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  • 1
    Language: English
    In: Proceedings of the National Academy of Sciences of the United States of America, 10 September 2013, Vol.110(37), pp.E3487-96
    Description: Small RNAs (sRNAs) constitute a large and heterogeneous class of bacterial gene expression regulators. Much like eukaryotic microRNAs, these sRNAs typically target multiple mRNAs through short seed pairing, thereby acting as global posttranscriptional regulators. In some bacteria, evidence for hundreds to possibly more than 1,000 different sRNAs has been obtained by transcriptome sequencing. However, the experimental identification of possible targets and, therefore, their confirmation as functional regulators of gene expression has remained laborious. Here, we present a strategy that integrates phylogenetic information to predict sRNA targets at the genomic scale and reconstructs regulatory networks upon functional enrichment and network analysis (CopraRNA, for Comparative Prediction Algorithm for sRNA Targets). Furthermore, CopraRNA precisely predicts the sRNA domains for target recognition and interaction. When applied to several model sRNAs, CopraRNA revealed additional targets and functions for the sRNAs CyaR, FnrS, RybB, RyhB, SgrS, and Spot42. Moreover, the mRNAs gdhA, lrp, marA, nagZ, ptsI, sdhA, and yobF-cspC were suggested as regulatory hubs targeted by up to seven different sRNAs. The verification of many previously undetected targets by CopraRNA, even for extensively investigated sRNAs, demonstrates its advantages and shows that CopraRNA-based analyses can compete with experimental target prediction approaches. A Web interface allows high-confidence target prediction and efficient classification of bacterial sRNAs.
    Keywords: E. Coli ; RNA–RNA Interaction ; Regulatory RNA ; RNA, Bacterial -- Genetics
    ISSN: 00278424
    E-ISSN: 1091-6490
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  • 2
    In: Nucleic Acids Research, 2017, Vol. 45(W1), pp.W435-W439
    Description: The IntaRNA algorithm enables fast and accurate prediction of RNA–RNA hybrids by incorporating seed constraints and interaction site accessibility. Here, we introduce IntaRNA v2, which enables enhanced parameterization as well as fully customizable control over the prediction modes and output formats. Based on up to date benchmark data, the enhanced predictive quality is shown and further improvements due to more restrictive seed constraints are highlighted. The extended web interface provides visualizations of the new minimal energy profiles for RNA–RNA interactions. These allow a detailed investigation of interaction alternatives and can reveal potential interaction site multiplicity. IntaRNA v2 is freely available (source and binary), and distributed via the conda package manager. Furthermore, it has been included into the Galaxy workflow framework and its already established web interface enables ad hoc usage.
    Keywords: Web Server Issue;
    ISSN: 0305-1048
    E-ISSN: 1362-4962
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  • 3
    Language: English
    In: Chemistry – A European Journal, 08 July 2013, Vol.19(28), pp.9319-9324
    Description: Marine myxobacteria (, , , ) are phylogenetically distant from their terrestrial counterparts. Salimabromide is the first natural product from the / clade of obligatory marine myxobacteria. Salimabromide has a new tetracyclic carbon skeleton, comprising a brominated benzene ring, a furano lactone residue, and a cyclohexane ring, bridged by a seven‐membered cyclic moiety. The absolute configuration was deduced from experimental and calculated CD data. Salimabromide revealed antibiotic activity towards . Salimabromide () is the first natural product from the / clade of obligate marine myxobacteria. Salimabromide has a new tetracyclic carbon skeleton, comprising a brominated benzene ring, a furano lactone residue, and a cyclohexane ring bridged by a seven‐membered cyclic moiety (see figure). The absolute configuration was deduced from experimental and calculated circular dichroism (CD) data.
    Keywords: Enhygromyxa ; Myxobacteria ; Natural Products ; Nmr Spectroscopy ; Polyketides
    ISSN: 0947-6539
    E-ISSN: 1521-3765
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  • 4
    Language: English
    In: Nucleic acids research, 02 November 2018, Vol.46(19), pp.10082-10094
    Description: As the key enzyme of bacterial nitrogen assimilation, glutamine synthetase (GS) is tightly regulated. In cyanobacteria, GS activity is controlled by the interaction with inactivating protein factors IF7 and IF17 encoded by the genes gifA and gifB, respectively. We show that a glutamine-binding aptamer within the gifB 5' UTR of Synechocystis sp. PCC 6803 is critical for the expression of IF17. Binding of glutamine induced structural re-arrangements in this RNA element leading to enhanced protein synthesis in vivo and characterizing it as a riboswitch. Mutagenesis showed the riboswitch mechanism to contribute at least as much to the control of gene expression as the promoter-mediated transcriptional regulation. We suggest this and a structurally related but distinct element, to be designated type 1 and type 2 glutamine riboswitches. Extended biocomputational searches revealed that glutamine riboswitches are exclusively but frequently found in cyanobacterial genomes, where they are primarily associated with gifB homologs. Hence, this RNA-based sensing mechanism is common in cyanobacteria and establishes a regulatory feedback loop that couples the IF17-mediated GS inactivation to the intracellular glutamine levels. Together with the previously described sRNA NsiR4, these results show that non-coding RNA is an indispensable component in the control of nitrogen assimilation in cyanobacteria.
    Keywords: Glutamate-Ammonia Ligase -- Genetics ; Glutamine -- Genetics ; Riboswitch -- Genetics
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 5
    Language: English
    In: Nucleic acids research, July 2014, Vol.42(Web Server issue), pp.W119-23
    Description: CopraRNA (Comparative prediction algorithm for small RNA targets) is the most recent asset to the Freiburg RNA Tools webserver. It incorporates and extends the functionality of the existing tool IntaRNA (Interacting RNAs) in order to predict targets, interaction domains and consequently the regulatory networks of bacterial small RNA molecules. The CopraRNA prediction results are accompanied by extensive postprocessing methods such as functional enrichment analysis and visualization of interacting regions. Here, we introduce the functionality of the CopraRNA and IntaRNA webservers and give detailed explanations on their postprocessing functionalities. Both tools are freely accessible at http://rna.informatik.uni-freiburg.de.
    Keywords: Software ; RNA, Bacterial -- Chemistry ; RNA, Small Untranslated -- Chemistry
    ISSN: 03051048
    E-ISSN: 1362-4962
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  • 6
    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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  • 7
    Language: English
    In: EMBO journal: European Molecular Biology Organization, 2016, Issue 9, pp.991-1011
    Description: The molecular roles of many RNA‐binding proteins in bacterial post‐transcriptional gene regulation are not well understood. Approaches combining in vivo UV crosslinking with RNA deep sequencing (CLIP‐seq) have begun to revolutionize the transcriptome‐wide mapping of eukaryotic RNA‐binding protein target sites. We have applied CLIP‐seq to chart the target landscape of two major bacterial post‐transcriptional regulators, Hfq and CsrA, in the model pathogen Salmonella Typhimurium. By detecting binding sites at single‐nucleotide resolution, we identify RNA 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–RNA interactions. Additionally, Hfq preferentially binds 5′ to sRNA‐target sites in mRNAs, and 3′ to seed sequences in sRNAs, reflecting a simple logic in how Hfq facilitates sRNA–mRNA interactions. Importantly, global knowledge of Hfq sites significantly improves sRNA‐target predictions. CsrA binds AUGGA sequences in apical loops and targets many Salmonella virulence mRNAs. Overall, our generic CLIP‐seq approach will bring new insights into post‐transcriptional gene regulation by RNA‐binding proteins in diverse bacterial species.
    Keywords: Clip ; Csra ; Hfq ; Non‐Coding Rna ; Peak Calling ; Post‐Transcriptional Control ; Small Rna ; Terminator ; Translation
    ISSN: 0261-4189
    Source: Fundación Dialnet
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  • 8
    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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  • 9
    Language: English
    In: Methods in molecular biology (Clifton, N.J.), 2018, Vol.1737, pp.3-30
    Description: Computational methods can often facilitate the functional characterization of individual sRNAs and furthermore allow high-throughput analysis on large numbers of sRNA candidates. This chapter outlines a potential workflow for computational sRNA analyses and describes in detail methods for homolog detection, target prediction, and functional characterization based on enrichment analysis. The cyanobacterial sRNA IsaR1 is used as a specific example. All methods are available as webservers and easily accessible for nonexpert users.
    Keywords: Computational Methods ; Cyanobacteria ; Functional Characterization ; Isar1 ; Target Prediction ; Srna Conservation ; Genome, Bacterial ; Computational Biology -- Methods ; Cyanobacteria -- Genetics ; Genomics -- Methods ; RNA, Bacterial -- Genetics ; RNA, Small Untranslated -- Genetics
    E-ISSN: 1940-6029
    Source: MEDLINE/PubMed (U.S. National Library of Medicine)
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  • 10
    Language: English
    In: Journal of Pharmaceutical and Biomedical Analysis, 2011, Vol.56(5), pp.944-949
    Description: Fusing complex data from two disparate sources has been demonstrated to improve the accuracy in quantifying active ingredients in mixtures of pharmaceutical powders. A four-component simplex-centroid design was used to prepare blended powder mixtures of acetaminophen, caffeine, aspirin and ibuprofen. The blends were analyzed by Fourier transform infra-red spectroscopy (FTIR) and powder X-ray diffraction (PXRD). The FTIR and PXRD data were preprocessed and combined using two different data fusion methods: fusion of preprocessed data (FPD) and fusion of principal component scores (FPCS). A partial least square (PLS) model built on the FPD did not improve the root mean square error of prediction. However, a PLS model built on the FPCS yielded better accuracy prediction than PLS models built on individual FTIR and PXRD data sets. The improvement in prediction accuracy of the FPCS may be attributed to the removal of noise and data reduction associated with using PCA as a preprocessing tool. The present approach demonstrates the usefulness of data fusion for the information management of large data sets from disparate sources.
    Keywords: Data Fusion ; Multivariate Analysis ; Pharmaceutical Powder Mixtures ; Fourier Transform Infrared Spectroscopy ; Powder X-Ray Diffraction ; Pharmacy, Therapeutics, & Pharmacology
    ISSN: 0731-7085
    E-ISSN: 1873-264X
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