that regulates gene expression at the post-transcriptional level in Gram-negative bacteria. We have previously shown that Escherichia coli Hfq Protein, and more precisely its C-terminal region (CTR), self-assembles into an amyloid-like structure in vitro. In the present work, we present evidence that Hfq unambiguously forms amyloid structures also in vivo. Taking into account the role of this Protein in bacterial adaptation and virulence, our work opens possibilities to target Hfq amyloid self-assembly and cell location, with important potential to block bacterial adaptation and treat infections.
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The Bacterial Amyloid-Like Hfq Promotes In Vitro DNA Alignment
Microorganisms, 2019Co-Authors: Frank Wien, Denis Martinez, Etienne Le Brun, Nykola C. Jones, Soren Vronning Hoffmann, Jehan Waeytens, Melanie Berbon, Birgit Habenstein, Véronique ArluisonAbstract:The Hfq Protein is reported to be involved in environmental adaptation and virulence of several bacteria. In Gram-negative bacteria, Hfq mediates the interaction between regulatory noncoding RNAs and their target mRNAs. Besides these RNA-related functions, Hfq is also associated with DNA and is a part of the bacterial chromatin. Its precise role in DNA structuration is, however, unclear and whether Hfq plays a direct role in DNA-related processes such as replication or recombination is controversial. In previous works, we showed that Escherichia coli Hfq, or more precisely its amyloid-like C-terminal region (CTR), induces DNA compaction into a condensed form. In this paper, we evidence a new property for Hfq; precisely we show that its CTR influences double helix structure and base tilting, resulting in a strong local alignment of nucleoProtein Hfq:DNA fibers. The significance of this alignment is discussed in terms of chromatin structuration and possible functional consequences on evolutionary processes and adaptation to environment.
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The Escherichia Coli Hfq Protein: An Unattended DNA-Transactions Regulator.
Frontiers in molecular biosciences, 2016Co-Authors: Grzegorz M. Cech, Wilfried Grange, Véronique Arluison, Agnieszka Szalewska-pałasz, Krzysztof Kubiak, Antoine Malabirade, Grzegorz WęgrzynAbstract:The Hfq Protein was discovered in Escherichia coli as a host factor for bacteriophage Qβ RNA replication. Subsequent studies indicated that Hfq is a pleiotropic regulator of bacterial gene expression. The regulatory role of Hfq is ascribed mainly to its function as an RNA-chaperone, facilitating interactions between bacterial noncoding RNA and its mRNA target. Thus, it modulates mRNA translation and stability. Nevertheless, Hfq is able to interact with DNA as well. Its role in the regulation of DNA-related processes has been demonstrated. In this mini-review, it is discussed how Hfq interacts with DNA and what is the role of this Protein in regulation of DNA transactions. Particularly, Hfq has been demonstrated to be involved in the control of ColE1 plasmid DNA replication, transposition, and possibly also transcription. Possible mechanisms of these Hfq-mediated regulations are described and discussed.
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Hfq Protein deficiency in Escherichia coli affects ColE1-like but not λ plasmid DNA replication.
Plasmid, 2014Co-Authors: Grzegorz M. Cech, Véronique Arluison, Grzegorz Węgrzyn, Bartosz Pakuła, Dominika Kamrowska, Agnieszka Szalewska-pałaszAbstract:Abstract Hfq is a nucleic acid-binding Protein involved in controlling several aspects of RNA metabolism. It achieves this regulatory function by modulating the translational activity and stability of different mRNAs, generally via interactions with stress-related small regulatory sRNAs. However, besides its role in the coordination of translation of bacterial mRNA, Hfq is also a nucleoid-associated DNA-binding Protein. Motivated by the above property of Hfq, we investigated if Hfq gene mutation has implications for the regulation of DNA replication. Efficiency of ColE1-like (pMB1- and p15A replicons) and bacteriophage λ-derived plasmids’ replication has been investigated in wild-type strain and otherwise isogenic Hfq mutant of Escherichia coli. Significant differences in plasmid amount and kinetics of plasmid DNA synthesis were observed between the two tested bacterial hosts for ColE1-like replicons, but not for λ plasmid. Furthermore, ColE1-like plasmids replicated more efficiently in wild-type cells than in the Hfq mutant in the early exponential phase of growth, but less efficiently in late exponential and early stationary phases. Hfq levels in the wild-type host, estimated by Western-blotting, were increased at the latter phases relative to the former one. Moreover, effects of the Hfq mutation on ColE1-like plasmid replication were impaired in the absence of the rom gene, coding for a Protein enhancing RNA I–RNA II interactions during the control of the replication initiation. These results are discussed in the light of a potential mechanism by which Hfq Protein may influence replication of some, but not all, replicons in E. coli.
Jörg Vogel - One of the best experts on this subject based on the ideXlab platform.
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Recognition of the small regulatory RNA RydC by the bacterial Hfq Protein
eLife, 2014Co-Authors: Daniela Dimastrogiovanni, Jörg Vogel, Kathrin S. Fröhlich, Katarzyna J Bandyra, Heather A Bruce, Susann Hohensee, Ben F. LuisiAbstract:A crucial step in the production of Proteins is the translation of messenger RNA molecules. Other RNA molecules called small RNAs are also involved in this process: these small RNAs bind to the messenger RNA molecules to either increase or decrease the production of Proteins. Bacteria and other microorganisms use small RNA molecules to help them respond to stress conditions and to changes in their environment, such as fluctuations in temperature or the availability of nutrients. The ability to rapidly adapt to these changes enables bacteria to withstand harmful conditions and to make efficient use of resources available to them. Many small RNA molecules use a Protein called Hfq to help them interact with their target messenger RNAs. In some cases this Protein protects the small RNA molecules when they are not bound to their targets. Hfq also helps the small RNA to bind to the messenger RNA, and then recruits other enzymes that eventually degrade the complex formed by the different RNA molecules. Previous research has shown that six Hfq subunits combine to form a ring-shaped structure and has also provided some clues about the way in which Hfq can recognise a short stretch of a small RNA molecule, but the precise details of the interaction between them are not fully understood. Now Dimastrogiovanni et al. have used a technique called X-ray crystallography to visualize the interaction between Hfq and a small RNA molecule called RydC. These experiments reveal that a particular region of RydC adopts a structure known as a pseudoknot and that this structure is critical for the interactions between the RydC molecules and the Hfq ring. Dimastrogiovanni et al. find that one RydC molecule interacts with one Hfq ring, and they identify the contact points between the RydC molecule and different regions of the Hfq ring. Based on this information, Dimastrogiovanni et al. propose a model for how the RydC:Hfq complex is likely to interact with a messenger RNA molecule. The next step will be to test this model in experiments.
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Deep sequencing of Salmonella RNA associated with heterologous Hfq Proteins in vivo reveals small RNAs as a major target class and identifies RNA processing phenotypes.
RNA biology, 2009Co-Authors: Alexandra Sittka, Cynthia M. Sharma, Katarzyna Rolle, Jörg VogelAbstract:The bacterial Sm-like Protein, Hfq, is a key factor for the stability and function of small non-coding RNAs (sRNAs) in Escherichia coli. Homologues of this Protein have been predicted in many distantly related organisms yet their functional conservation as sRNA-binding Proteins has not entirely been clear. To address this, we expressed in Salmonella the Hfq Proteins of two eubacteria (Neisseria meningitides, Aquifex aeolicus) and an archaeon (Methanocaldococcus jannaschii), and analyzed the associated RNA by deep sequencing. This in vivo approach identified endogenous Salmonella sRNAs as a major target of the foreign Hfq Proteins. New Salmonella sRNA species were also identified, and some of these accumulated specifically in the presence of a foreign Hfq Protein. In addition, we observed specific RNA processing defects, e.g., suppression of precursor processing of SraH sRNA by Methanocaldococcus Hfq, or aberrant accumulation of extracytoplasmic target mRNAs of the Salmonella GcvB, MicA or RybB sRNAs. Taken together, our study provides evidence of a conserved inherent sRNA-binding property of Hfq, which may facilitate the lateral transmission of regulatory sRNAs among distantly related species. It also suggests that the expression of heterologous RNA-binding Proteins combined with deep sequencing analysis of RNA ligands can be used as a molecular tool to dissect individual steps of RNA metabolism in vivo.
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Multiple target regulation by small noncoding RNAs rewires gene expression at the post-transcriptional level.
Research in microbiology, 2009Co-Authors: Kai Papenfort, Jörg VogelAbstract:Small noncoding RNAs (sRNAs), often in conjunction with Hfq Protein, have increasingly been shown to regulate multiple rather than individual mRNAs, thereby reprogramming gene expression at the post-transcriptional level. This review summarizes how and when several such regulators (CyaR, DsrA, GcvB, OmrAB, RNAIII, RybB, RyhB) act upon multiple targets.
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Hfq dependent regulation of ompa synthesis is mediated by an antisense rna
Genes & Development, 2005Co-Authors: Klas I Udekwu, Johan Reimegard, Fabien Darfeuille, Erik Holmqvist, Jörg Vogel, Gerhart E H WagnerAbstract:This paper shows that the small RNA MicA (previously SraD) is an antisense regulator of ompA in Escherichia coli. MicA accumulates upon entry into stationary phase and down-regulates the level of ompA mRNA. Regulation of ompA (outer membrane Protein A), previously attributed to Hfq/mRNA binding, is lost upon deletion of the micA gene, whereas overexpression of MicA inhibits the synthesis of OmpA. In vitro, MicA binds to the ompA mRNA leader. Enzymatic and chemical probing was used to map the structures of MicA, the ompA mRNA leader, and the complex formed upon binding. MicA binding generates a footprint across the ompA Shine-Dalgarno sequence, consistent with a 12 + 4 base-pair interaction, which is additionally supported by the effect of mutations in vivo and by bioinformatics analysis of enterobacterial micA/ompA homolog sequences. MicA is conserved in many enterobacteria, as is its ompA target site. In vitro toeprinting confirmed that binding of MicA specifically interferes with ribosome binding. We propose that MicA, when present at high levels, blocks ribosome binding at the ompA translation start site, which—in line with previous work—secondarily facilitates RNase E cleavage and subsequent mRNA decay. MicA requires the presence of the Hfq Protein, although the mechanistic basis for this remains unclear.
Udo Blasi - One of the best experts on this subject based on the ideXlab platform.
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Detection of small RNAs in Pseudomonas aeruginosa by RNomics and structure-based bioinformatic tools.
Microbiology (Reading England), 2008Co-Authors: Elisabeth Sonnleitner, Udo Blasi, Theresa Sorger-domenigg, Monika J Madej, Sven Findeiss, Jörg Hackermüller, Alexander Hüttenhofer, Peter F Stadler, Isabella MollAbstract:Inactivation of the Pseudomonas aeruginosa (PAO1) Hfq gene, encoding the Sm-like Hfq Protein, resulted in pleiotropic effects that included an attenuated virulence. As regulation by Hfq often involves the action of small regulatory RNAs (sRNAs), we have used a shotgun cloning approach (RNomics) and bioinformatic tools to identify sRNAs in strain PAO1. For cDNA library construction, total RNA was extracted from PAO1 cultures either grown to stationary phase or exposed to human serum. The cDNA libraries were generated from small-sized RNAs of PAO1 after co-immunoprecipitation with Hfq. Of 400 sequenced cDNA clones, 11 mapped to intergenic regions. Band-shift assays and Northern blot analyses performed with two selected sRNAs confirmed that Hfq binds to and affects the steady-state levels of these RNAs. A proteome study performed upon overproduction of one sRNA, PhrS, implicated it in riboregulation. PhrS contains an ORF, and evidence for its translation is presented. In addition, based on surveys with structure-based bioinformatic tools, we provide an electronic compilation of putative sRNA and non-coding RNA genes of PAO1 based on their evolutionarily conserved structure.
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Functional effects of variants of the RNA chaperone Hfq.
Biochemical and biophysical research communications, 2004Co-Authors: Elisabeth Sonnleitner, Isabella Moll, Johanna Napetschnig, Taras Afonyushkin, Karin Ecker, Branislav Večerek, Vladimir R. Kaberdin, Udo BlasiAbstract:The ring-shaped RNA chaperone Hfq has recently received much attention owing to its multiple roles in RNA metabolism. In this study we have performed a mutational analysis of the Escherichia coli Hfq gene, and have studied the effects of amino acid substitutions at several positions in the Hfq Protein as well as of C-terminal truncations on its role in phage Qβ replication, in repression of a target mRNA, and on the stability of the small regulatory RNA DsrA. These functional studies provided insights into the interaction of Hfq with RNA and suggested a role for the C-terminus of Hfq in DsrA stability.
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Crystallization of Hfq Protein: a bacterial gene-expression regulator.
Acta crystallographica. Section D Biological crystallography, 2003Co-Authors: Ioulia M. Vassilieva, Isabella Moll, Alexey D Nikulin, Udo Blasi, Maria B GarberAbstract:Hfq Protein from Escherichia coli (EcoHfq) has been overproduced in E. coli, purified to homogeneity and crystallized using the hanging-drop vapour-diffusion technique. Crystallization conditions for EcoHfq were found which yielded X-ray quality crystals. Crystals of EcoHfq and of Cd-, Hg- and Se-containing derivatives grew in two months, with unit-cell parameters a = b = 127.41, c = 170.36 A. The crystals belong to space group I4 and diffract to 2.1 A resolution. Two hexamers are predicted per asymmetric unit.
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RNA chaperone activity of the Sm‐like Hfq Protein
EMBO reports, 2003Co-Authors: Isabella Moll, David Leitsch, Tanja Steinhauser, Udo BlasiAbstract:The Escherichia coli Sm‐like host factor I (Hfq) Protein is thought to function in post‐transcriptional regulation by modulating the function of small regulatory RNAs. Hfq also interferes with ribosome binding on E. coli ompA messenger RNA, indicating that Hfq also interacts with mRNAs. In this study, we have used stimulation of group I intron splicing in vivo and a modified in vitro toeprinting assay to determine whether Hfq acts as an RNA chaperone. Hfq was able to rescue an RNA ‘folding trap’ in a splicing defective T4 bacteriophage td gene in vivo . Enzymatic analysis showed that Hfq affects the accessibility of the ompA start codon, as well a s other bases within the ribosome‐binding site, explaining its negative effect on ribosome binding. We also show that the Hfq‐induced structural changes in ompA mRNA are maintained after proteolytic digestion of the Protein, which classifies Hfq as an RNA chaperone.
Mikołaj Olejniczak - One of the best experts on this subject based on the ideXlab platform.
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Determinants of RNA recognition by the FinO domain of the Escherichia coli ProQ Protein
2020Co-Authors: Ewa M Stein, Joanna Kwiatkowska, Maciej M Basczok, Chandra M Gravel, Katherine E. Berry, Mikołaj OlejniczakAbstract:The regulation of gene expression by small RNAs in Escherichia coli depends on RNA binding Proteins Hfq and ProQ, which bind mostly distinct RNA pools. To understand how ProQ discriminates between RNA substrates, we compared its binding to six different RNA molecules. Full-length ProQ bound all six RNAs similarly, while the isolated N-terminal FinO domain (NTD) of ProQ specifically recognized RNAs with Rho-independent terminators. Analysis of malM 3ʹ-UTR mutants showed that tight RNA binding by the ProQ NTD required a terminator hairpin of at least two base pairs preceding an 3ʹ oligoU tail of at least four uridine residues. Substitution of an A-rich sequence on the 5ʹ side of the terminator to uridines strengthened the binding of several ProQ-specific RNAs to the Hfq Protein, but not to the ProQ NTD. Substitution of the motif in the malM-3ʹ and cspE-3ʹ RNAs also conferred the ability to bind Hfq in E. coli cells, as measured using a three-hybrid assay. In summary, these data suggest that the ProQ NTD specifically recognizes 3ʹ intrinsic terminators of RNA substrates, and that the discrimination between RNA ligands by E. coli ProQ and Hfq depends both on positive determinants for binding to ProQ and negative determinants against binding to Hfq.
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The structure of fadL mRNA and its interactions with RybB sRNA
Acta biochimica Polonica, 2016Co-Authors: Agata Groszewska, Zuzanna Wroblewska, Mikołaj OlejniczakAbstract:Small bacterial RNAs (sRNAs) regulate translation by pairing with complementary sequences in their target mRNAs, in a process which is often dependent on the Hfq Protein. Here, the structure probing of a 95-nt long fragment of Salmonella fadL mRNA showed that the annealing of sRNA RybB to the coding sequence of fadL induced local rearrangements in mRNA structure. The filter retention data showed that Hfq bound RybB and fadL with tight affinities. Moreover, Hfq increased the rate of RybB annealing to fadL mRNA. Overall, the data showed that the Hfq Protein directly participates in RybB interactions with fadL mRNA.
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Contributions of the Hfq Protein to translation regulation by small noncoding RNAs binding to the mRNA coding sequence.
Acta biochimica Polonica, 2016Co-Authors: Zuzanna Wroblewska, Mikołaj OlejniczakAbstract:The bacterial Sm-like Protein Hfq is involved in the regulation of translation by small noncoding RNAs (sRNAs), which affect bacterial cell’s response to changing environmental conditions. sRNAs bind to complementary sequences in their target mRNAs to activate or repress translation. The majority of sRNAs bind to the 5ʹ-untranslated mRNA regions. However, recent studies showed that sRNAs can also regulate translation by binding to the mRNA coding sequence, even far downstream of AUG start codon. This review aims to summarize our current understanding of the contributions of Hfq to translation regulation by sRNAs binding the mRNA coding sequence.
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Structure of Bacterial Regulatory RNAs Determines Their Performance in Competition for the Chaperone Protein Hfq
Biochemistry, 2015Co-Authors: Ewelina M Małecka, Joanna Teresa Stróżecka, Daria Sobańska, Mikołaj OlejniczakAbstract:Bacterial regulatory RNAs require the chaperone Protein Hfq to enable their pairing to mRNAs. Recent data showed that there is a hierarchy among sRNAs in the competition for access to Hfq, which could be important for the tuning of sRNA-dependent translation regulation. Here, seven structurally different sRNAs were compared using filter-based competition assays. Moreover, chimeric sRNA constructs were designed to identify structure elements important for competition performance. The data showed that besides the 3'-terminal oligouridine sequences also the 5'-terminal structure elements of sRNAs were essential for their competition performance. When the binding of sRNAs to Hfq mutants was compared, the data showed the important role of the proximal and rim sites of Hfq for the binding of six out of seven sRNAs. However, ChiX sRNA, which was the most efficient competitor, bound Hfq in a unique way using the opposite-distal and proximal-faces of this ring-shaped Protein. The data indicated that the simultaneous binding to the opposite faces of Hfq was enabled by separate adenosine-rich and uridine-rich sequences in the long, single-stranded region of ChiX. Overall, the results suggest that the individual structural composition of sRNAs serves to tune their performance to different levels resulting in a hierarchy of sRNAs in the competition for access to the Hfq Protein.
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Despite similar binding to the Hfq Protein regulatory RNAs widely differ in their competition performance.
Biochemistry, 2011Co-Authors: Mikołaj OlejniczakAbstract:The binding of nine noncoding regulatory RNAs (sRNAs) to the E. coli Hfq Protein was compared using a high-throughput double filter retention assay. Despite the fact that these sRNAs have different lengths, sequences and secondary structures their Hfq binding affinities were surprisingly uniform. The analysis of sRNAs binding to Hfq mutants showed that the proximal face of Hfq, known as the binding site for DsrA RNA, is a universal sRNA binding site. Moreover, all sRNAs bound Hfq with similar association rates limited only by the rate of diffusion, while the rates of dissociation, measured in the dilution experiments, were uniformly slow. Despite that, the data showed that there was a hierarchy of sRNAs in regard to their performance in competition for access to Hfq and in their ability to facilitate the dissociation of other sRNAs from Hfq. The sRNAs also differed in their salt dependence of binding to this Protein. Overall, the results suggest that despite the uniform binding of different sRNAs to the same site on Hfq their exchange on this Protein is dependent on the identities of the competing sRNAs.
Gisela Storz - One of the best experts on this subject based on the ideXlab platform.
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Protection against deleterious nitrogen compounds: role of σS-dependent small RNAs encoded adjacent to sdiA.
Nucleic acids research, 2016Co-Authors: Yue Hao, Taylor B. Updegrove, Natasha N. Livingston, Gisela StorzAbstract:Here, we report the characterization of a set of small, regulatory RNAs (sRNAs) expressed from an Escherichia coli locus we have denoted sdsN located adjacent to the LuxR-homolog gene sdiA Two longer sRNAs, SdsN137 and SdsN178 are transcribed from two σ(S)-dependent promoters but share the same terminator. Low temperature, rich nitrogen sources and the Crl and NarP transcription factors differentially affect the levels of the SdsN transcripts. Whole genome expression analysis after pulse overexpression of SdsN137 and assays of lacZ fusions revealed that the SdsN137 directly represses the synthesis of the nitroreductase NfsA, which catalyzes the reduction of the nitrogroup (NO2) in nitroaromatic compounds and the flavohemoglobin HmpA, which has aerobic nitric oxide (NO) dioxygenase activity. Consistent with this regulation, SdsN137 confers resistance to nitrofurans. In addition, SdsN137 negatively regulates synthesis of NarP. Interestingly, SdsN178 is defective at regulating the above targets due to unusual binding to the Hfq Protein, but cleavage leads to a shorter form, SdsN124, able to repress nfsA and hmpA.
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Controlling mRNA stability and translation with small, noncoding RNAs.
Current opinion in microbiology, 2004Co-Authors: Gisela Storz, Jason A. Opdyke, Aixia ZhangAbstract:Recent studies have lead to the identification of more than 50 small regulatory RNAs in Escherichia coli. Only a subset of these RNAs has been characterized. However, it is clear that many of the RNAs, such as the MicF, OxyS, DsrA, Spot42 and RyhB RNAs, act by basepairing to activate or repress translation or to destabilize mRNAs. Basepairing between these regulatory RNAs and their target mRNAs requires the Sm-like Hfq Protein which most likely functions as an RNA chaperone to increase RNA unfolding or local target RNA concentration. Here we summarize the physiological roles of the basepairing RNAs, examine their prevalence in bacteria and discuss unresolved questions regarding their mechanisms of action.
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The Sm-like Hfq Protein Increases OxyS RNA Interaction with Target mRNAs
Molecular cell, 2002Co-Authors: Aixia Zhang, Karen M. Wassarman, Joaquin Ortega, Alasdair C. Steven, Gisela StorzAbstract:The Escherichia coli host factor I, Hfq, binds to many small regulatory RNAs and is required for OxyS RNA repression of fhlA and rpoS mRNA translation. Here we report that Hfq is a bacterial homolog of the Sm and Sm-like Proteins integral to RNA processing and mRNA degradation complexes in eukaryotic cells. Hfq exhibits the hallmark features of Sm and Sm-like Proteins: the Sm1 sequence motif, a multisubunit ring structure (in this case a homomeric hexamer), and preferential binding to polyU. We also show that Hfq increases the OxyS RNA interaction with its target messages and propose that the enhancement of RNA-RNA pairing may be a general function of Hfq, Sm, and Sm-like Proteins.
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identification of novel small rnas using comparative genomics and microarrays
Genes & Development, 2001Co-Authors: Karen M. Wassarman, Gisela Storz, Francis Repoila, Carsten Rosenow, Susan GottesmanAbstract:A burgeoning list of small RNAs with a variety of regulatory functions has been identified in both prokaryotic and eukaryotic cells. However, it remains difficult to identify small RNAs by sequence inspection. We used the high conservation of small RNAs among closely related bacterial species, as well as analysis of transcripts detected by high-density oligonucleotide probe arrays, to predict the presence of novel small RNA genes in the intergenic regions of the Escherichia coli genome. The existence of 23 distinct new RNA species was confirmed by Northern analysis. Of these, six are predicted to encode short ORFs, whereas 17 are likely to be novel functional small RNAs. We discovered that many of these small RNAs interact with the RNA-binding Protein Hfq, pointing to a global role of the Hfq Protein in facilitating small RNA function. The approaches used here should allow identification of small RNAs in other organisms.