1
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McBroome J, de Bernardi Schneider A, Roemer C, Wolfinger MT, Hinrichs AS, O'Toole AN, Ruis C, Turakhia Y, Rambaut A, Corbett-Detig R. A framework for automated scalable designation of viral pathogen lineages from genomic data. Nat Microbiol 2024; 9:550-560. [PMID: 38316930 PMCID: PMC10847047 DOI: 10.1038/s41564-023-01587-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/06/2023] [Accepted: 12/13/2023] [Indexed: 02/07/2024]
Abstract
Pathogen lineage nomenclature systems are a key component of effective communication and collaboration for researchers and public health workers. Since February 2021, the Pango dynamic lineage nomenclature for SARS-CoV-2 has been sustained by crowdsourced lineage proposals as new isolates were sequenced. This approach is vulnerable to time-critical delays as well as regional and personal bias. Here we developed a simple heuristic approach for dividing phylogenetic trees into lineages, including the prioritization of key mutations or genes. Our implementation is efficient on extremely large phylogenetic trees consisting of millions of sequences and produces similar results to existing manually curated lineage designations when applied to SARS-CoV-2 and other viruses including chikungunya virus, Venezuelan equine encephalitis virus complex and Zika virus. This method offers a simple, automated and consistent approach to pathogen nomenclature that can assist researchers in developing and maintaining phylogeny-based classifications in the face of ever-increasing genomic datasets.
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Affiliation(s)
- Jakob McBroome
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
| | - Adriano de Bernardi Schneider
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Cornelius Roemer
- Biozentrum, University of Basel, Basel, Switzerland
- Swiss Institute of Bioinformatics, Basel, Switzerland
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- RNA Forecast e.U., Vienna, Austria
- Bioinformatics Group, Department of Computer Science, University of Freiburg, Freiburg, Germany
| | - Angie S Hinrichs
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA
| | - Aine Niamh O'Toole
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Christopher Ruis
- Molecular Immunity Unit, MRC Laboratory of Molecular Biology, Department of Medicine, University of Cambridge, Cambridge, UK
- Department of Veterinary Medicine, University of Cambridge, Cambridge, UK
- Cambridge Centre for AI in Medicine, University of Cambridge, Cambridge, UK
| | - Yatish Turakhia
- Department of Electrical and Computer Engineering, University of California San Diego, San Diego, CA, USA
| | - Andrew Rambaut
- Institute of Ecology and Evolution, University of Edinburgh, Edinburgh, UK
| | - Russell Corbett-Detig
- Department of Biomolecular Engineering, University of California Santa Cruz, Santa Cruz, CA, USA.
- Genomics Institute, University of California Santa Cruz, Santa Cruz, CA, USA.
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2
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Gemmill DL, Nelson CR, Badmalia MD, Pereira HS, Kerr L, Wolfinger MT, Patel TR. The 3' terminal region of Zika virus RNA contains a conserved G-quadruplex and is unfolded by human DDX17. Biochem Cell Biol 2024; 102:96-105. [PMID: 37774422 DOI: 10.1139/bcb-2023-0036] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/01/2023] Open
Abstract
Zika virus (ZIKV) infection remains a worldwide concern, and currently no effective treatments or vaccines are available. Novel therapeutics are an avenue of interest that could probe viral RNA-human protein communication to stop viral replication. One specific RNA structure, G-quadruplexes (G4s), possess various roles in viruses and all domains of life, including transcription and translation regulation and genome stability, and serves as nucleation points for RNA liquid-liquid phase separation. Previous G4 studies on ZIKV using a quadruplex forming G-rich sequences Mapper located a potential G-quadruplex sequence in the 3' terminal region (TR) and was validated structurally using a 25-mer oligo. It is currently unknown if this structure is conserved and maintained in a large ZIKV RNA transcript and its specific roles in viral replication. Using bioinformatic analysis and biochemical assays, we demonstrate that the ZIKV 3' TR G4 is conserved across all ZIKV isolates and maintains its structure in a 3' TR full-length transcript. We further established the G4 formation using pyridostatin and the BG4 G4-recognizing antibody binding assays. Our study also demonstrates that the human DEAD-box helicases, DDX3X132-607 and DDX17135-555, bind to the 3' TR and that DDX17135-555 unfolds the G4 present in the 3' TR. These findings provide a path forward in potential therapeutic targeting of DDX3X or DDX17's binding to the 3' TR G4 region for novel treatments against ZIKV.
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Affiliation(s)
- Dannielle L Gemmill
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Corey R Nelson
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Higor S Pereira
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Liam Kerr
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- RNA Forecast e.U., 1140 Vienna, Austria
| | - Trushar R Patel
- Alberta RNA Research and Training Institute & Department of Chemistry and Biochemistry, University of Lethbridge, Lethbridge, AB T1K 3M4, Canada
- Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada
- Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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3
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Mrozowich T, Park SM, Waldl M, Henrickson A, Tersteeg S, Nelson CR, De Klerk A, Demeler B, Hofacker IL, Wolfinger MT, Patel TR. Investigating RNA-RNA interactions through computational and biophysical analysis. Nucleic Acids Res 2023; 51:4588-4601. [PMID: 36999609 DOI: 10.1093/nar/gkad223] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2022] [Revised: 02/24/2023] [Accepted: 03/15/2023] [Indexed: 04/01/2023] Open
Abstract
Numerous viruses utilize essential long-range RNA-RNA genome interactions, specifically flaviviruses. Using Japanese encephalitis virus (JEV) as a model system, we computationally predicted and then biophysically validated and characterized its long-range RNA-RNA genomic interaction. Using multiple RNA computation assessment programs, we determine the primary RNA-RNA interacting site among JEV isolates and numerous related viruses. Following in vitro transcription of RNA, we provide, for the first time, characterization of an RNA-RNA interaction using size-exclusion chromatography coupled with multi-angle light scattering and analytical ultracentrifugation. Next, we demonstrate that the 5' and 3' terminal regions of JEV interact with nM affinity using microscale thermophoresis, and this affinity is significantly reduced when the conserved cyclization sequence is not present. Furthermore, we perform computational kinetic analyses validating the cyclization sequence as the primary driver of this RNA-RNA interaction. Finally, we examined the 3D structure of the interaction using small-angle X-ray scattering, revealing a flexible yet stable interaction. This pathway can be adapted and utilized to study various viral and human long-non-coding RNA-RNA interactions and determine their binding affinities, a critical pharmacological property of designing potential therapeutics.
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Affiliation(s)
- Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Sean M Park
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Maria Waldl
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- Center of Anatomy & Cell Biology, Division of Cell & Developmental Biology, Medical, University of Vienna, Schwarzspanierstrasse 17, 1090, Vienna, Austria
- Vienna Doctoral School in Chemistry (DoSChem), University of Vienna, Währinger Strasse 42, 1090 Vienna, Austria
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Scott Tersteeg
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Corey R Nelson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Anneke De Klerk
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
- Department of Chemistry and Biochemistry, University of Montana, Missoula, MT59812, USA
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
- Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna Austria
- RNA Forecast e.U., 1100 Vienna, Austria
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, ABT1K 3M4, Canada
- Li Ka Shing Institute of Virology, University of Alberta, Edmonton T6G 2E1, Alberta, Canada
- Department of Microbiology, Immunology & Infectious Diseases, Cumming School of Medicine, University of Calgary, Calgary T2N 4N1, Canada
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4
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Ochsenreiter R, Wolfinger MT. Strukturierte RNAs in Viren. Biospektrum (Heidelb) 2023; 29:156-158. [PMID: 37073323 PMCID: PMC10101536 DOI: 10.1007/s12268-023-1907-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/20/2023]
Abstract
Evolutionarily conserved RNAs in untranslated regions are key regulators of the viral life cycle. Exoribonuclease-resistant RNAs (xrRNAs) are particularly interesting examples of structurally conserved elements because they actively dysregulate the messenger RNA (mRNA) degradation machinery of host cells, thereby mediating viral pathogenicity. We review the principles of RNA structure conservation in viruses and discuss potential applications of xrRNAs in synthetic biology and future mRNA vaccines.
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Affiliation(s)
| | - Michael T. Wolfinger
- Institut für Theoretische Chemie, Universität Wien, Wien, Österreich
- Arbeitsgruppe Bioinformatik und Computational Biology, Fakultät für Informatik, Universität Wien, Währinger Strasse 29, A-1090 Wien, Österreich
- RNA Forecast E. U., Wien, Österreich
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5
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Darai N, Mahalapbutr P, Wolschann P, Lee VS, Wolfinger MT, Rungrotmongkol T. Theoretical studies on RNA recognition by Musashi 1 RNA-binding protein. Sci Rep 2022; 12:12137. [PMID: 35840700 PMCID: PMC9287312 DOI: 10.1038/s41598-022-16252-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/23/2022] [Accepted: 07/07/2022] [Indexed: 01/12/2023] Open
Abstract
The Musashi (MSI) family of RNA-binding proteins, comprising the two homologs Musashi-1 (MSI1) and Musashi-2 (MSI2), typically regulates translation and is involved in cell proliferation and tumorigenesis. MSI proteins contain two ribonucleoprotein-like RNA-binding domains, RBD1 and RBD2, that bind single-stranded RNA motifs with a central UAG trinucleotide with high affinity and specificity. The finding that MSI also promotes the replication of Zika virus, a neurotropic Flavivirus, has triggered further investigations of the biochemical principles behind MSI–RNA interactions. However, a detailed molecular understanding of the specificity of MSI RBD1/2 interaction with RNA is still missing. Here, we performed computational studies of MSI1–RNA association complexes, investigating different RNA pentamer motifs using molecular dynamics simulations with binding free energy calculations based on the solvated interaction energy method. Simulations with Alphafold2 suggest that predicted MSI protein structures are highly similar to experimentally determined structures. The binding free energies show that two out of four RNA pentamers exhibit a considerably higher binding affinity to MSI1 RBD1 and RBD2, respectively. The obtained structural information on MSI1 RBD1 and RBD2 will be useful for a detailed functional and mechanistic understanding of this type of RNA–protein interactions.
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Affiliation(s)
- Nitchakan Darai
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand
| | - Panupong Mahalapbutr
- Department of Biochemistry, Faculty of Medicine, Khon Kaen University, Khon Kaen, 40002, Thailand
| | - Peter Wolschann
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria
| | - Vannajan Sanghiran Lee
- Department of Chemistry, Faculty of Science, University of Malaya, 50603, Kuala Lumpur, Malaysia
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Strasse 17, 1090, Vienna, Austria. .,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Währinger Strasse 29, 1090, Vienna, Austria.
| | - Thanyada Rungrotmongkol
- Program in Bioinformatics and Computational Biology, Graduate School, Chulalongkorn University, Bangkok, 10330, Thailand. .,Center of Excellence in Biocatalyst and Sustainable Biotechnology, Faculty of Science, Chulalongkorn University, Bangkok, 10330, Thailand.
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6
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Kutschera LS, Wolfinger MT. Evolutionary traits of Tick-borne encephalitis virus: Pervasive non-coding RNA structure conservation and molecular epidemiology. Virus Evol 2022; 8:veac051. [PMID: 35822110 PMCID: PMC9272599 DOI: 10.1093/ve/veac051] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2021] [Revised: 04/14/2022] [Accepted: 06/09/2022] [Indexed: 12/17/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is the aetiological agent of tick-borne
encephalitis, an infectious disease of the central nervous system that is often associated
with severe sequelae in humans. While TBEV is typically classified into three subtypes,
recent evidence suggests a more varied range of TBEV subtypes and lineages that differ
substantially in the architecture of their 3ʹ untranslated region (3ʹUTR). Building on
comparative genomic approaches and thermodynamic modelling, we characterize the TBEV UTR
structureome diversity and propose a unified picture of pervasive non-coding RNA structure
conservation. Moreover, we provide an updated phylogeny of TBEV, building on more than 220
publicly available complete genomes, and investigate the molecular epidemiology and
phylodynamics with Nextstrain, a web-based visualization framework for real-time pathogen
evolution.
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Affiliation(s)
- Lena S Kutschera
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währinger Straße 17, Vienna 1090, Austria
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7
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Flamm C, Wielach J, Wolfinger MT, Badelt S, Lorenz R, Hofacker IL. Caveats to Deep Learning Approaches to RNA Secondary Structure Prediction. Front Bioinform 2022; 2:835422. [PMID: 36304289 PMCID: PMC9580944 DOI: 10.3389/fbinf.2022.835422] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2021] [Accepted: 06/09/2022] [Indexed: 11/18/2022] Open
Abstract
Machine learning (ML) and in particular deep learning techniques have gained popularity for predicting structures from biopolymer sequences. An interesting case is the prediction of RNA secondary structures, where well established biophysics based methods exist. The accuracy of these classical methods is limited due to lack of experimental parameters and certain simplifying assumptions and has seen little improvement over the last decade. This makes RNA folding an attractive target for machine learning and consequently several deep learning models have been proposed in recent years. However, for ML approaches to be competitive for de-novo structure prediction, the models must not just demonstrate good phenomenological fits, but be able to learn a (complex) biophysical model. In this contribution we discuss limitations of current approaches, in particular due to biases in the training data. Furthermore, we propose to study capabilities and limitations of ML models by first applying them on synthetic data (obtained from a simplified biophysical model) that can be generated in arbitrary amounts and where all biases can be controlled. We assume that a deep learning model that performs well on these synthetic, would also perform well on real data, and vice versa. We apply this idea by testing several ML models of varying complexity. Finally, we show that the best models are capable of capturing many, but not all, properties of RNA secondary structures. Most severely, the number of predicted base pairs scales quadratically with sequence length, even though a secondary structure can only accommodate a linear number of pairs.
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Affiliation(s)
- Christoph Flamm
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Julia Wielach
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T. Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Stefan Badelt
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ronny Lorenz
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ivo L. Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- *Correspondence: Ivo L. Hofacker,
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8
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Rozner M, Nukarinen E, Wolfinger MT, Amman F, Weckwerth W, Bläsi U, Sonnleitner E. Rewiring of Gene Expression in Pseudomonas aeruginosa During Diauxic Growth Reveals an Indirect Regulation of the MexGHI-OpmD Efflux Pump by Hfq. Front Microbiol 2022; 13:919539. [PMID: 35832820 PMCID: PMC9272787 DOI: 10.3389/fmicb.2022.919539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2022] [Accepted: 05/25/2022] [Indexed: 11/13/2022] Open
Abstract
In Pseudomonas aeruginosa, the RNA chaperone Hfq and the catabolite repression protein Crc act in concert to regulate numerous genes during carbon catabolite repression (CCR). After alleviation of CCR, the RNA CrcZ sequesters Hfq/Crc, which leads to a rewiring of gene expression to ensure the consumption of less preferred carbon and nitrogen sources. Here, we performed a multiomics approach by assessing the transcriptome, translatome, and proteome in parallel in P. aeruginosa strain O1 during and after relief of CCR. As Hfq function is impeded by the RNA CrcZ upon relief of CCR, and Hfq is known to impact antibiotic susceptibility in P. aeruginosa, emphasis was laid on links between CCR and antibiotic susceptibility. To this end, we show that the mexGHI-opmD operon encoding an efflux pump for the antibiotic norfloxacin and the virulence factor 5-Methyl-phenazine is upregulated after alleviation of CCR, resulting in a decreased susceptibility to the antibiotic norfloxacin. A model for indirect regulation of the mexGHI-opmD operon by Hfq is presented.
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Affiliation(s)
- Marlena Rozner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
| | - Ella Nukarinen
- Molecular Systems Biology, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
| | - Michael T. Wolfinger
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Wolfram Weckwerth
- Molecular Systems Biology, Department of Functional and Evolutionary Ecology, Faculty of Life Sciences, University of Vienna, Vienna, Austria
- Vienna Metabolomics Center, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- *Correspondence: Udo Bläsi,
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna Biocenter (VBC), University of Vienna, Vienna, Austria
- Elisabeth Sonnleitner,
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9
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D'Souza MH, Mrozowich T, Badmalia MD, Geeraert M, Frederickson A, Henrickson A, Demeler B, Wolfinger MT, Patel TR. Biophysical characterisation of human LincRNA-p21 sense and antisense Alu inverted repeats. Nucleic Acids Res 2022; 50:5881-5898. [PMID: 35639511 PMCID: PMC9177966 DOI: 10.1093/nar/gkac414] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2021] [Revised: 04/26/2022] [Accepted: 05/09/2022] [Indexed: 12/05/2022] Open
Abstract
Human Long Intergenic Noncoding RNA-p21 (LincRNA-p21) is a regulatory noncoding RNA that plays an important role in promoting apoptosis. LincRNA-p21 is also critical in down-regulating many p53 target genes through its interaction with a p53 repressive complex. The interaction between LincRNA-p21 and the repressive complex is likely dependent on the RNA tertiary structure. Previous studies have determined the two-dimensional secondary structures of the sense and antisense human LincRNA-p21 AluSx1 IRs using SHAPE. However, there were no insights into its three-dimensional structure. Therefore, we in vitro transcribed the sense and antisense regions of LincRNA-p21 AluSx1 Inverted Repeats (IRs) and performed analytical ultracentrifugation, size exclusion chromatography, light scattering, and small angle X-ray scattering (SAXS) studies. Based on these studies, we determined low-resolution, three-dimensional structures of sense and antisense LincRNA-p21. By adapting previously known two-dimensional information, we calculated their sense and antisense high-resolution models and determined that they agree with the low-resolution structures determined using SAXS. Thus, our integrated approach provides insights into the structure of LincRNA-p21 Alu IRs. Our study also offers a viable pipeline for combining the secondary structure information with biophysical and computational studies to obtain high-resolution atomistic models for long noncoding RNAs.
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Affiliation(s)
- Michael H D'Souza
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Tyler Mrozowich
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Maulik D Badmalia
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Mitchell Geeraert
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Angela Frederickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Amy Henrickson
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Borries Demeler
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada.,Department of Chemistry and Biochemistry, University of Montana, Missoula, MT 59812, USA.,NorthWest Biophysics Consortium, University of Lethbridge, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada
| | - Michael T Wolfinger
- Bioinformatics and Computational Biology, Faculty of Computer Science, Währingerstrasse 29, 1090 Vienna, Austria.,Department of Theoretical Chemistry, University of Vienna, Währingerstrasse 17, 1090 Vienna, Austria
| | - Trushar R Patel
- Department of Chemistry and Biochemistry, Alberta RNA Research and Training Institute, University of Lethbridge, 4401 University Drive, Lethbridge, AB T1K 3M4, Canada.,Department of Microbiology, Immunology and Infectious Disease, Cumming School of Medicine, University of Calgary, Calgary, AB T2N 1N4, Canada.,Li Ka Shing Institute of Virology and Discovery Lab, University of Alberta, Edmonton, AB T6G 2E1, Canada
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10
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Gosavi D, Wower I, Beckmann IK, Hofacker IL, Wower J, Wolfinger MT, Sztuba-Solinska J. Insights into the secondary and tertiary structure of the Bovine Viral Diarrhea Virus Internal Ribosome Entry Site. RNA Biol 2022; 19:496-506. [PMID: 35380920 PMCID: PMC8986297 DOI: 10.1080/15476286.2022.2058818] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022] Open
Abstract
The internal ribosome entry site (IRES) RNA of bovine viral diarrhoea virus (BVDV), an economically significant Pestivirus, is required for the cap-independent translation of viral genomic RNA. Thus, it is essential for viral replication and pathogenesis. We applied a combination of high-throughput biochemical RNA structure probing (SHAPE-MaP) and in silico modelling approaches to gain insight into the secondary and tertiary structures of BVDV IRES RNA. Our study demonstrated that BVDV IRES RNA in solution forms a modular architecture composed of three distinct structural domains (I-III). Two regions within domain III are represented in tertiary interactions to form an H-type pseudoknot. Computational modelling of the pseudoknot motif provided a fine-grained picture of the tertiary structure and local arrangement of helices in the BVDV IRES. Furthermore, comparative genomics and consensus structure predictions revealed that the pseudoknot is evolutionarily conserved among many Pestivirus species. These studies provide detailed insight into the structural arrangement of BVDV IRES RNA H-type pseudoknot and encompassing motifs that likely contribute to the optimal functionality of viral cap-independent translation element.
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Affiliation(s)
- Devadatta Gosavi
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States
| | - Iwona Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - Irene K Beckmann
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Jacek Wower
- Department of Animal and Dairy Sciences, Auburn University, Auburn, AL, United States
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Joanna Sztuba-Solinska
- Department of Biological Sciences, Auburn University, 120 W. Samford Ave, Rouse Life Sciences Building, Auburn, AL, United States.,Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
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11
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Mrozowich T, Park SM, Wolfinger MT, Patel TR. Investigating flaviviral genomic cyclization. Biophys J 2022. [DOI: 10.1016/j.bpj.2021.11.1203] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022] Open
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12
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Cianciulli Sesso A, Lilić B, Amman F, Wolfinger MT, Sonnleitner E, Bläsi U. Gene Expression Profiling of Pseudomonas aeruginosa Upon Exposure to Colistin and Tobramycin. Front Microbiol 2021; 12:626715. [PMID: 33995291 PMCID: PMC8120321 DOI: 10.3389/fmicb.2021.626715] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 03/31/2021] [Indexed: 11/22/2022] Open
Abstract
Pseudomonas aeruginosa (Pae) is notorious for its high-level resistance toward clinically used antibiotics. In fact, Pae has rendered most antimicrobials ineffective, leaving polymyxins and aminoglycosides as last resort antibiotics. Although several resistance mechanisms of Pae are known toward these drugs, a profounder knowledge of hitherto unidentified factors and pathways appears crucial to develop novel strategies to increase their efficacy. Here, we have performed for the first time transcriptome analyses and ribosome profiling in parallel with strain PA14 grown in synthetic cystic fibrosis medium upon exposure to polymyxin E (colistin) and tobramycin. This approach did not only confirm known mechanisms involved in colistin and tobramycin susceptibility but revealed also as yet unknown functions/pathways. Colistin treatment resulted primarily in an anti-oxidative stress response and in the de-regulation of the MexT and AlgU regulons, whereas exposure to tobramycin led predominantly to a rewiring of the expression of multiple amino acid catabolic genes, lower tricarboxylic acid (TCA) cycle genes, type II and VI secretion system genes and genes involved in bacterial motility and attachment, which could potentially lead to a decrease in drug uptake. Moreover, we report that the adverse effects of tobramycin on translation are countered with enhanced expression of genes involved in stalled ribosome rescue, tRNA methylation and type II toxin-antitoxin (TA) systems.
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Affiliation(s)
- Anastasia Cianciulli Sesso
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Branislav Lilić
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Elisabeth Sonnleitner
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Max Perutz Labs, Vienna Biocenter (VBC), Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna, Austria
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13
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Harima H, Orba Y, Torii S, Qiu Y, Kajihara M, Eto Y, Matsuta N, Hang'ombe BM, Eshita Y, Uemura K, Matsuno K, Sasaki M, Yoshii K, Nakao R, Hall WW, Takada A, Abe T, Wolfinger MT, Simuunza M, Sawa H. An African tick flavivirus forming an independent clade exhibits unique exoribonuclease-resistant RNA structures in the genomic 3'-untranslated region. Sci Rep 2021; 11:4883. [PMID: 33649491 PMCID: PMC7921595 DOI: 10.1038/s41598-021-84365-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2020] [Accepted: 02/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne flaviviruses (TBFVs) infect mammalian hosts through tick bites and can cause various serious illnesses, such as encephalitis and hemorrhagic fevers, both in humans and animals. Despite their importance to public health, there is limited epidemiological information on TBFV infection in Africa. Herein, we report that a novel flavivirus, Mpulungu flavivirus (MPFV), was discovered in a Rhipicephalus muhsamae tick in Zambia. MPFV was found to be genetically related to Ngoye virus detected in ticks in Senegal, and these viruses formed a unique lineage in the genus Flavivirus. Analyses of dinucleotide contents of flaviviruses indicated that MPFV was similar to those of other TBFVs with a typical vertebrate genome signature, suggesting that MPFV may infect vertebrate hosts. Bioinformatic analyses of the secondary structures in the 3′-untranslated regions (UTRs) revealed that MPFV exhibited unique exoribonuclease-resistant RNA (xrRNA) structures. Utilizing biochemical approaches, we clarified that two xrRNA structures of MPFV in the 3′-UTR could prevent exoribonuclease activity. In summary, our findings provide new information regarding the geographical distribution of TBFV and xrRNA structures in the 3′-UTR of flaviviruses.
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Affiliation(s)
- Hayato Harima
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yasuko Orba
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Shiho Torii
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yongjin Qiu
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Masahiro Kajihara
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Yoshiki Eto
- Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Naoya Matsuta
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Bernard M Hang'ombe
- Department of Para-Clinical Studies, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia
| | - Yuki Eshita
- Hokudai Center for Zoonosis Control in Zambia, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Uemura
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Drug Discovery and Disease Research Laboratory, Shionogi & Co., Ltd., Osaka, Japan
| | - Keita Matsuno
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Unit of Risk Analysis and Management, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Michihito Sasaki
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan
| | - Kentaro Yoshii
- Laboratory of Public Health, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan.,National Research Center for the Control and Prevention of Infectious Diseases (CCPID), Nagasaki University, Nagasaki, Japan
| | - Ryo Nakao
- Laboratory of Parasitology, Faculty of Veterinary Medicine, Hokkaido University, Sapporo, Japan
| | - William W Hall
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,National Virus Reference Laboratory, School of Medicine, University College Dublin, Dublin, Ireland.,Centre for Research in Infectious Diseases, School of Medicine, University College Dublin, Dublin, Ireland.,Global Virus Network, Baltimore, MD, USA
| | - Ayato Takada
- International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Division of Global Epidemiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan.,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Takashi Abe
- Department of Electrical and Information Engineering, Graduate School of Science and Technology, Niigata University, Niigata, Japan
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Martin Simuunza
- Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia.,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia
| | - Hirofumi Sawa
- Division of Molecular Pathobiology, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,International Collaboration Unit, Research Center for Zoonosis Control, Hokkaido University, Sapporo, Japan. .,Africa Center of Excellence for Infectious Diseases of Humans and Animals, The University of Zambia, Lusaka, Zambia. .,Global Virus Network, Baltimore, MD, USA. .,Department of Disease Control, School of Veterinary Medicine, The University of Zambia, Lusaka, Zambia.
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14
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Popa A, Genger JW, Nicholson MD, Penz T, Schmid D, Aberle SW, Agerer B, Lercher A, Endler L, Colaço H, Smyth M, Schuster M, Grau ML, Martínez-Jiménez F, Pich O, Borena W, Pawelka E, Keszei Z, Senekowitsch M, Laine J, Aberle JH, Redlberger-Fritz M, Karolyi M, Zoufaly A, Maritschnik S, Borkovec M, Hufnagl P, Nairz M, Weiss G, Wolfinger MT, von Laer D, Superti-Furga G, Lopez-Bigas N, Puchhammer-Stöckl E, Allerberger F, Michor F, Bock C, Bergthaler A. Genomic epidemiology of superspreading events in Austria reveals mutational dynamics and transmission properties of SARS-CoV-2. Sci Transl Med 2020; 12:eabe2555. [PMID: 33229462 PMCID: PMC7857414 DOI: 10.1126/scitranslmed.abe2555] [Citation(s) in RCA: 154] [Impact Index Per Article: 38.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 11/16/2020] [Indexed: 12/17/2022]
Abstract
Superspreading events shaped the coronavirus disease 2019 (COVID-19) pandemic, and their rapid identification and containment are essential for disease control. Here, we provide a national-scale analysis of severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) superspreading during the first wave of infections in Austria, a country that played a major role in initial virus transmissions in Europe. Capitalizing on Austria's well-developed epidemiological surveillance system, we identified major SARS-CoV-2 clusters during the first wave of infections and performed deep whole-genome sequencing of more than 500 virus samples. Phylogenetic-epidemiological analysis enabled the reconstruction of superspreading events and charts a map of tourism-related viral spread originating from Austria in spring 2020. Moreover, we exploited epidemiologically well-defined clusters to quantify SARS-CoV-2 mutational dynamics, including the observation of low-frequency mutations that progressed to fixation within the infection chain. Time-resolved virus sequencing unveiled viral mutation dynamics within individuals with COVID-19, and epidemiologically validated infector-infectee pairs enabled us to determine an average transmission bottleneck size of 103 SARS-CoV-2 particles. In conclusion, this study illustrates the power of combining epidemiological analysis with deep viral genome sequencing to unravel the spread of SARS-CoV-2 and to gain fundamental insights into mutational dynamics and transmission properties.
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Affiliation(s)
- Alexandra Popa
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jakob-Wendelin Genger
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Michael D Nicholson
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
| | - Thomas Penz
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Daniela Schmid
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Stephan W Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | - Benedikt Agerer
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Alexander Lercher
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Lukas Endler
- Bioinformatics and Biostatistics Platform, Department of Biomedical Sciences, University of Veterinary Medicine, 1210 Vienna, Austria
| | - Henrique Colaço
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Mark Smyth
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Michael Schuster
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Miguel L Grau
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
| | | | - Oriol Pich
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
| | - Wegene Borena
- Institute of Virology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Erich Pawelka
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Zsofia Keszei
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Martin Senekowitsch
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Jan Laine
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
| | - Judith H Aberle
- Center for Virology, Medical University of Vienna, 1090 Vienna, Austria
| | | | - Mario Karolyi
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | - Alexander Zoufaly
- Department of Medicine IV, Kaiser Franz Josef Hospital, 1100 Vienna, Austria
| | | | - Martin Borkovec
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Peter Hufnagl
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Manfred Nairz
- Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Günter Weiss
- Department of Internal Medicine II, Medical University of Innsbruck, 6020 Innsbruck, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria
- Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, 1090 Vienna, Austria
| | - Dorothee von Laer
- Institute of Virology, Medical University Innsbruck, 6020 Innsbruck, Austria
| | - Giulio Superti-Furga
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Center for Physiology and Pharmacology, Medical University of Vienna, 1090 Vienna, Austria
| | - Nuria Lopez-Bigas
- Institute for Research in Biomedicine (IRB), 08028 Barcelona, Spain
- Institució Catalana de Recerca i Estudis Avançats (ICREA), Barcelona, Spain
| | | | - Franz Allerberger
- Austrian Agency for Health and Food Safety (AGES), 1220 Vienna, Austria
| | - Franziska Michor
- Department of Data Sciences, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Biostatistics, Harvard T.H. Chan School of Public Health, Boston, MA, USA
- Department of Stem Cell and Regenerative Biology, Harvard University, Cambridge, MA 02138, USA
- Broad Institute of MIT and Harvard, Cambridge, MA, USA
- Ludwig Center at Harvard, Boston, MA, USA
- Center for Cancer Evolution, Dana-Farber Cancer Institute, Boston, MA, USA
| | - Christoph Bock
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria
- Department of Laboratory Medicine, Medical University of Vienna, 1090 Vienna, Austria
| | - Andreas Bergthaler
- CeMM Research Center for Molecular Medicine of the Austrian Academy of Sciences, 1090 Vienna, Austria.
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15
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Sonnleitner E, Pusic P, Wolfinger MT, Bläsi U. Distinctive Regulation of Carbapenem Susceptibility in Pseudomonas aeruginosa by Hfq. Front Microbiol 2020; 11:1001. [PMID: 32528439 PMCID: PMC7264166 DOI: 10.3389/fmicb.2020.01001] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2020] [Accepted: 04/24/2020] [Indexed: 12/29/2022] Open
Abstract
Carbapenems are often the antibiotics of choice to combat life threatening infections caused by the opportunistic human pathogen Pseudomonas aeruginosa. The outer membrane porins OprD and OpdP serve as entry ports for carbapenems. Here, we report that the RNA chaperone Hfq governs post-transcriptional regulation of the oprD and opdP genes in a distinctive manner. Hfq together with the recently described small regulatory RNAs (sRNAs) ErsA and Sr0161 is shown to mediate translational repression of oprD, whereas opdP appears not to be regulated by sRNAs. At variance, our data indicate that opdP is translationally repressed by a regulatory complex consisting of Hfq and the catabolite repression protein Crc, an assembly known to be key to carbon catabolite repression in P. aeruginosa. The regulatory RNA CrcZ, which is up-regulated during growth of P. aeruginosa on less preferred carbon sources, is known to sequester Hfq, which relieves Hfq-mediated translational repression of genes. The differential carbapenem susceptibility during growth on different carbon sources can thus be understood in light of Hfq-dependent oprD/opdP regulation and of the antagonizing function of the CrcZ RNA on Hfq regulatory complexes.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Petra Pusic
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, Faculty of Chemistry, University of Vienna, Vienna, Austria.,Research Group Bioinformatics and Computational Biology, Faculty of Computer Science, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max Perutz Labs, Vienna BioCenter (VBC), University of Vienna, Vienna, Austria
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16
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Sonnleitner E, Wulf A, Campagne S, Pei XY, Wolfinger MT, Forlani G, Prindl K, Abdou L, Resch A, Allain FHT, Luisi BF, Urlaub H, Bläsi U. Interplay between the catabolite repression control protein Crc, Hfq and RNA in Hfq-dependent translational regulation in Pseudomonas aeruginosa. Nucleic Acids Res 2019; 46:1470-1485. [PMID: 29244160 PMCID: PMC5815094 DOI: 10.1093/nar/gkx1245] [Citation(s) in RCA: 58] [Impact Index Per Article: 11.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2017] [Accepted: 12/01/2017] [Indexed: 12/23/2022] Open
Abstract
In Pseudomonas aeruginosa the RNA chaperone Hfq and the catabolite repression control protein (Crc) act as post-transcriptional regulators during carbon catabolite repression (CCR). In this regard Crc is required for full-fledged Hfq-mediated translational repression of catabolic genes. RNAseq based transcriptome analyses revealed a significant overlap between the Crc and Hfq regulons, which in conjunction with genetic data supported a concerted action of both proteins. Biochemical and biophysical approaches further suggest that Crc and Hfq form an assembly in the presence of RNAs containing A-rich motifs, and that Crc interacts with both, Hfq and RNA. Through these interactions, Crc enhances the stability of Hfq/Crc/RNA complexes, which can explain its facilitating role in Hfq-mediated translational repression. Hence, these studies revealed for the first time insights into how an interacting protein can modulate Hfq function. Moreover, Crc is shown to interfere with binding of a regulatory RNA to Hfq, which bears implications for riboregulation. These results are discussed in terms of a working model, wherein Crc prioritizes the function of Hfq toward utilization of favored carbon sources.
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Affiliation(s)
- Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Alexander Wulf
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany
| | - Sébastien Campagne
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Xue-Yuan Pei
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Michael T Wolfinger
- Institute of Theoretical Chemistry, University of Vienna, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, 1090 Vienna, Austria
| | - Giada Forlani
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Konstantin Prindl
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Laetitia Abdou
- Department of Fundamental Microbiology, University of Lausanne, 1015 Lausanne, Switzerland
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Frederic H-T Allain
- Institute of Molecular Biology and Biophysics, ETH Zürich, 8093 Zürich, Switzerland
| | - Ben F Luisi
- Department of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK
| | - Henning Urlaub
- Biophysical Mass Spectrometry Group, Max Planck Institute for Biophysical Chemistry, 37077 Göttingen, Germany.,Bioanalytics, Institute for Clinical Chemistry, University Medical Center Göttingen, 37075 Göttingen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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17
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Abstract
Zika virus (ZIKV) belongs to a class of neurotropic viruses that have the ability to cause congenital infection, which can result in microcephaly or fetal demise. Recently, the RNA-binding protein Musashi-1 (Msi1), which mediates the maintenance and self-renewal of stem cells and acts as a translational regulator, has been associated with promoting ZIKV replication, neurotropism, and pathology. Msi1 predominantly binds to single-stranded motifs in the 3' untranslated region (UTR) of RNA that contain a UAG trinucleotide in their core. We systematically analyzed the properties of Musashi binding elements (MBEs) in the 3'UTR of flaviviruses with a thermodynamic model for RNA folding. Our results indicate that MBEs in ZIKV 3'UTRs occur predominantly in unpaired, single-stranded structural context, thus corroborating experimental observations by a biophysical model of RNA structure formation. Statistical analysis and comparison with related viruses show that ZIKV MBEs are maximally accessible among mosquito-borne flaviviruses. Our study addresses the broader question of whether other emerging arboviruses can cause similar neurotropic effects through the same mechanism in the developing fetus by establishing a link between the biophysical properties of viral RNA and teratogenicity. Moreover, our thermodynamic model can explain recent experimental findings and predict the Msi1-related neurotropic potential of other viruses.
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Affiliation(s)
- Adriano de Bernardi Schneider
- Department of Medicine, University of California San Diego, 220 Dickinson St, Suite A, San Diego, CA, 92103, United States of America
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090, Vienna, Austria.
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18
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Bassani F, Zink IA, Pribasnig T, Wolfinger MT, Romagnoli A, Resch A, Schleper C, Bläsi U, La Teana A. Indications for a moonlighting function of translation factor aIF5A in the crenarchaeum Sulfolobus solfataricus. RNA Biol 2019; 16:675-685. [PMID: 30777488 PMCID: PMC6546411 DOI: 10.1080/15476286.2019.1582953] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 01/14/2019] [Accepted: 02/08/2019] [Indexed: 01/02/2023] Open
Abstract
Translation factor a/eIF5A is highly conserved in Eukarya and Archaea. The eukaryal eIF5A protein is required for transit of ribosomes across consecutive proline codons, whereas the function of the archaeal orthologue remains unknown. Here, we provide a first hint for an involvement of Sulfolobus solfataricus (Sso) aIF5A in translation. CRISPR-mediated knock down of the aif5A gene resulted in strong growth retardation, underlining a pivotal function. Moreover, in vitro studies revealed that Sso aIF5A is endowed with endoribonucleolytic activity. Thus, aIF5A appears to be a moonlighting protein that might be involved in protein synthesis as well as in RNA metabolism.
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Affiliation(s)
- Flavia Bassani
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Isabelle Anna Zink
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Thomas Pribasnig
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | | | - Alice Romagnoli
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
| | - Armin Resch
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Christa Schleper
- Division of Archaea Biology and Ecogenomics, Department of Ecogenomics and Systems Biology, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Anna La Teana
- Department of Life and Environmental Sciences, Polytechnic University of Marche, Ancona, Italy
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19
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Ochsenreiter R, Hofacker IL, Wolfinger MT. Functional RNA Structures in the 3'UTR of Tick-Borne, Insect-Specific and No-Known-Vector Flaviviruses. Viruses 2019; 11:E298. [PMID: 30909641 PMCID: PMC6466055 DOI: 10.3390/v11030298] [Citation(s) in RCA: 40] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2019] [Revised: 03/19/2019] [Accepted: 03/20/2019] [Indexed: 12/21/2022] Open
Abstract
Untranslated regions (UTRs) of flaviviruses contain a large number of RNA structural elements involved in mediating the viral life cycle, including cyclisation, replication, and encapsidation. Here we report on a comparative genomics approach to characterize evolutionarily conserved RNAs in the 3 ' UTR of tick-borne, insect-specific and no-known-vector flaviviruses in silico. Our data support the wide distribution of previously experimentally characterized exoribonuclease resistant RNAs (xrRNAs) within tick-borne and no-known-vector flaviviruses and provide evidence for the existence of a cascade of duplicated RNA structures within insect-specific flaviviruses. On a broader scale, our findings indicate that viral 3 ' UTRs represent a flexible scaffold for evolution to come up with novel xrRNAs.
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Affiliation(s)
- Roman Ochsenreiter
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- Department of Theoretical Chemistry, University of Vienna, Währingerstraße 17, 1090 Vienna, Austria.
- Research Group BCB, Faculty of Computer Science, University of Vienna, Währingerstraße 29, 1090 Vienna, Austria.
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Pusic P, Sonnleitner E, Krennmayr B, Heitzinger DA, Wolfinger MT, Resch A, Bläsi U. Harnessing Metabolic Regulation to Increase Hfq-Dependent Antibiotic Susceptibility in Pseudomonas aeruginosa. Front Microbiol 2018; 9:2709. [PMID: 30473687 PMCID: PMC6237836 DOI: 10.3389/fmicb.2018.02709] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2018] [Accepted: 10/23/2018] [Indexed: 01/04/2023] Open
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa is responsible for ~ 10% of hospital-acquired infections worldwide. It is notorious for its high level resistance toward many antibiotics, and the number of multi-drug resistant clinical isolates is steadily increasing. A better understanding of the molecular mechanisms underlying drug resistance is crucial for the development of novel antimicrobials and alternative strategies such as enhanced sensitization of bacteria to antibiotics in use. In P. aeruginosa several uptake channels for amino-acids and carbon sources can serve simultaneously as entry ports for antibiotics. The respective genes are often controlled by carbon catabolite repression (CCR). We have recently shown that Hfq in concert with Crc acts as a translational repressor during CCR. This function is counteracted by the regulatory RNA CrcZ, which functions as a decoy to abrogate Hfq-mediated translational repression of catabolic genes. Here, we report an increased susceptibility of P. aeruginosa hfq deletion strains to different classes of antibiotics. Transcriptome analyses indicated that Hfq impacts on different mechanisms known to be involved in antibiotic susceptibility, viz import and efflux, energy metabolism, cell wall and LPS composition as well as on the c-di-GMP levels. Furthermore, we show that sequestration of Hfq by CrcZ, which was over-produced or induced by non-preferred carbon-sources, enhances the sensitivity toward antibiotics. Thus, controlled synthesis of CrcZ could provide a means to (re)sensitize P. aeruginosa to different classes of antibiotics.
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Affiliation(s)
- Petra Pusic
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Elisabeth Sonnleitner
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Beatrice Krennmayr
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Dorothea A. Heitzinger
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
| | | | - Armin Resch
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
| | - Udo Bläsi
- Max F. Perutz Laboratories, Department of Microbiology, Immunobiology and Genetics, Vienna Biocenter, University of Vienna, Vienna, Austria
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21
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Waldl M, Thiel BC, Ochsenreiter R, Holzenleiter A, de Araujo Oliveira JV, Walter MEMT, Wolfinger MT, Stadler PF. TERribly Difficult: Searching for Telomerase RNAs in Saccharomycetes. Genes (Basel) 2018; 9:genes9080372. [PMID: 30049970 PMCID: PMC6115765 DOI: 10.3390/genes9080372] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2018] [Revised: 07/17/2018] [Accepted: 07/18/2018] [Indexed: 11/20/2022] Open
Abstract
The telomerase RNA in yeasts is large, usually >1000 nt, and contains functional elements that have been extensively studied experimentally in several disparate species. Nevertheless, they are very difficult to detect by homology-based methods and so far have escaped annotation in the majority of the genomes of Saccharomycotina. This is a consequence of sequences that evolve rapidly at nucleotide level, are subject to large variations in size, and are highly plastic with respect to their secondary structures. Here, we report on a survey that was aimed at closing this gap in RNA annotation. Despite considerable efforts and the combination of a variety of different methods, it was only partially successful. While 27 new telomerase RNAs were identified, we had to restrict our efforts to the subgroup Saccharomycetacea because even this narrow subgroup was diverse enough to require different search models for different phylogenetic subgroups. More distant branches of the Saccharomycotina remain without annotated telomerase RNA.
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Affiliation(s)
- Maria Waldl
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Bernhard C Thiel
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Roman Ochsenreiter
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
| | - Alexander Holzenleiter
- BioInformatics Group, Fakultät CB Hochschule Mittweida, Technikumplatz 17, D-09648 Mittweida, Germany.
- Bioinformatics Group, Department of Computer Science, and Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstraße 16-18, D-04107 Leipzig, Germany.
| | - João Victor de Araujo Oliveira
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário⁻Asa Norte, Brasília, DF CEP: 70910-900, Brazil.
| | - Maria Emília M T Walter
- Departamento de Ciência da Computação, Instituto de Ciências Exatas, Universidade de Brasília, Campus Universitário⁻Asa Norte, Brasília, DF CEP: 70910-900, Brazil.
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
- Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria.
| | - Peter F Stadler
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Wien, Austria.
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Competence Center for Scalable Data Services and Solutions, and Leipzig Research Center for Civilization Diseases, Universität Leipzig, D-04107 Leipzig, Germany.
- Max Planck Institute for Mathematics in the Sciences, Inselstraße 22, D-04103 Leipzig, Germany.
- Santa Fe Institute, 1399 Hyde Park Rd., Santa Fe, NM 87501, USA.
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22
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Findeiß S, Hammer S, Wolfinger MT, Kühnl F, Flamm C, Hofacker IL. In silico design of ligand triggered RNA switches. Methods 2018; 143:90-101. [PMID: 29660485 DOI: 10.1016/j.ymeth.2018.04.003] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2017] [Revised: 03/06/2018] [Accepted: 04/06/2018] [Indexed: 02/06/2023] Open
Abstract
This contribution sketches a work flow to design an RNA switch that is able to adapt two structural conformations in a ligand-dependent way. A well characterized RNA aptamer, i.e., knowing its Kd and adaptive structural features, is an essential ingredient of the described design process. We exemplify the principles using the well-known theophylline aptamer throughout this work. The aptamer in its ligand-binding competent structure represents one structural conformation of the switch while an alternative fold that disrupts the binding-competent structure forms the other conformation. To keep it simple we do not incorporate any regulatory mechanism to control transcription or translation. We elucidate a commonly used design process by explicitly dissecting and explaining the necessary steps in detail. We developed a novel objective function which specifies the mechanistics of this simple, ligand-triggered riboswitch and describe an extensive in silico analysis pipeline to evaluate important kinetic properties of the designed sequences. This protocol and the developed software can be easily extended or adapted to fit novel design scenarios and thus can serve as a template for future needs.
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Affiliation(s)
- Sven Findeiß
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria.
| | - Stefan Hammer
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
| | - Michael T Wolfinger
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria; Medical University of Vienna, Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria
| | - Felix Kühnl
- Bioinformatics, Institute of Computer Science, and Interdisciplinary Center for Bioinformatics, Leipzig University, Härtelstraße 16-18, 04107 Leipzig, Germany
| | - Christoph Flamm
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
| | - Ivo L Hofacker
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstraße 29, 1090 Vienna, Austria; University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstraße 17, 1090 Vienna, Austria
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23
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Tata M, Amman F, Pawar V, Wolfinger MT, Weiss S, Häussler S, Bläsi U. The Anaerobically Induced sRNA PaiI Affects Denitrification in Pseudomonas aeruginosa PA14. Front Microbiol 2017; 8:2312. [PMID: 29218039 PMCID: PMC5703892 DOI: 10.3389/fmicb.2017.02312] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2017] [Accepted: 11/08/2017] [Indexed: 01/08/2023] Open
Abstract
Pseudomonas aeruginosa is an opportunistic pathogen that can thrive by anaerobic respiration in the lungs of cystic fibrosis patients using nitrate as terminal electron acceptor. Here, we report the identification and characterization of the small RNA PaiI in the P. aeruginosa strain 14 (PA14). PaiI is anaerobically induced in the presence of nitrate and depends on the two-component system NarXL. Our studies revealed that PaiI is required for efficient denitrification affecting the conversion of nitrite to nitric oxide. In the absence of PaiI anaerobic growth was impaired on glucose, which can be reconciled with a decreased uptake of the carbon source under these conditions. The importance of PaiI for anaerobic growth is further underlined by the observation that a paiI deletion mutant was impaired in growth in murine tumors.
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Affiliation(s)
- Muralidhar Tata
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
| | - Fabian Amman
- Institute of Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Vinay Pawar
- Institute of Immunology, Hannover Medical School, Hannover, Germany.,Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany
| | | | - Siegfried Weiss
- Institute of Immunology, Hannover Medical School, Hannover, Germany
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Braunschweig, Germany.,Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, Hannover, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, University of Vienna, Vienna, Austria
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24
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Märtens B, Hou L, Amman F, Wolfinger MT, Evguenieva-Hackenberg E, Bläsi U. The SmAP1/2 proteins of the crenarchaeon Sulfolobus solfataricus interact with the exosome and stimulate A-rich tailing of transcripts. Nucleic Acids Res 2017; 45:7938-7949. [PMID: 28520934 PMCID: PMC5570065 DOI: 10.1093/nar/gkx437] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2016] [Accepted: 05/03/2017] [Indexed: 01/26/2023] Open
Abstract
The conserved Sm and Sm-like proteins are involved in different aspects of RNA metabolism. Here, we explored the interactome of SmAP1 and SmAP2 of the crenarchaeon Sulfolobus solfataricus (Sso) to shed light on their physiological function(s). Both, SmAP1 and SmAP2 co-purified with several proteins involved in RNA-processing/modification, translation and protein turnover as well as with components of the exosome involved in 3΄ to 5΄ degradation of RNA. In follow-up studies a direct interaction with the poly(A) binding and accessory exosomal subunit DnaG was demonstrated. Moreover, elevated levels of both SmAPs resulted in increased abundance of the soluble exosome fraction, suggesting that they affect the subcellular localization of the exosome in the cell. The increased solubility of the exosome was accompanied by augmented levels of RNAs with A-rich tails that were further characterized using RNASeq. Hence, the observation that the Sso SmAPs impact on the activity of the exosome revealed a hitherto unrecognized function of SmAPs in archaea.
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Affiliation(s)
- Birgit Märtens
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
| | - Linlin Hou
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17/3, 1090 Vienna, Austria.,Center for Anatomy and Cell Biology, Medical University of Vienna, Währingerstraße 13, 1090 Vienna, Austria
| | - Elena Evguenieva-Hackenberg
- Institute of Microbiology and Molecular Biology, Justus Liebig University Gießen, Heinrich-Buff-Ring 26-32, 35392 Gießen, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Vienna Biocenter, Dr. Bohrgasse 9, 1030 Vienna, Austria
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25
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Helmling C, Wacker A, Wolfinger MT, Hofacker IL, Hengesbach M, Fürtig B, Schwalbe H. NMR Structural Profiling of Transcriptional Intermediates Reveals Riboswitch Regulation by Metastable RNA Conformations. J Am Chem Soc 2017; 139:2647-2656. [PMID: 28134517 DOI: 10.1021/jacs.6b10429] [Citation(s) in RCA: 35] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Gene repression induced by the formation of transcriptional terminators represents a prime example for the coupling of RNA synthesis, folding, and regulation. In this context, mapping the changes in available conformational space of transcription intermediates during RNA synthesis is important to understand riboswitch function. A majority of riboswitches, an important class of small metabolite-sensing regulatory RNAs, act as transcriptional regulators, but the dependence of ligand binding and the subsequent allosteric conformational switch on mRNA transcript length has not yet been investigated. We show a strict fine-tuning of binding and sequence-dependent alterations of conformational space by structural analysis of all relevant transcription intermediates at single-nucleotide resolution for the I-A type 2'dG-sensing riboswitch from Mesoplasma florum by NMR spectroscopy. Our results provide a general framework to dissect the coupling of synthesis and folding essential for riboswitch function, revealing the importance of metastable states for RNA-based gene regulation.
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Affiliation(s)
- Christina Helmling
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Anna Wacker
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Michael T Wolfinger
- Medical University of Vienna , Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria
| | | | - Martin Hengesbach
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Boris Fürtig
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
| | - Harald Schwalbe
- Institute for Organic Chemisty and Chemical Biology, Center for Biomolecular Magnetic Resonance (BMRZ), Johann Wolfgang Goethe-Universität , Frankfurt/M. 60438, Germany
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26
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Tajaddod M, Tanzer A, Licht K, Wolfinger MT, Badelt S, Huber F, Pusch O, Schopoff S, Janisiw M, Hofacker I, Jantsch MF. Transcriptome-wide effects of inverted SINEs on gene expression and their impact on RNA polymerase II activity. Genome Biol 2016; 17:220. [PMID: 27782844 PMCID: PMC5080714 DOI: 10.1186/s13059-016-1083-0] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/21/2016] [Accepted: 10/10/2016] [Indexed: 01/23/2023] Open
Abstract
BACKGROUND Short interspersed elements (SINEs) represent the most abundant group of non-long-terminal repeat transposable elements in mammalian genomes. In primates, Alu elements are the most prominent and homogenous representatives of SINEs. Due to their frequent insertion within or close to coding regions, SINEs have been suggested to play a crucial role during genome evolution. Moreover, Alu elements within mRNAs have also been reported to control gene expression at different levels. RESULTS Here, we undertake a genome-wide analysis of insertion patterns of human Alus within transcribed portions of the genome. Multiple, nearby insertions of SINEs within one transcript are more abundant in tandem orientation than in inverted orientation. Indeed, analysis of transcriptome-wide expression levels of 15 ENCODE cell lines suggests a cis-repressive effect of inverted Alu elements on gene expression. Using reporter assays, we show that the negative effect of inverted SINEs on gene expression is independent of known sensors of double-stranded RNAs. Instead, transcriptional elongation seems impaired, leading to reduced mRNA levels. CONCLUSIONS Our study suggests that there is a bias against multiple SINE insertions that can promote intramolecular base pairing within a transcript. Moreover, at a genome-wide level, mRNAs harboring inverted SINEs are less expressed than mRNAs harboring single or tandemly arranged SINEs. Finally, we demonstrate a novel mechanism by which inverted SINEs can impact on gene expression by interfering with RNA polymerase II.
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Affiliation(s)
- Mansoureh Tajaddod
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, Vienna, A-1030, Austria
| | - Andrea Tanzer
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna, A-1090, Austria
| | - Konstantin Licht
- Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria
| | - Michael T Wolfinger
- Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna, A-1090, Austria
| | - Stefan Badelt
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna, A-1090, Austria
| | - Florian Huber
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, Vienna, A-1030, Austria
- Present address: Center for molecular biology of the University Heidelberg, Im Neuenheimer Feld 282, Heidelberg, D-69120, Germany
| | - Oliver Pusch
- Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria
| | - Sandy Schopoff
- Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr Gasse 9/5, Vienna, A-1030, Austria
| | - Michael Janisiw
- Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria
| | - Ivo Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Währinger Strasse 17, Vienna, A-1090, Austria
| | - Michael F Jantsch
- Department of Cell and Developmental Biology, Medical University of Vienna, Schwarzspanierstrasse 17, Vienna, A-1090, Austria.
- Department of Cell and Developmental Biology, Medical University of Vienna, Center of Anatomy and Cell Biology, Schwarzspanierstrasse 17, Vienna, A-1090, Austria.
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27
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Lorenz R, Wolfinger MT, Tanzer A, Hofacker IL. Predicting RNA secondary structures from sequence and probing data. Methods 2016; 103:86-98. [PMID: 27064083 DOI: 10.1016/j.ymeth.2016.04.004] [Citation(s) in RCA: 66] [Impact Index Per Article: 8.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2015] [Revised: 03/29/2016] [Accepted: 04/04/2016] [Indexed: 01/08/2023] Open
Abstract
RNA secondary structures have proven essential for understanding the regulatory functions performed by RNA such as microRNAs, bacterial small RNAs, or riboswitches. This success is in part due to the availability of efficient computational methods for predicting RNA secondary structures. Recent advances focus on dealing with the inherent uncertainty of prediction by considering the ensemble of possible structures rather than the single most stable one. Moreover, the advent of high-throughput structural probing has spurred the development of computational methods that incorporate such experimental data as auxiliary information.
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Affiliation(s)
- Ronny Lorenz
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Michael T Wolfinger
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; Medical University of Vienna, Center for Anatomy and Cell Biology, Währingerstraße 13, 1090 Vienna, Austria.
| | - Andrea Tanzer
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Ivo L Hofacker
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria; University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
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28
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Sauert M, Wolfinger MT, Vesper O, Müller C, Byrgazov K, Moll I. The MazF-regulon: a toolbox for the post-transcriptional stress response in Escherichia coli. Nucleic Acids Res 2016; 44:6660-75. [PMID: 26908653 PMCID: PMC5001579 DOI: 10.1093/nar/gkw115] [Citation(s) in RCA: 44] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2015] [Accepted: 02/17/2016] [Indexed: 12/22/2022] Open
Abstract
Flexible adaptation to environmental stress is vital for bacteria. An energy-efficient post-transcriptional stress response mechanism in Escherichia coli is governed by the toxin MazF. After stress-induced activation the endoribonuclease MazF processes a distinct subset of transcripts as well as the 16S ribosomal RNA in the context of mature ribosomes. As these 'stress-ribosomes' are specific for the MazF-processed mRNAs, the translational program is changed. To identify this 'MazF-regulon' we employed Poly-seq (polysome fractionation coupled with RNA-seq analysis) and analyzed alterations introduced into the transcriptome and translatome after mazF overexpression. Unexpectedly, our results reveal that the corresponding protein products are involved in all cellular processes and do not particularly contribute to the general stress response. Moreover, our findings suggest that translational reprogramming serves as a fast-track reaction to harsh stress and highlight the so far underestimated significance of selective translation as a global regulatory mechanism in gene expression. Considering the reported implication of toxin-antitoxin (TA) systems in persistence, our results indicate that MazF acts as a prime effector during harsh stress that potentially introduces translational heterogeneity within a bacterial population thereby stimulating persister cell formation.
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Affiliation(s)
- Martina Sauert
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Michael T Wolfinger
- Max F. Perutz Laboratories, Department of Biochemistry and Molecular Cell Biology, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/5, A-1030 Vienna, Austria Max F. Perutz Laboratories, Center for Integrative Bioinformatics Vienna, University of Vienna, Medical University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9, A-1030 Vienna, Austria Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090 Vienna, Austria
| | - Oliver Vesper
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Christian Müller
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Konstantin Byrgazov
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
| | - Isabella Moll
- Max F. Perutz Laboratories, Center for Molecular Biology, Department of Microbiology, Immunobiology and Genetics, University of Vienna, Vienna Biocenter (VBC), Dr. Bohr-Gasse 9/4, A-1030 Vienna, Austria
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29
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Tata M, Wolfinger MT, Amman F, Roschanski N, Dötsch A, Sonnleitner E, Häussler S, Bläsi U. RNASeq Based Transcriptional Profiling of Pseudomonas aeruginosa PA14 after Short- and Long-Term Anoxic Cultivation in Synthetic Cystic Fibrosis Sputum Medium. PLoS One 2016; 11:e0147811. [PMID: 26821182 PMCID: PMC4731081 DOI: 10.1371/journal.pone.0147811] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2015] [Accepted: 01/08/2016] [Indexed: 01/22/2023] Open
Abstract
The opportunistic human pathogen Pseudomonas aeruginosa can thrive under microaerophilic to anaerobic conditions in the lungs of cystic fibrosis patients. RNASeq based comparative RNA profiling of the clinical isolate PA14 cultured in synthetic cystic fibrosis medium was performed after planktonic growth (OD600 = 2.0; P), 30 min after shift to anaerobiosis (A-30) and after anaerobic biofilm growth for 96h (B-96) with the aim to reveal differentially regulated functions impacting on sustained anoxic biofilm formation as well as on tolerance towards different antibiotics. Most notably, functions involved in sulfur metabolism were found to be up-regulated in B-96 cells when compared to A-30 cells. Based on the transcriptome studies a set of transposon mutants were screened, which revealed novel functions involved in anoxic biofilm growth.In addition, these studies revealed a decreased and an increased abundance of the oprD and the mexCD-oprJ operon transcripts, respectively, in B-96 cells, which may explain their increased tolerance towards meropenem and to antibiotics that are expelled by the MexCD-OprD efflux pump. The OprI protein has been implicated as a target for cationic antimicrobial peptides, such as SMAP-29. The transcriptome and subsequent Northern-blot analyses showed that the abundance of the oprI transcript encoding the OprI protein is strongly decreased in B-96 cells. However, follow up studies revealed that the susceptibility of a constructed PA14ΔoprI mutant towards SMAP-29 was indistinguishable from the parental wild-type strain, which questions OprI as a target for this antimicrobial peptide in strain PA14.
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Affiliation(s)
- Muralidhar Tata
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Michael T. Wolfinger
- Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria
| | - Fabian Amman
- Department of Chromosome Biology, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Institute for Theoretical Chemistry, University of Vienna Währinger Straße 17, 1090 Vienna, Austria
| | - Nicole Roschanski
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- Free University Berlin, Institute of Animal Hygiene and Environmental Health, Robert-von-Ostertag-Str. 7–13, 14163 Berlin, Germany
| | - Andreas Dötsch
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
| | - Elisabeth Sonnleitner
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
| | - Susanne Häussler
- Department of Molecular Bacteriology, Helmholtz Center for Infection Research, Inhoffenstraße 7, 38124 Braunschweig, Germany
- Institute of Molecular Bacteriology, Twincore, Center for Experimental and Clinical Infection Research, Feodor-Lynen-Straße 7, 30625 Hannover, Germany
| | - Udo Bläsi
- Department of Microbiology, Immunobiology and Genetics, Max F. Perutz Laboratories, Center of Molecular Biology, University of Vienna, Dr. Bohr-Gasse 9, 1030 Vienna, Austria
- * E-mail:
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Abstract
Summary: Chemical mapping experiments allow for nucleotide resolution assessment of RNA structure. We demonstrate that different strategies of integrating probing data with thermodynamics-based RNA secondary structure prediction algorithms can be implemented by means of soft constraints. This amounts to incorporating suitable pseudo-energies into the standard energy model for RNA secondary structures. As a showcase application for this new feature of the ViennaRNA Package we compare three distinct, previously published strategies to utilize SHAPE reactivities for structure prediction. The new tool is benchmarked on a set of RNAs with known reference structure. Availability and implementation: The capability for SHAPE directed RNA folding is part of the upcoming release of the ViennaRNA Package 2.2, for which a preliminary release is already freely available at http://www.tbi.univie.ac.at/RNA. Contact: michael.wolfinger@univie.ac.at Supplementary information:Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Ronny Lorenz
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Dominik Luntzer
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Peter F Stadler
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
| | - Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria, Institute for Theoretical Chemistry, University of Vienna, Vienna, Austria
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Abstract
Recent achievements in next-generation sequencing (NGS) technologies lead to a high demand for reuseable software components to easily compile customized analysis workflows for big genomics data. We present ViennaNGS, an integrated collection of Perl modules focused on building efficient pipelines for NGS data processing. It comes with functionality for extracting and converting features from common NGS file formats, computation and evaluation of read mapping statistics, as well as normalization of RNA abundance. Moreover, ViennaNGS provides software components for identification and characterization of splice junctions from RNA-seq data, parsing and condensing sequence motif data, automated construction of Assembly and Track Hubs for the UCSC genome browser, as well as wrapper routines for a set of commonly used NGS command line tools.
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Affiliation(s)
- Michael T Wolfinger
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria ; Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria ; Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
| | - Jörg Fallmann
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria
| | - Florian Eggenhofer
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria
| | - Fabian Amman
- Institute for Theoretical Chemistry, University of Vienna, Währingerstraße 17, A-1090, Vienna, Austria ; Department of Chromosome Biology, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, Dr. Bohr-Gasse 9, A-1030 Vienna, Austria
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Mann M, Kucharík M, Flamm C, Wolfinger MT. Memory-efficient RNA energy landscape exploration. Bioinformatics 2014; 30:2584-91. [PMID: 24833804 PMCID: PMC4155248 DOI: 10.1093/bioinformatics/btu337] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2014] [Revised: 04/25/2014] [Accepted: 05/08/2014] [Indexed: 02/01/2023] Open
Abstract
MOTIVATION Energy landscapes provide a valuable means for studying the folding dynamics of short RNA molecules in detail by modeling all possible structures and their transitions. Higher abstraction levels based on a macro-state decomposition of the landscape enable the study of larger systems; however, they are still restricted by huge memory requirements of exact approaches. RESULTS We present a highly parallelizable local enumeration scheme that enables the computation of exact macro-state transition models with highly reduced memory requirements. The approach is evaluated on RNA secondary structure landscapes using a gradient basin definition for macro-states. Furthermore, we demonstrate the need for exact transition models by comparing two barrier-based approaches, and perform a detailed investigation of gradient basins in RNA energy landscapes. AVAILABILITY AND IMPLEMENTATION Source code is part of the C++ Energy Landscape Library available at http://www.bioinf.uni-freiburg.de/Software/.
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Affiliation(s)
- Martin Mann
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Marcel Kucharík
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Christoph Flamm
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
| | - Michael T Wolfinger
- Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria Bioinformatics Group, Department of Computer Science, University of Freiburg, 79110 Freiburg, Germany, Institute for Theoretical Chemistry, University of Vienna, 1090 Vienna, Center for Integrative Bioinformatics Vienna, Max F. Perutz Laboratories, University of Vienna, Medical University of Vienna, and Department of Biochemistry and Molecular Cell Biology, Max F. Perutz Laboratories, University of Vienna, A-1030 Vienna, Austria
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Amman F, Wolfinger MT, Lorenz R, Hofacker IL, Stadler PF, Findeiß S. TSSAR: TSS annotation regime for dRNA-seq data. BMC Bioinformatics 2014; 15:89. [PMID: 24674136 PMCID: PMC4098767 DOI: 10.1186/1471-2105-15-89] [Citation(s) in RCA: 41] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/19/2013] [Accepted: 03/24/2014] [Indexed: 12/27/2022] Open
Abstract
BACKGROUND Differential RNA sequencing (dRNA-seq) is a high-throughput screening technique designed to examine the architecture of bacterial operons in general and the precise position of transcription start sites (TSS) in particular. Hitherto, dRNA-seq data were analyzed by visualizing the sequencing reads mapped to the reference genome and manually annotating reliable positions. This is very labor intensive and, due to the subjectivity, biased. RESULTS Here, we present TSSAR, a tool for automated de novo TSS annotation from dRNA-seq data that respects the statistics of dRNA-seq libraries. TSSAR uses the premise that the number of sequencing reads starting at a certain genomic position within a transcriptional active region follows a Poisson distribution with a parameter that depends on the local strength of expression. The differences of two dRNA-seq library counts thus follow a Skellam distribution. This provides a statistical basis to identify significantly enriched primary transcripts.We assessed the performance by analyzing a publicly available dRNA-seq data set using TSSAR and two simple approaches that utilize user-defined score cutoffs. We evaluated the power of reproducing the manual TSS annotation. Furthermore, the same data set was used to reproduce 74 experimentally validated TSS in H. pylori from reliable techniques such as RACE or primer extension. Both analyses showed that TSSAR outperforms the static cutoff-dependent approaches. CONCLUSIONS Having an automated and efficient tool for analyzing dRNA-seq data facilitates the use of the dRNA-seq technique and promotes its application to more sophisticated analysis. For instance, monitoring the plasticity and dynamics of the transcriptomal architecture triggered by different stimuli and growth conditions becomes possible.The main asset of a novel tool for dRNA-seq analysis that reaches out to a broad user community is usability. As such, we provide TSSAR both as intuitive RESTful Web service ( http://rna.tbi.univie.ac.at/TSSAR) together with a set of post-processing and analysis tools, as well as a stand-alone version for use in high-throughput dRNA-seq data analysis pipelines.
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Affiliation(s)
- Fabian Amman
- Bioinformatics Group, Department of Computer Science and the Interdisciplinary Center for Bioinformatic, University of Leipzig, Härtelstraße 16-18, 04107 Leipzig, Germany.
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Hofacker IL, Flamm C, Heine C, Wolfinger MT, Scheuermann G, Stadler PF. BarMap: RNA folding on dynamic energy landscapes. RNA 2010; 16:1308-1316. [PMID: 20504954 PMCID: PMC2885680 DOI: 10.1261/rna.2093310] [Citation(s) in RCA: 39] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/17/2010] [Accepted: 03/24/2010] [Indexed: 05/29/2023]
Abstract
Dynamical changes of RNA secondary structures play an important role in the function of many regulatory RNAs. Such kinetic effects, especially in time-variable and externally triggered systems, are usually investigated by means of extensive and expensive simulations of large sets of individual folding trajectories. Here we describe the theoretical foundations of a generic approach that not only allows the direct computation of approximate population densities but also reduces the efforts required to analyze the folding energy landscapes to a one-time preprocessing step. The basic idea is to consider the kinetics on individual landscapes and to model external triggers and environmental changes as small but discrete changes in the landscapes. A "barmap" links macrostates of temporally adjacent landscapes and defines the transfer of population densities from one "snapshot" to the next. Implemented in the BarMap software, this approach makes it feasible to study folding processes at the level of basins, saddle points, and barriers for many nonstationary scenarios, including temperature changes, cotranscriptional folding, refolding in consequence to degradation, and mechanically constrained kinetics, as in the case of the translocation of a polymer through a pore.
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Affiliation(s)
- Ivo L Hofacker
- Institute for Theoretical Chemistry, University of Vienna, 1090 Wien, Austria.
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Geis M, Flamm C, Wolfinger MT, Tanzer A, Hofacker IL, Middendorf M, Mandl C, Stadler PF, Thurner C. Folding kinetics of large RNAs. J Mol Biol 2008; 379:160-73. [PMID: 18440024 DOI: 10.1016/j.jmb.2008.02.064] [Citation(s) in RCA: 64] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2007] [Revised: 02/08/2008] [Accepted: 02/27/2008] [Indexed: 11/29/2022]
Abstract
We introduce here a heuristic approach to kinetic RNA folding that constructs secondary structures by stepwise combination of building blocks. These blocks correspond to subsequences and their thermodynamically optimal structures. These are determined by the standard dynamic programming approach to RNA folding. Folding trajectories are modeled at base-pair resolution using the Morgan-Higgs heuristic and a barrier tree-based heuristic to connect combinations of the local building blocks. Implemented in the program Kinwalker, the algorithm allows co-transcriptional folding and can be used to fold sequences of up to about 1500 nucleotides in length. A detailed comparison with several well-studied examples from the literature, including the delayed folding of bacteriophage cloverleaf structures, the adenine sensing riboswitch, and the hok RNA, shows an excellent agreement of predicted trajectories and experimental evidence. The software is available as part of the ViennaRNA Package.
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Affiliation(s)
- Michael Geis
- Interdisciplinary Center for Bioinformatics, University of Leipzig, Härtelstrasse 16-18, 04107 Leipzig, Germany.
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