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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 20 March 2012, Vol.109(12), pp.4621-6
    Description: The conserved RNA-binding protein Hfq and its associated small regulatory RNAs (sRNAs) are increasingly recognized as the players of a large network of posttranscriptional control of gene expression in Gram-negative bacteria. The role of Hfq in this network is to facilitate base pairing between sRNAs and their trans-encoded target mRNAs. Although the number of known sRNA-mRNA interactions has grown steadily, cellular factors that influence Hfq, the mediator of these interactions, have remained unknown. We report that RelA, a protein long known as the central regulator of the bacterial-stringent response, acts on Hfq and thereby affects the physiological activity of RyhB sRNA as a regulator of iron homeostasis. RyhB requires RelA in vivo to arrest growth during iron depletion and to down-regulate a subset of its target mRNAs (fdoG, nuoA, and sodA), whereas the sodB and sdhC targets are barely affected by RelA. In vitro studies with recombinant proteins show that RelA enhances multimerization of Hfq monomers and stimulates Hfq binding of RyhB and other sRNAs. Hfq from polysomes extracted from wild-type cells binds RyhB in vitro, whereas Hfq from polysomes of a relA mutant strain shows no binding. We propose that, by increasing the level of the hexameric form of Hfq, RelA enables binding of RNAs whose affinity for Hfq is low. Our results suggest that, under specific conditions and/or environments, Hfq concentrations are limiting for RNA binding, which thereby provides an opportunity for cellular proteins such as RelA to impact sRNA-mediated responses by modulating the activity of Hfq.
    Keywords: Escherichia Coli -- Metabolism ; Escherichia Coli Proteins -- Physiology ; Host Factor 1 Protein -- Physiology ; Ligases -- Physiology ; RNA, Bacterial -- Metabolism ; RNA-Binding Proteins -- Physiology
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 2012, Vol.109(12), pp.4621-4626
    Description: The conserved RNA-binding protein Hfq and its associated small regulatory RNAs (sRNAs) are increasingly recognized as the players of a large network of posttranscriptional control of gene expression in Gram-negative bacteria. The role of Hfq in this network is to facilitate base pairing between sRNAs and their trans-encoded target mRNAs. Although the number of known sRNA–mRNA interactions has grown steadily, cellular factors that influence Hfq, the mediator of these interactions, have remained unknown. We report that RelA, a protein long known as the central regulator of the bacterial-stringent response, acts on Hfq and thereby affects the physiological activity of RyhB sRNA as a regulator of iron homeostasis. RyhB requires RelA in vivo to arrest growth during iron depletion and to down-regulate a subset of its target mRNAs (fdoG, nuoA, and sodA), whereas the sodB and sdhC targets are barely affected by RelA. In vitro studies with recombinant proteins show that RelA enhances multimerization of Hfq monomers and stimulates Hfq binding of RyhB and other sRNAs. Hfq from polysomes extracted from wild-type cells binds RyhB in vitro, whereas Hfq from polysomes of a relA mutant strain shows no binding. We propose that, by increasing the level of the hexameric form of Hfq, RelA enables binding of RNAs whose affinity for Hfq is low. Our results suggest that, under specific conditions and/or environments, Hfq concentrations are limiting for RNA binding, which thereby provides an opportunity for cellular proteins such as RelA to impact sRNA-mediated responses by modulating the activity of Hfq. ; p. 4621-4626.
    Keywords: Polyribosomes ; In Vitro Studies ; Messenger Rna ; Gram-Negative Bacteria ; Gene Expression ; Recombinant Proteins
    ISSN: 0027-8424
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  • 3
    Language: English
    In: Nucleic acids research, January 2014, Vol.42(1), pp.622-30
    Description: Previously, we described a novel pH-responsive RNA element in Escherichia coli that resides in the 5' untranslated region of the alx gene and controls its translation in a pH-dependent manner. Under normal growth conditions, this RNA region forms a translationally inactive structure, but when transcribed under alkaline conditions, it forms an active structure producing the Alx protein. We identified two distinct transcriptional pause sites and proposed that pausing at these sites interfered with the formation of the inactive structure while facilitating folding of the active one. Alkali increases the longevity of pausing at these sites, thereby promoting folding of the translationally active form of alx RNA. We show here that mutations that modify the extent and/or position of pausing, although silent with regard to structure stability per se, greatly influence the dynamics of folding and thereby translation. Our data illustrate the mechanistic design of alx regulation, relying on precise temporal and spatial characteristics. We propose that this unique design provides an opportunity for environmental signals such as pH to introduce structural changes in the RNA and thereby modulate expression.
    Keywords: Gene Expression Regulation, Bacterial ; Regulatory Sequences, Ribonucleic Acid ; Transcription, Genetic ; Escherichia Coli Proteins -- Genetics ; RNA, Bacterial -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 4
    In: EMBO Journal, 01 February 2018, Vol.37(3), pp.413-426
    Description: To maintain genome integrity, organisms employ damage response, the underlying principles of which are conserved from bacteria to humans. The bacterial small OxyS of is induced upon oxidative stress and has been implicated in protecting cells from damage; however, the mechanism by which OxyS confers genome stability remained unknown. Here, we revealed an OxyS‐induced molecular checkpoint relay, leading to temporary cell cycle arrest to allow damage repair. By repressing the expression of the essential transcription termination factor , OxyS enables read‐through transcription into a cryptic prophage encoding . The KilR protein interferes with the function of the major cell division protein FtsZ, thus imposing growth arrest. This transient growth inhibition facilitates damage repair, enabling cellular recovery, thereby increasing viability following stress. The OxyS‐mediated growth arrest represents a novel tier of defense, introducing a new regulatory concept into bacterial stress response. The oxidative stress‐induced bacterial small OxyS protects genome integrity by unknown mechanisms. Identification of its downstream targets reveals a cell division inhibitory mechanism that parallels damage checkpoints of eukaryotic cells. Escherichia coli OxyS inhibits expression of the NusG transcription termination factor. NusG repression facilitates read‐through transcription of prophage‐encoded KilR protein. KilR interferes with the function of the cell division protein FtsZ to impose temporary growth arrest. Transient cell cycle arrest allows extra time for DNA damage repair and increases cellular viability after oxidative stress. Repression of the bacterial termination factor nusG by an oxidative stress‐induced allows read‐through transcription of a prophage‐encoded FtsZ inhibitor, delaying cell division to allow stress recovery.
    Keywords: Cell Cycle Arrest ; Checkpoint ; Escherichia Coli ; Prophage ; Small Rna
    ISSN: 0261-4189
    E-ISSN: 1460-2075
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  • 5
    Language: English
    In: Research in Microbiology, June, 2011, Vol.162(5), p.461(9)
    Description: To link to full-text access for this article, visit this link: http://dx.doi.org/10.1016/j.resmic.2011.03.005 Byline: Michael Ionescu (a), Maya Elgrably-Weiss (b), Tal Elad (a), Aviram Rasouly (c), Sharon Yagur-Kroll (a), Shimshon Belkin (a) Abstract: The Escherichia coli yjbEFGH operon, encoding genes involved in exopolysaccharide production, has previously been shown to be induced by osmotic stress and to be negatively regulated by I.sup.38. Promoter analysis suggested that like most E. coli genes, its transcription is driven by the housekeeping sigma factor I.sup.70. Indeed, manipulation of any of the other five alternative sigma factors did not affect its induction by osmotic stress. Surprisingly, when assayed in a strain expressing low levels of I.sup.70, yjbEFGH induction in response to osmotic stress was higher than in a strain expressing normal levels of I.sup.70. Similar phenomena were observed in the I.sup.70-driven promoters of sulA, uvrA, recA, fecI, entC and lacZ, the transcription of which is directly controlled by a repressor protein (LexA, Fur and LacI), but not in promoters of the housekeeping genes ftsA and ftsY, or in I.sup.38-driven treA promoter. Since transcription factors are generally present in the cell in low numbers, we hypothesize that a decrease in I.sup.70, that drives the expression of lexA, fur and lacI as well, further diminishes their number in the cell and thus de-represses the induction of genes which are subjected to their repression. Author Affiliation: (a) Department of Plant and Environmental Sciences, The Alexander Silberman Institute of Life Sciences, The Hebrew University of Jerusalem, Edmond J. Safra Campus, Givat Ram, Jerusalem 91904, Israel (b) Department of Microbiology and Molecular Genetics, IMRIC, The Hebrew University-Hadassah Medical School, Jerusalem 91120, Israel (c) Department of Molecular Microbiology and Biotechnology, The George S. Wise Faculty of Life Sciences, Tel Aviv University, Tel Aviv 69978, Israel Article History: Received 1 October 2010; Accepted 14 February 2011
    Keywords: Escherichia Coli -- Analysis ; Dna Binding Proteins -- Analysis
    ISSN: 0923-2508
    Source: Cengage Learning, Inc.
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  • 6
    Language: English
    In: Research in Microbiology, 2011, Vol.162(5), pp.461-469
    Description: The Escherichia coli yjbEFGH operon, encoding genes involved in exopolysaccharide production, has previously been shown to be induced by osmotic stress and to be negatively regulated by σ 38. Promoter analysis suggested that like most E. coli genes, its transcription is driven by the housekeeping sigma factor σ 70. Indeed, manipulation of any of the other five alternative sigma factors did not affect its induction by osmotic stress. Surprisingly, when assayed in a strain expressing low levels of σ 70, yjbEFGH induction in response to osmotic stress was higher than in a strain expressing normal levels of σ 70. Similar phenomena were observed in the σ 70-driven promoters of sulA, uvrA, recA, fecI, entC and lacZ, the transcription of which is directly controlled by a repressor protein (LexA, Fur and LacI), but not in promoters of the housekeeping genes ftsA and ftsY, or in σ 38-driven treA promoter. Since transcription factors are generally present in the cell in low numbers, we hypothesize that a decrease in σ 70, that drives the expression of lexA, fur and lacI as well, further diminishes their number in the cell and thus de-represses the induction of genes which are subjected to their repression.
    Keywords: Sigma Factor ; Yjbefgh ; Rpod ; Transcriptional Fusion
    ISSN: 0923-2508
    E-ISSN: 17697123
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  • 7
    In: The Journal of Bacteriology, 2002, Vol. 184(14), p.3774
    Description: The first committed step in the biosynthesis of heme, an important cofactor of two catalases and a number of cytochromes, is catalyzed by the hemA gene product. Salmonella enterica serovar Typhimurium hemA26::Tn10d (hemA26) was identified in a genetic screen of insertion mutants that were sensitive to hydrogen peroxide. Here we show that the hemA26 mutant respires at half the rate of wild-type cells and is highly susceptible to the effects of oxygen species. Exposure of the hemA26 strain to hydrogen peroxide results in extensive DNA damage and cell death. The chelation of intracellular free iron fully abrogates the sensitivity of this mutant, indicating that the DNA damage results from the iron-catalyzed formation of hydroxyl radicals. The inactivation of heme synthesis does not change the amount of intracellular iron, but by diminishing the rate of respiration, it apparently increases the amount of reducing equivalents available to drive the Fenton reaction. We also report that hydrogen peroxide has opposite effects on the expression of hemA and hemH, the first and last genes of heme biosynthesis pathway, respectively. hemA mRNA levels decrease, while the transcription of hemH is induced by hydrogen peroxide, in an oxyR-dependent manner. The oxyR-dependent induction is suppressed under conditions that accelerate the Fenton reaction by a mechanism that is not yet understood.
    Keywords: Biology;
    ISSN: 0021-9193
    ISSN: 00219193
    E-ISSN: 10985530
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  • 8
    In: Journal of Bacteriology, July, 2002, Vol.184(13-14), p.3774(11)
    Description: Research has been conducted on Salmonella enterica serovar Typhimurium hemA gene. Results demonstrate that hemA-deficient cell exposure to hydrogen peroxide leads to the iron-dependent DNA damage and cell death.
    Keywords: Bacteriology -- Research ; Oxidation-reduction Reactions -- Physiological Aspects ; Dna Damage -- Genetic Aspects ; Gene Mutation -- Physiological Aspects ; Salmonella Typhimurium -- Genetic Aspects ; Cell Death -- Genetic Aspects ; Iron (Metal) -- Physiological Aspects ; Hydrogen Peroxide -- Physiological Aspects
    ISSN: 0021-9193
    Source: Cengage Learning, Inc.
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  • 9
    Language: English
    In: PLoS Genetics, 01 April 2016, Vol.12(4), p.e1005975
    Description: While an increasing number of conserved small regulatory RNAs (sRNAs) are known to function in general bacterial physiology, the roles and modes of action of sRNAs from horizontally acquired genomic regions remain little understood. The IsrK sRNA of Gifsy-1 prophage of Salmonella belongs to the latter class. This regulatory RNA exists in two isoforms. The first forms, when a portion of transcripts originating from isrK promoter reads-through the IsrK transcription-terminator producing a translationally inactive mRNA target. Acting in trans, the second isoform, short IsrK RNA, binds the inactive transcript rendering it translationally active. By switching on translation of the first isoform, short IsrK indirectly activates the production of AntQ, an antiterminator protein located upstream of isrK. Expression of antQ globally interferes with transcription termination resulting in bacterial growth arrest and ultimately cell death. Escherichia coli and Salmonella cells expressing AntQ display condensed chromatin morphology and localization of UvrD to the nucleoid. The toxic phenotype of AntQ can be rescued by co-expression of the transcription termination factor, Rho, or RNase H, which protects genomic DNA from breaks by resolving R-loops. We propose that AntQ causes conflicts between transcription and replication machineries and thus promotes DNA damage. The isrK locus represents a unique example of an island-encoded sRNA that exerts a highly complex regulatory mechanism to tune the expression of a toxic protein.
    Keywords: Biology
    ISSN: 1553-7390
    E-ISSN: 1553-7404
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  • 10
    Language: English
    In: PLoS Genetics, 01 April 2017, Vol.13(4), p.e1006725
    Description: [This corrects the article DOI: 10.1371/journal.pgen.1005975.].
    Keywords: Biology
    E-ISSN: 1553-7404
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