1
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Greenwood T, Heitsch CE. How Parameters Influence SHAPE-Directed Predictions. Methods Mol Biol 2024; 2726:105-124. [PMID: 38780729 DOI: 10.1007/978-1-0716-3519-3_5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 05/25/2024]
Abstract
The structure of an RNA sequence encodes information about its biological function. Dynamic programming algorithms are often used to predict the conformation of an RNA molecule from its sequence alone, and adding experimental data as auxiliary information improves prediction accuracy. This auxiliary data is typically incorporated into the nearest neighbor thermodynamic model22 by converting the data into pseudoenergies. Here, we look at how much of the space of possible structures auxiliary data allows prediction methods to explore. We find that for a large class of RNA sequences, auxiliary data shifts the predictions significantly. Additionally, we find that predictions are highly sensitive to the parameters which define the auxiliary data pseudoenergies. In fact, the parameter space can typically be partitioned into regions where different structural predictions predominate.
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2
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Quansah M, Fetter L, Fineran A, Colling HV, Silver K, Rowland TJ, Bonham AJ. Rapid and Quantitative Detection of Lung Cancer Biomarker ENOX2 Using a Novel Aptamer in an Electrochemical DNA-Based (E-DNA) Biosensor. BIOSENSORS 2023; 13:675. [PMID: 37504074 PMCID: PMC10377175 DOI: 10.3390/bios13070675] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Revised: 06/16/2023] [Accepted: 06/23/2023] [Indexed: 07/29/2023]
Abstract
To overcome early cancer detection challenges, diagnostic tools enabling more sensitive, rapid, and noninvasive detection are necessary. An attractive cancer target for diagnostic blood tests is human Ecto-NOX disulfide-thiol exchanger 2 (ENOX2), expressed in most human cancer types and regularly shed into blood sera. Here, we developed an electrochemical DNA-based (E-DNA) biosensor that rapidly detects physiologically relevant levels of ENOX2. To identify ENOX2-binding aptamers that could potentially be used in a biosensor, recombinantly expressed ENOX2 was used as a binding target in an oligonucleotide library pull-down that generated a highly enriched ENOX2-binding aptamer. This candidate aptamer sensitively bound ENOX2 via gel mobility shift assays. To enable this aptamer to function in an ENOX2 E-DNA biosensor, the aptamer sequence was modified to adopt two conformations, one capable of ENOX2 binding, and one with disrupted ENOX2 binding. Upon ENOX2 introduction, a conformational shift to the ENOX2 binding state resulted in changed dynamics of a redox reporter molecule, which generated a rapid, significant, and target-specific electrical current readout change. ENOX2 biosensor sensitivity was at or below the diagnostic range. The ENOX2 E-DNA biosensor design presented here may enable the development of more sensitive, rapid, diagnostic tools for early cancer detection.
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Affiliation(s)
- Mary Quansah
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA
| | - Lisa Fetter
- Program in Biomolecular Science and Engineering, University of California Santa Barbara, Santa Barbara, CA 93106, USA
| | - Autumn Fineran
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA
| | - Haley V Colling
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA
| | - Keaton Silver
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA
| | - Teisha J Rowland
- Department of Molecular, Cellular, and Developmental Biology, University of Colorado, Boulder, CO 80309, USA
| | - Andrew J Bonham
- Department of Chemistry & Biochemistry, Metropolitan State University of Denver, Denver, CO 80204, USA
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3
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Raicu AM, Kadiyala D, Niblock M, Jain A, Yang Y, Bird KM, Bertholf K, Seenivasan A, Siddiq M, Arnosti DN. The Cynosure of CtBP: Evolution of a Bilaterian Transcriptional Corepressor. Mol Biol Evol 2023; 40:msad003. [PMID: 36625090 PMCID: PMC9907507 DOI: 10.1093/molbev/msad003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2022] [Revised: 12/16/2022] [Accepted: 01/03/2023] [Indexed: 01/11/2023] Open
Abstract
Evolution of sequence-specific transcription factors clearly drives lineage-specific innovations, but less is known about how changes in the central transcriptional machinery may contribute to evolutionary transformations. In particular, transcriptional regulators are rich in intrinsically disordered regions that appear to be magnets for evolutionary innovation. The C-terminal Binding Protein (CtBP) is a transcriptional corepressor derived from an ancestral lineage of alpha hydroxyacid dehydrogenases; it is found in mammals and invertebrates, and features a core NAD-binding domain as well as an unstructured C-terminus (CTD) of unknown function. CtBP can act on promoters and enhancers to repress transcription through chromatin-linked mechanisms. Our comparative phylogenetic study shows that CtBP is a bilaterian innovation whose CTD of about 100 residues is present in almost all orthologs. CtBP CTDs contain conserved blocks of residues and retain a predicted disordered property, despite having variations in the primary sequence. Interestingly, the structure of the C-terminus has undergone radical transformation independently in certain lineages including flatworms and nematodes. Also contributing to CTD diversity is the production of myriad alternative RNA splicing products, including the production of "short" tailless forms of CtBP in Drosophila. Additional diversity stems from multiple gene duplications in vertebrates, where up to five CtBP orthologs have been observed. Vertebrate lineages show fewer major modifications in the unstructured CTD, possibly because gene regulatory constraints of the vertebrate body plan place specific constraints on this domain. Our study highlights the rich regulatory potential of this previously unstudied domain of a central transcriptional regulator.
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Affiliation(s)
- Ana-Maria Raicu
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
| | - Dhruva Kadiyala
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Madeline Niblock
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | | | - Yahui Yang
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kalynn M Bird
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Kayla Bertholf
- Biochemistry and Molecular Biology Program, College of Wooster
| | - Akshay Seenivasan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
| | - Mohammad Siddiq
- Department of Molecular, Cellular, and Developmental Biology, University of Michigan, Ann Arbor, Michigan
- Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, Michigan
| | - David N Arnosti
- Cell and Molecular Biology Program, Michigan State University, East Lansing, Michigan
- Department of Biochemistry and Molecular Biology, Michigan State University, East Lansing, Michigan
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4
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Tutukina MN, Dakhnovets AI, Kaznadzey AD, Gelfand MS, Ozoline ON. Sense and antisense RNA products of the uxuR gene can affect motility and chemotaxis acting independent of the UxuR protein. Front Mol Biosci 2023; 10:1121376. [PMID: 36936992 PMCID: PMC10016265 DOI: 10.3389/fmolb.2023.1121376] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2022] [Accepted: 02/06/2023] [Indexed: 02/19/2023] Open
Abstract
Small non-coding and antisense RNAs are widespread in all kingdoms of life, however, the diversity of their functions in bacteria is largely unknown. Here, we study RNAs synthesised from divergent promoters located in the 3'-end of the uxuR gene, encoding transcription factor regulating hexuronate metabolism in Escherichia coli. These overlapping promoters were predicted in silico with rather high scores, effectively bound RNA polymerase in vitro and in vivo and were capable of initiating transcription in sense and antisense directions. The genome-wide correlation between in silico promoter scores and RNA polymerase binding in vitro and in vivo was higher for promoters located on the antisense strands of the genes, however, sense promoters within the uxuR gene were more active. Both regulatory RNAs synthesised from the divergent promoters inhibited expression of genes associated with the E. coli motility and chemotaxis independent of a carbon source on which bacteria had been grown. Direct effects of these RNAs were confirmed for the fliA gene encoding σ28 subunit of RNA polymerase. In addition to intracellular sRNAs, promoters located within the uxuR gene could initiate synthesis of transcripts found in the fraction of RNAs secreted in the extracellular medium. Their profile was also carbon-independent suggesting that intragenic uxuR transcripts have a specific regulatory role not directly related to the function of the protein in which gene they are encoded.
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Affiliation(s)
- Maria N. Tutukina
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
| | - Artemiy I. Dakhnovets
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- Department of Biotechnology, M. V. Lomonosov Moscow State University, Moscow, Russia
| | - Anna D. Kaznadzey
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Mikhail S. Gelfand
- Center for Molecular and Cellular Biology, Skolkovo Institute of Science and Technology, Moscow, Russia
- RTC “Bioinformatics”, A. A. Kharkevich Institute for Information Transmission Problems RAS, Moscow, Russia
| | - Olga N. Ozoline
- Lab of Functional Genomics and Cellular Stress, Institute of Cell Biophysics RAS, FRC PRCBR, Pushchino, Russia
- *Correspondence: Maria N. Tutukina, , Olga N. Ozoline,
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5
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Wilson SL, Shen SY, Harmon L, Burgener JM, Triche T, Bratman SV, De Carvalho DD, Hoffman MM. Sensitive and reproducible cell-free methylome quantification with synthetic spike-in controls. CELL REPORTS METHODS 2022; 2:100294. [PMID: 36160046 PMCID: PMC9499995 DOI: 10.1016/j.crmeth.2022.100294] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 05/17/2022] [Accepted: 08/19/2022] [Indexed: 06/16/2023]
Abstract
Cell-free methylated DNA immunoprecipitation sequencing (cfMeDIP-seq) identifies genomic regions with DNA methylation, using a protocol adapted to work with low-input DNA samples and with cell-free DNA (cfDNA). We developed a set of synthetic spike-in DNA controls for cfMeDIP-seq to provide a simple and inexpensive reference for quantitative normalization. We designed 54 DNA fragments with combinations of methylation status (methylated and unmethylated), fragment length (80 bp, 160 bp, 320 bp), G + C content (35%, 50%, 65%), and fraction of CpG dinucleotides within the fragment (1/80 bp, 1/40 bp, 1/20 bp). Using 0.01 ng of spike-in controls enables training a generalized linear model that absolutely quantifies methylated cfDNA in MeDIP-seq experiments. It mitigates batch effects and corrects for biases in enrichment due to known biophysical properties of DNA fragments and other technical biases.
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Affiliation(s)
- Samantha L. Wilson
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | - Shu Yi Shen
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
| | | | - Justin M. Burgener
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Tim Triche
- Van Andel Institute, Grand Rapids, MI, USA
| | - Scott V. Bratman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Daniel D. De Carvalho
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
| | - Michael M. Hoffman
- Princess Margaret Cancer Centre, University Health Network, Toronto, ON, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, ON, Canada
- Department of Computer Science, University of Toronto, Toronto, ON, Canada
- Vector Institute for Artificial Intelligence, Toronto, ON, Canada
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6
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SantaLucia J, Sozhamannan S, Gans JD, Koehler JW, Soong R, Lin NJ, Xie G, Olson V, Roth K, Beck L. Appendix Q: Recommendations for Developing Molecular Assays for Microbial Pathogen Detection Using Modern In Silico Approaches. J AOAC Int 2021; 103:882-899. [PMID: 33241357 PMCID: PMC8370429 DOI: 10.1093/jaoacint/qsaa045] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2020] [Accepted: 03/19/2020] [Indexed: 11/13/2022]
Affiliation(s)
| | - Shanmuga Sozhamannan
- Logistics Management Institute supporting Defense Biological Product Assurance Office (DBPAO), Joint Project Leads (JPL) Chemical, Biological, Radiological, and Nuclear Defense (CBRND) Enabling Biotechnologies (EB)
| | | | - Jeffrey W Koehler
- U.S. Army Medical Research Institute of Infectious Diseases (USAMRIID)
| | | | - Nancy J Lin
- National Institute of Standards and Technology (NIST)
| | - Gary Xie
- Los Alamos National Laboratory (LANL)
| | | | | | - Linda Beck
- Joint Research and Development, Inc. (JRAD) supporting Joint Program Executive Office (JPEO) JPL CBRND EB; Deputy Under Secretary of the Army, Test and Evaluation (DUSA TE)
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7
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Andrews RJ, O’Leary CA, Tompkins VS, Peterson JM, Haniff H, Williams C, Disney MD, Moss WN. A map of the SARS-CoV-2 RNA structurome. NAR Genom Bioinform 2021; 3:lqab043. [PMID: 34046592 PMCID: PMC8140738 DOI: 10.1093/nargab/lqab043] [Citation(s) in RCA: 39] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2021] [Revised: 04/06/2021] [Accepted: 04/28/2021] [Indexed: 12/11/2022] Open
Abstract
SARS-CoV-2 has exploded throughout the human population. To facilitate efforts to gain insights into SARS-CoV-2 biology and to target the virus therapeutically, it is essential to have a roadmap of likely functional regions embedded in its RNA genome. In this report, we used a bioinformatics approach, ScanFold, to deduce the local RNA structural landscape of the SARS-CoV-2 genome with the highest likelihood of being functional. We recapitulate previously-known elements of RNA structure and provide a model for the folding of an essential frameshift signal. Our results find that SARS-CoV-2 is greatly enriched in unusually stable and likely evolutionarily ordered RNA structure, which provides a large reservoir of potential drug targets for RNA-binding small molecules. Results are enhanced via the re-analyses of publicly-available genome-wide biochemical structure probing datasets that are broadly in agreement with our models. Additionally, ScanFold was updated to incorporate experimental data as constraints in the analysis to facilitate comparisons between ScanFold and other RNA modelling approaches. Ultimately, ScanFold was able to identify eight highly structured/conserved motifs in SARS-CoV-2 that agree with experimental data, without explicitly using these data. All results are made available via a public database (the RNAStructuromeDB: https://structurome.bb.iastate.edu/sars-cov-2) and model comparisons are readily viewable at https://structurome.bb.iastate.edu/sars-cov-2-global-model-comparisons.
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Affiliation(s)
- Ryan J Andrews
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Collin A O’Leary
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Van S Tompkins
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
| | - Hafeez S Haniff
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | | | - Matthew D Disney
- Department of Chemistry, The Scripps Research Institute, Jupiter, FL 33458, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA 50011, USA
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8
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Schmidt K, Weidmann CA, Hilimire TA, Yee E, Hatfield BM, Schneekloth JS, Weeks KM, Novina CD. Targeting the Oncogenic Long Non-coding RNA SLNCR1 by Blocking Its Sequence-Specific Binding to the Androgen Receptor. Cell Rep 2021; 30:541-554.e5. [PMID: 31940495 DOI: 10.1016/j.celrep.2019.12.011] [Citation(s) in RCA: 43] [Impact Index Per Article: 14.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2018] [Revised: 08/30/2018] [Accepted: 12/04/2019] [Indexed: 02/07/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) are critical regulators of numerous physiological processes and diseases, especially cancers. However, development of lncRNA-based therapies is limited because the mechanisms of many lncRNAs are obscure, and interactions with functional partners, including proteins, remain uncharacterized. The lncRNA SLNCR1 binds to and regulates the androgen receptor (AR) to mediate melanoma invasion and proliferation in an androgen-independent manner. Here, we use biochemical analyses coupled with selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) RNA structure probing to show that the N-terminal domain of AR binds a pyrimidine-rich motif in an unstructured region of SLNCR1. This motif is predictive of AR binding, as we identify an AR-binding motif in lncRNA HOXA11-AS-203. Oligonucleotides that bind either the AR N-terminal domain or the AR RNA motif block the SLNCR1-AR interaction and reduce SLNCR1-mediated melanoma invasion. Delivery of oligos that block SLNCR1-AR interaction thus represent a plausible therapeutic strategy.
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Affiliation(s)
- Karyn Schmidt
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA
| | - Chase A Weidmann
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Thomas A Hilimire
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Elaine Yee
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA
| | - Breanne M Hatfield
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - John S Schneekloth
- Chemical Biology Laboratory, National Cancer Institute, Frederick, MD 21702, USA
| | - Kevin M Weeks
- Department of Chemistry, University of North Carolina at Chapel Hill, Chapel Hill, NC 27599-3290, USA
| | - Carl D Novina
- Department of Cancer Immunology and Virology, Dana-Farber Cancer Institute, Boston, MA, USA; Department of Medicine, Harvard Medical School, Boston, MA 02115, USA; Broad Institute of Harvard and MIT, Cambridge, MA 02141, USA.
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9
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Stepanov VG, Fox GE. Expansion segments in bacterial and archaeal 5S ribosomal RNAs. RNA (NEW YORK, N.Y.) 2021; 27:133-150. [PMID: 33184227 PMCID: PMC7812874 DOI: 10.1261/rna.077123.120] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/28/2020] [Accepted: 11/09/2020] [Indexed: 05/10/2023]
Abstract
The large ribosomal RNAs of eukaryotes frequently contain expansion sequences that add to the size of the rRNAs but do not affect their overall structural layout and are compatible with major ribosomal function as an mRNA translation machine. The expansion of prokaryotic ribosomal RNAs is much less explored. In order to obtain more insight into the structural variability of these conserved molecules, we herein report the results of a comprehensive search for the expansion sequences in prokaryotic 5S rRNAs. Overall, 89 expanded 5S rRNAs of 15 structural types were identified in 15 archaeal and 36 bacterial genomes. Expansion segments ranging in length from 13 to 109 residues were found to be distributed among 17 insertion sites. The strains harboring the expanded 5S rRNAs belong to the bacterial orders Clostridiales, Halanaerobiales, Thermoanaerobacterales, and Alteromonadales as well as the archael order Halobacterales When several copies of a 5S rRNA gene are present in a genome, the expanded versions may coexist with normal 5S rRNA genes. The insertion sequences are typically capable of forming extended helices, which do not seemingly interfere with folding of the conserved core. The expanded 5S rRNAs have largely been overlooked in 5S rRNA databases.
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MESH Headings
- Alteromonadaceae/classification
- Alteromonadaceae/genetics
- Alteromonadaceae/metabolism
- Base Pairing
- Base Sequence
- Clostridiales/classification
- Clostridiales/genetics
- Clostridiales/metabolism
- Firmicutes/classification
- Firmicutes/genetics
- Firmicutes/metabolism
- Genome, Archaeal
- Genome, Bacterial
- Halobacteriales/classification
- Halobacteriales/genetics
- Halobacteriales/metabolism
- Nucleic Acid Conformation
- Phylogeny
- RNA, Archaeal/chemistry
- RNA, Archaeal/genetics
- RNA, Archaeal/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Ribosomal, 5S/chemistry
- RNA, Ribosomal, 5S/genetics
- RNA, Ribosomal, 5S/metabolism
- Thermoanaerobacterium/classification
- Thermoanaerobacterium/genetics
- Thermoanaerobacterium/metabolism
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Affiliation(s)
- Victor G Stepanov
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
| | - George E Fox
- Department of Biology and Biochemistry, University of Houston, Houston, Texas 77204-5001, USA
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10
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Tickner ZJ, Zhong G, Sheptack KR, Farzan M. Selection of High-Affinity RNA Aptamers That Distinguish between Doxycycline and Tetracycline. Biochemistry 2020; 59:3473-3486. [PMID: 32857495 DOI: 10.1021/acs.biochem.0c00586] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
Oligonucleotide aptamers are found in prokaryotes and eukaryotes, and they can be selected from large synthetic libraries to bind protein or small-molecule ligands with high affinities and specificities. Aptamers can function as biosensors, as protein recognition elements, and as components of riboswitches allowing ligand-dependent control of gene expression. One of the best studied laboratory-selected aptamers binds the antibiotic tetracycline, but it binds with a much lower affinity to the closely related but more bioavailable antibiotic doxycycline. Here we report enrichment of doxycycline binding aptamers from a selectively randomized library of tetracycline aptamer variants over four selection rounds. Selected aptamers distinguish between doxycycline, which they bind with dissociation constants of approximately 7 nM, and tetracycline, which they bind undetectably. They thus function as orthogonal complements to the original tetracycline aptamer. Unexpectedly, doxycycline aptamers adopt a conformation distinct from that of the tetracycline aptamer and depend on constant regions originally installed as primer binding sites. We show that the fluorescence emission intensity of doxycycline increases upon aptamer binding, permitting their use as biosensors. This new class of aptamers can be used in multiple contexts where doxycycline detection, or doxycycline-mediated regulation, is necessary.
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Affiliation(s)
- Zachary J Tickner
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Guocai Zhong
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Kelly R Sheptack
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
| | - Michael Farzan
- Department of Immunology and Microbiology, The Scripps Research Institute, Jupiter, Florida 33458, United States
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11
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Singh A, Pandey M, Nandakumar D, Raney KD, Yin YW, Patel SS. Excessive excision of correct nucleotides during DNA synthesis explained by replication hurdles. EMBO J 2020; 39:e103367. [PMID: 32037587 PMCID: PMC7073461 DOI: 10.15252/embj.2019103367] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2019] [Revised: 12/23/2019] [Accepted: 01/07/2020] [Indexed: 11/25/2022] Open
Abstract
The proofreading exonuclease activity of replicative DNA polymerase excises misincorporated nucleotides during DNA synthesis, but these events are rare. Therefore, we were surprised to find that T7 replisome excised nearly 7% of correctly incorporated nucleotides during leading and lagging strand syntheses. Similar observations with two other DNA polymerases establish its generality. We show that excessive excision of correctly incorporated nucleotides is not due to events such as processive degradation of nascent DNA or spontaneous partitioning of primer‐end to the exonuclease site as a “cost of proofreading”. Instead, we show that replication hurdles, including secondary structures in template, slowed helicase, or uncoupled helicase–polymerase, increase DNA reannealing and polymerase backtracking, and generate frayed primer‐ends that are shuttled to the exonuclease site and excised efficiently. Our studies indicate that active‐site shuttling occurs at a high frequency, and we propose that it serves as a proofreading mechanism to protect primer‐ends from mutagenic extensions.
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Affiliation(s)
- Anupam Singh
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Manjula Pandey
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Divya Nandakumar
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
| | - Kevin D Raney
- Department of Biochemistry and Molecular Biology, The University of Arkansas for Medical Sciences, Little Rock, AR, USA
| | - Y Whitney Yin
- Department of Pharmacology and Toxicology, Sealy Center for Structural Biology, University of Texas Medical Branch, Galveston, TX, USA
| | - Smita S Patel
- Department of Biochemistry and Molecular Biology, Robert Wood Johnson Medical School, Rutgers University, Piscataway, NJ, USA
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12
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Shilo A, Tosto FA, Rausch JW, Le Grice SFJ, Misteli T. Interplay of primary sequence, position and secondary RNA structure determines alternative splicing of LMNA in a pre-mature aging syndrome. Nucleic Acids Res 2019; 47:5922-5935. [PMID: 31006814 DOI: 10.1093/nar/gkz259] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Revised: 03/25/2019] [Accepted: 04/01/2019] [Indexed: 11/14/2022] Open
Abstract
Aberrant splicing in exon 11 of the LMNA gene causes the premature aging disorder Hutchinson-Gilford Progeria Syndrome. A de novo C1824T mutation activates an internal alternative 5' splice site, resulting in formation of the disease-causing progerin protein. The underlying mechanism for this 5' splice site selection is unknown. Here, we have applied a combination of targeted mutational analysis in a cell-based system and structural mapping by SHAPE-MaP to comprehensively probe the contributions of primary sequence, secondary RNA structure and linear splice site position in determining in vivo mechanisms of splice site choice in LMNA. While splice site choice is in part defined by sequence complementarity to U1 snRNA, we identify RNA secondary structural elements near the alternative 5' splice sites and show that splice site choice is significantly influenced by the structural context of the available splice sites. Furthermore, relative positioning of the competing sites within the primary sequence of the pre-mRNA is a predictor of 5' splice site usage, with the distal position favored over the proximal, regardless of sequence composition. Together, these results demonstrate that 5' splice site selection in LMNA is determined by an intricate interplay among RNA sequence, secondary structure and splice site position.
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Affiliation(s)
- Asaf Shilo
- Cell Biology of Genomes, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Frances Anne Tosto
- Cell Biology of Genomes, National Cancer Institute, NIH, Bethesda, MD 20892, USA
| | - Jason W Rausch
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Stuart F J Le Grice
- Basic Research Laboratory, National Cancer Institute, NIH, Frederick, MD 21702, USA
| | - Tom Misteli
- Cell Biology of Genomes, National Cancer Institute, NIH, Bethesda, MD 20892, USA
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13
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Bakre AA, Maleki A, Tripp RA. MicroRNA and Nonsense Transcripts as Putative Viral Evasion Mechanisms. Front Cell Infect Microbiol 2019; 9:152. [PMID: 31139579 PMCID: PMC6519394 DOI: 10.3389/fcimb.2019.00152] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2019] [Accepted: 04/23/2019] [Indexed: 12/25/2022] Open
Abstract
Viral proteins encode numerous antiviral activities to modify the host immunity. In this article, we hypothesize that viral genomes and gene transcripts interfere with host gene expression using passive mechanisms to deregulate host microRNA (miRNA) activity. We postulate that various RNA viruses mimic or block binding between a host miRNA and its target transcript, a phenomenon mediated by the miRNA seed site at the 5′ end of miRNA. Virus-encoded miRNA seed sponges (vSSs) can potentially bind to host miRNA seed sites and prevent interaction with their native targets thereby relieving native miRNA suppression. In contrast, virus-encoded miRNA seed mimics (vSMs) may mediate considerable downregulation of host miRNA activity. We analyzed genomes from diverse RNA viruses for vSS and vSM signatures and found an abundance of these motifs indicating that this may be a mechanism of deceiving host immunity. Employing respiratory syncytial virus and measles virus as models, we reveal that regions surrounding vSS or vSM motifs have features characteristics of pre-miRNA templates and show that RSV viral transcripts are processed into small RNAs that may behave as vSS or vSM effectors. These data suggest that complex molecular interactions likely occur at the host-virus interface. Identifying the mechanisms in the network of interactions between the host and viral transcripts can help uncover ways to improve vaccine efficacy, therapeutics, and potentially mitigate the adverse events that may be associated with some vaccines.
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Affiliation(s)
- Abhijeet A Bakre
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
| | - Ali Maleki
- Department of Virology, Faculty of Medical Sciences, Tarbiat Modares University, Tehran, Iran
| | - Ralph A Tripp
- Department of Infectious Diseases, College of Veterinary Medicine, University of Georgia, Athens, GA, United States
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14
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Alikina OV, Glazunova OA, Bykov AA, Kiselev SS, Tutukina MN, Shavkunov KS, Ozoline ON. A cohabiting bacterium alters the spectrum of short RNAs secreted by Escherichia coli. FEMS Microbiol Lett 2018; 365:5146451. [PMID: 30376063 DOI: 10.1093/femsle/fny262] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 10/28/2018] [Indexed: 02/07/2023] Open
Abstract
Recently, it has been found that bacteria secrete short RNAs able to affect gene expression in eukaryotic cells, while certain mammalian microRNAs shape the gut microbiome altering bacterial transcriptome. The involvement of bacterial RNAs in communication with other bacteria is also expected, but has not been documented yet. Here, we compared the fractions of extremely short (12-22 nucleotides) RNAs secreted by Escherichia coli grown in a pure culture and jointly with bacteria of the Paenibacillus genus. Besides fragments of rRNAs and tRNAs, abundant in all samples, secreted oligonucleotides (exoRNAs) predominantly contained GC-rich fragments of messenger and antisense RNAs processed from regions with stable secondary structures. They differed in composition from oligonucleotides of intracellular fraction, where fragments of small regulatory RNAs were prevalent. Both fractions contained RNAs capable of forming complementary duplexes, while for exoRNA samples a higher percentage of 3΄-end modified RNAs and different endonuclease cleavage were detected. The presence of a cohabiting bacterium altered the spectrum of E. coli exoRNAs, indicating a population-dependent control over their composition. Possible mechanisms of this effect are discussed.
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MESH Headings
- Biological Transport
- Escherichia coli/chemistry
- Escherichia coli/genetics
- Escherichia coli/metabolism
- Genome, Bacterial
- Nucleic Acid Conformation
- RNA, Antisense/chemistry
- RNA, Antisense/genetics
- RNA, Antisense/metabolism
- RNA, Bacterial/chemistry
- RNA, Bacterial/genetics
- RNA, Bacterial/metabolism
- RNA, Messenger/chemistry
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Ribosomal/chemistry
- RNA, Ribosomal/genetics
- RNA, Ribosomal/metabolism
- RNA, Transfer/chemistry
- RNA, Transfer/genetics
- RNA, Transfer/metabolism
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Affiliation(s)
- Olga V Alikina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga A Glazunova
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Alexandr A Bykov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Sergey S Kiselev
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Maria N Tutukina
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Konstantin S Shavkunov
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
| | - Olga N Ozoline
- Institute of Cell Biophysics of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
- Pushchino Research Center of Russian Academy of Sciences, Pushchino, Moscow Region, 142290, Russian Federation
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15
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Deforges J, de Breyne S, Ameur M, Ulryck N, Chamond N, Saaidi A, Ponty Y, Ohlmann T, Sargueil B. Two ribosome recruitment sites direct multiple translation events within HIV1 Gag open reading frame. Nucleic Acids Res 2017; 45:7382-7400. [PMID: 28449096 PMCID: PMC5499600 DOI: 10.1093/nar/gkx303] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2017] [Accepted: 04/12/2017] [Indexed: 02/06/2023] Open
Abstract
In the late phase of the HIV virus cycle, the unspliced genomic RNA is exported to the cytoplasm for the necessary translation of the Gag and Gag-pol polyproteins. Three distinct translation initiation mechanisms ensuring Gag production have been described with little rationale for their multiplicity. The Gag-IRES has the singularity to be located within Gag ORF and to directly interact with ribosomal 40S. Aiming at elucidating the specificity and the relevance of this interaction, we probed HIV-1 Gag-IRES structure and developed an innovative integrative modelling strategy to take into account all the gathered information. We propose a novel Gag-IRES secondary structure strongly supported by all experimental data. We further demonstrate the presence of two regions within Gag-IRES that independently and directly interact with the ribosome. Importantly, these binding sites are functionally relevant to Gag translation both in vitro and ex vivo. This work provides insight into the Gag-IRES molecular mechanism and gives compelling evidence for its physiological importance. It allows us to propose original hypotheses about the IRES physiological role and conservation among primate lentiviruses.
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Affiliation(s)
- Jules Deforges
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Sylvain de Breyne
- CIRI (International Center for Infectiology Research), INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5308, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Melissa Ameur
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Nathalie Ulryck
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Nathalie Chamond
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
| | - Afaf Saaidi
- CNRS UMR 7161, Laboratoire de Recherche en Informatique de l'Ecole Polytechnique (LIX), Ecole Polytechnique, 1 rue Estienne d'Orves, 91120 Palaiseau, France.,AMIB, Inria Saclay, bat Alan Turing, 1 rue Estienne d'Orves, 91120 Palaiseau, France
| | - Yann Ponty
- CNRS UMR 7161, Laboratoire de Recherche en Informatique de l'Ecole Polytechnique (LIX), Ecole Polytechnique, 1 rue Estienne d'Orves, 91120 Palaiseau, France.,AMIB, Inria Saclay, bat Alan Turing, 1 rue Estienne d'Orves, 91120 Palaiseau, France
| | - Theophile Ohlmann
- CIRI (International Center for Infectiology Research), INSERM U1111, Ecole Normale Supérieure de Lyon, Université Claude Bernard Lyon 1, CNRS UMR 5308, 46 allée d'Italie, 69364 Lyon Cedex 07, France
| | - Bruno Sargueil
- CNRS UMR 8015, Laboratoire de cristallographie et RMN Biologiques, Université Paris Descartes, 4 avenue de l'Observatoire, 75270 Paris Cedex 06, France
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