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  • 1
    Language: English
    In: Molecular Cell, 10 October 2013, Vol.52(1), pp.4-7
    Description: Three papers in this issue of report on the structure and functional activity of type III CRISPR-Cas effector complexes, revealing novel and conserved features of the ribonucleoprotein particles that underlie prokaryotic genome defense. The new structures suggest that type I and type III complexes follow the same architectural principles and are most likely descendants of a common ancestor, the differences in RNA and protein sequences and structure of individual components notwithstanding.
    Keywords: Biology
    ISSN: 1097-2765
    E-ISSN: 1097-4164
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  • 2
    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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  • 3
    Language: English
    In: Molecular microbiology, 2010, Vol.76(4), pp.990-1009
    Description: Small non-coding RNAs (sRNAs) have been found to regulate gene expression in all three kingdoms of life. So far, relatively little is known about sRNAs from Gram-positive bacteria. SR1 is a regulatory sRNA from the Bacillus subtilis chromosome that inhibits by base-pairing translation initiation of ahrC mRNA encoding a transcriptional activator of the arginine catabolic operons. Here we present a novel target of SR1, the glycolytic gapA operon. Both microarray and Northern blot analyses show that the amount of gapA operon mRNA is significantly higher in the presence of SR1 when cells were grown in complex medium until stationary phase. Translational lacZ fusions and toeprinting analyses demonstrate that SR1 does not promote translation of gapA mRNA. By contrast, the half-life of gapA operon mRNA is strongly reduced in the sr1 knockout strain. SR1 does not act as a base-pairing sRNA on gapA operon mRNA. Instead, we demonstrate that the 39 aa peptide encoded by SR1, SR1P, is responsible for the effect of SR1 on the gapA operon. We show that SR1P binds GapA, thereby stabilizing the gapA operon mRNA by a hitherto unknown mechanism. SR1 is the first dual-function sRNA found in B. subtilis. ; Includes references ; p. 990-1009.
    Keywords: Messenger Rna ; Peptides ; Gene Expression;
    ISSN: 0950-382X
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  • 4
    Language: English
    In: Nucleic acids research, 02 June 2017, Vol.45(10), pp.6147-6167
    Description: Neisseria meningitidis is a human commensal that can also cause life-threatening meningitis and septicemia. Despite growing evidence for RNA-based regulation in meningococci, their transcriptome structure and output of regulatory small RNAs (sRNAs) are incompletely understood. Using dRNA-seq, we have mapped at single-nucleotide resolution the primary transcriptome of N. meningitidis strain 8013. Annotation of 1625 transcriptional start sites defines transcription units for most protein-coding genes but also reveals a paucity of classical σ70-type promoters, suggesting the existence of activators that compensate for the lack of -35 consensus sequences in N. meningitidis. The transcriptome maps also reveal 65 candidate sRNAs, a third of which were validated by northern blot analysis. Immunoprecipitation with the RNA chaperone Hfq drafts an unexpectedly large post-transcriptional regulatory network in this organism, comprising 23 sRNAs and hundreds of potential mRNA targets. Based on this data, using a newly developed gfp reporter system we validate an Hfq-dependent mRNA repression of the putative colonization factor PrpB by the two trans-acting sRNAs RcoF1/2. Our genome-wide RNA compendium will allow for a better understanding of meningococcal transcriptome organization and riboregulation with implications for colonization of the human nasopharynx.
    Keywords: Gene Expression Regulation, Bacterial ; Transcriptome ; Bacterial Proteins -- Metabolism ; Host Factor 1 Protein -- Metabolism ; Micrornas -- Genetics ; Molecular Chaperones -- Metabolism ; Neisseria Meningitidis -- Genetics ; RNA, Bacterial -- Genetics ; RNA, Messenger -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 5
    In: Molecular Microbiology, October 2006, Vol.62(2), pp.520-536
    Description: Whereas about 70 small non‐coding RNAs have been found in the genome, relatively little is known about regulatory RNAs from Gram‐positive bacteria. Here, we demonstrate that the recently identified small untranslated RNA SR1 from the genome is a regulatory RNA involved in fine‐tuning of arginine catabolism. 2D protein gel electrophoresis indicated three possible SR1 targets that are regulated by the transcriptional activator AhrC, which was shown to be the primary target of SR1. pairing studies and an reporter gene test demonstrated a specific interaction between SR1 and mRNA. This interaction did not lead to degradation of mRNA, but inhibited translation at a post‐initiation stage. Our data show that the Hfq chaperone was not required for the stabilization of SR1 . The amount of SR1 was increased upon addition of ‐arginine and ‐ornithine, but not ‐citrulline or ‐proline.
    Keywords: Arginine -- Genetic Aspects ; Genomics -- Genetic Aspects;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 6
    Language: English
    In: RNA Biology, 01 April 2012, Vol.9(4), pp.361-363
    Keywords: Anatomy & Physiology
    ISSN: 1547-6286
    E-ISSN: 1555-8584
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  • 7
    In: Molecular Microbiology, May 2010, Vol.76(4), pp.990-1009
    Description: Small non‐coding RNAs (sRNAs) have been found to regulate gene expression in all three kingdoms of life. So far, relatively little is known about sRNAs from Gram‐positive bacteria. SR1 is a regulatory sRNA from the chromosome that inhibits by base‐pairing translation initiation of mRNA encoding a transcriptional activator of the arginine catabolic operons. Here we present a novel target of SR1, the glycolytic operon. Both microarray and Northern blot analyses show that the amount of operon mRNA is significantly higher in the presence of SR1 when cells were grown in complex medium until stationary phase. Translational fusions and toeprinting analyses demonstrate that SR1 does not promote translation of mRNA. By contrast, the half‐life of operon mRNA is strongly reduced in the knockout strain. SR1 does not act as a base‐pairing sRNA on operon mRNA. Instead, we demonstrate that the 39 aa peptide encoded by SR1, SR1P, is responsible for the effect of SR1 on the operon. We show that SR1P binds GapA, thereby stabilizing the operon mRNA by a hitherto unknown mechanism. SR1 is the first dual‐function sRNA found in .
    Keywords: Ribonucleic Acid–RNA ; Gram-Positive Bacteria ; Peptides ; Gene Expression ; Proteins ; Cells ; Microbiology;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 8
    Language: English
    In: Microbiology (Reading, England), February 2007, Vol.153(Pt 2), pp.420-7
    Description: Streptococcal plasmid pIP501 uses antisense RNA-mediated transcriptional attenuation to regulate its replication. Previous in vitro assays suggested that binding intermediates between RNAII (sense RNA) and RNAIII (antisense RNA) are sufficient for inhibition, and a U-turn structure on RNAII loop L1 was found to be crucial for the interaction with RNAIII. Here, sequence and structural requirements for an efficient RNAII-RNAIII interaction were investigated. A detailed probing of RNA secondary structure combined with in vitro single-round transcription assays indicated that complex formation between the two molecules progresses into the lower stems of both loop pairs of the sense and antisense RNAs, but that the complex between RNAII and RNAIII is not a full duplex. Stem-loops L3 and L4 were required to be linked to one other for efficient contact with the complementary loops L2 and L1 of the sense RNA, indicating a simultaneous interaction between these two loop pairs. Thereby, the sequence and length of the spacer connecting L3 and L4 were shown not to be important for inhibition.
    Keywords: Gene Expression Regulation, Bacterial ; Transcription, Genetic ; Plasmids -- Metabolism ; RNA -- Chemistry ; RNA, Antisense -- Metabolism
    ISSN: 1350-0872
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  • 9
    In: Molecular Microbiology, July 2007, Vol.65(2), pp.413-424
    Description: The translation of many heat shock and virulence genes is controlled by RNA thermometers. Usually, they are located in the 5′‐untranslated region (5′‐UTR) and block the Shine‐Dalgarno (SD) sequence by base pairing. Destabilization of the structure at elevated temperature permits ribosome binding and translation initiation. We have identified a new type of RNA thermometer in the 5′‐UTR of the gene, which codes for a small heat shock protein. Transcription of the gene is controlled by the alternative sigma factor σ. Additional translational control depends on a stretch of four uridines that pair with the SD sequence. Mutations in this region affect translation . Structure probing experiments demonstrate a temperature‐controlled opening of the SD region . Toeprinting (primer extension inhibition) shows that ribosome binding is dependent on high temperatures. Together with a postulated RNA thermometer upstream of the virulence gene (), the 5′‐UTR of might be the founding member of a new class of RNA thermometers that we propose to name ‘fourU’ thermometers.
    Keywords: Measuring Instruments ; Salmonella;
    ISSN: 0950-382X
    E-ISSN: 1365-2958
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  • 10
    Language: English
    In: Journal of Molecular Biology, 2003, Vol.333(5), pp.917-929
    Description: Antisense-RNA mediated gene regulation has been found and studied in detail mainly in prokaryotic accessory DNA elements. In spite of different regulatory mechanisms, in all cases a rapid interaction between antisense and target RNA has been shown to be crucial for efficient regulation. Recently, a sequence comparison revealed in 45 antisense RNA control systems a 5′ YUNR motif indicative for the formation of a U-turn structure in either an antisense or a target RNA loop and confirmed in the case of the hok/sok system of plasmid R1 its importance for regulation. Here, we demonstrate the importance of the 5′ YUNR motif in the target RNA (RNAII) loop L1 of the replication control system of plasmid pIP501. The effect of four individual mutations in L1 was studied in vivo and in vitro . Mutations that maintained the putative U-turn or swapped it from sense to antisense RNA were silent, whereas mutations that eliminated the 5′-YUNR motif showed two- to threefold elevated copy numbers in vivo in correlation with three- to fourfold reduced inhibition rate constants of the complementary RNAIII species in vitro , whereas the half-lives of all RNAIII species were not affected. ENU probing experiments confirmed the U-turn structure for the silent mutation (N-C) and disruption of this structure upon alteration of the invariant U or inversion of the YUNR motif-containing loop. RNA secondary structure probing excluded loop size alterations as a reason for altered inhibition rates. Implications for the pathway and efficiency of RNAII/RNAIII interaction, and hence, pIP501 copy-number control, are discussed.
    Keywords: Antisense-RNA Mediated Transcriptional Attenuation ; Sense/Antisense-RNA Interaction ; U-Turn Loop Structure ; Plasmid Copy-Number Control ; Gram Positive Bacteria ; Biology ; Chemistry
    ISSN: 0022-2836
    E-ISSN: 1089-8638
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