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Secondary Structure of Influenza A Virus Genomic Segment 8 RNA Folded in a Cellular Environment. Int J Mol Sci 2022; 23:ijms23052452. [PMID: 35269600 PMCID: PMC8910647 DOI: 10.3390/ijms23052452] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2021] [Revised: 02/05/2022] [Accepted: 02/17/2022] [Indexed: 11/17/2022] Open
Abstract
Influenza A virus (IAV) is a member of the single-stranded RNA (ssRNA) family of viruses. The most recent global pandemic caused by the SARS-CoV-2 virus has shown the major threat that RNA viruses can pose to humanity. In comparison, influenza has an even higher pandemic potential as a result of its high rate of mutations within its relatively short (<13 kbp) genome, as well as its capability to undergo genetic reassortment. In light of this threat, and the fact that RNA structure is connected to a broad range of known biological functions, deeper investigation of viral RNA (vRNA) structures is of high interest. Here, for the first time, we propose a secondary structure for segment 8 vRNA (vRNA8) of A/California/04/2009 (H1N1) formed in the presence of cellular and viral components. This structure shows similarities with prior in vitro experiments. Additionally, we determined the location of several well-defined, conserved structural motifs of vRNA8 within IAV strains with possible functionality. These RNA motifs appear to fold independently of regional nucleoprotein (NP)-binding affinity, but a low or uneven distribution of NP in each motif region is noted. This research also highlights several accessible sites for oligonucleotide tools and small molecules in vRNA8 in a cellular environment that might be a target for influenza A virus inhibition on the RNA level.
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2
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Soszynska-Jozwiak M, Pszczola M, Piasecka J, Peterson JM, Moss WN, Taras-Goslinska K, Kierzek R, Kierzek E. Universal and strain specific structure features of segment 8 genomic RNA of influenza A virus-application of 4-thiouridine photocrosslinking. J Biol Chem 2021; 297:101245. [PMID: 34688660 PMCID: PMC8666676 DOI: 10.1016/j.jbc.2021.101245] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 09/22/2021] [Accepted: 09/23/2021] [Indexed: 11/24/2022] Open
Abstract
RNA structure in the influenza A virus (IAV) has been the focus of several studies that have shown connections between conserved secondary structure motifs and their biological function in the virus replication cycle. Questions have arisen on how to best recognize and understand the pandemic properties of IAV strains from an RNA perspective, but determination of the RNA secondary structure has been challenging. Herein, we used chemical mapping to determine the secondary structure of segment 8 viral RNA (vRNA) of the pandemic A/California/04/2009 (H1N1) strain of IAV. Additionally, this long, naturally occurring RNA served as a model to evaluate RNA mapping with 4-thiouridine (4sU) crosslinking. We explored 4-thiouridine as a probe of nucleotides in close proximity, through its incorporation into newly transcribed RNA and subsequent photoactivation. RNA secondary structural features both universal to type A strains and unique to the A/California/04/2009 (H1N1) strain were recognized. 4sU mapping confirmed and facilitated RNA structure prediction, according to several rules: 4sU photocross-linking forms efficiently in the double-stranded region of RNA with some flexibility, in the ends of helices, and across bulges and loops when their structural mobility is permitted. This method highlighted three-dimensional properties of segment 8 vRNA secondary structure motifs and allowed to propose several long-range three-dimensional interactions. 4sU mapping combined with chemical mapping and bioinformatic analysis could be used to enhance the RNA structure determination as well as recognition of target regions for antisense strategies or viral RNA detection.
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Affiliation(s)
| | - Maciej Pszczola
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Julita Piasecka
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jake M Peterson
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, Iowa, USA
| | | | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland.
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3
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Michalak P, Soszynska-Jozwiak M, Biala E, Moss WN, Kesy J, Szutkowska B, Lenartowicz E, Kierzek R, Kierzek E. Secondary structure of the segment 5 genomic RNA of influenza A virus and its application for designing antisense oligonucleotides. Sci Rep 2019; 9:3801. [PMID: 30846846 PMCID: PMC6406010 DOI: 10.1038/s41598-019-40443-7] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Accepted: 02/12/2019] [Indexed: 12/20/2022] Open
Abstract
Influenza virus causes seasonal epidemics and dangerous pandemic outbreaks. It is a single stranded (-)RNA virus with a segmented genome. Eight segments of genomic viral RNA (vRNA) form the virion, which are then transcribed and replicated in host cells. The secondary structure of vRNA is an important regulator of virus biology and can be a target for finding new therapeutics. In this paper, the secondary structure of segment 5 vRNA is determined based on chemical mapping data, free energy minimization and structure-sequence conservation analysis for type A influenza. The revealed secondary structure has circular folding with a previously reported panhandle motif and distinct novel domains. Conservations of base pairs is 87% on average with many structural motifs that are highly conserved. Isoenergetic microarray mapping was used to additionally validate secondary structure and to discover regions that easy bind short oligonucleotides. Antisense oligonucleotides, which were designed based on modeled secondary structure and microarray mapping, inhibit influenza A virus proliferation in MDCK cells. The most potent oligonucleotides lowered virus titer by ~90%. These results define universal for type A structured regions that could be important for virus function, as well as new targets for antisense therapeutics.
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Affiliation(s)
- Paula Michalak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ewa Biala
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, USA
| | - Julita Kesy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Barbara Szutkowska
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Lenartowicz
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland.
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Soszynska-Jozwiak M, Michalak P, Moss WN, Kierzek R, Kesy J, Kierzek E. Influenza virus segment 5 (+)RNA - secondary structure and new targets for antiviral strategies. Sci Rep 2017; 7:15041. [PMID: 29118447 PMCID: PMC5678188 DOI: 10.1038/s41598-017-15317-5] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2017] [Accepted: 10/24/2017] [Indexed: 01/05/2023] Open
Abstract
Influenza A virus is a threat for humans due to seasonal epidemics and occasional pandemics. This virus can generate new strains that are dangerous through nucleotide/amino acid changes or through segmental recombination of the viral RNA genome. It is important to gain wider knowledge about influenza virus RNA to create new strategies for drugs that will inhibit its spread. Here, we present the experimentally determined secondary structure of the influenza segment 5 (+)RNA. Two RNAs were studied: the full-length segment 5 (+)RNA and a shorter construct containing only the coding region. Chemical mapping data combined with thermodynamic energy minimization were used in secondary structure prediction. Sequence/structure analysis showed that the determined secondary structure of segment 5 (+)RNA is mostly conserved between influenza virus type A strains. Microarray mapping and RNase H cleavage identified accessible sites for oligonucleotides in the revealed secondary structure of segment 5 (+)RNA. Antisense oligonucleotides were designed based on the secondary structure model and tested against influenza virus in cell culture. Inhibition of influenza virus proliferation was noticed, identifying good targets for antisense strategies. Effective target sites fall within two domains, which are conserved in sequence/structure indicating their importance to the virus.
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Affiliation(s)
- Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Paula Michalak
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Walter N Moss
- Roy J. Carver Department of Biophysics, Biochemistry and Molecular Biology, Iowa State University, Ames, IA, 50011, United States of America
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Julita Kesy
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704, Poznan, Noskowskiego 12/14, Poland.
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5
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Secondary structure model of the naked segment 7 influenza A virus genomic RNA. Biochem J 2016; 473:4327-4348. [PMID: 27694388 DOI: 10.1042/bcj20160651] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/04/2016] [Revised: 09/25/2016] [Accepted: 09/30/2016] [Indexed: 11/17/2022]
Abstract
The influenza A virus (IAV) genome comprises eight negative-sense viral (v)RNA segments. The seventh segment of the genome encodes two essential viral proteins and is specifically packaged alongside the other seven vRNAs. To gain insights into the possible roles of RNA structure both within and without virions, a secondary structure model of a naked (protein-free) segment 7 vRNA (vRNA7) has been determined using chemical mapping and thermodynamic energy minimization. The proposed structure model was validated using microarray mapping, RNase H cleavage and comparative sequence analysis. Additionally, the detailed structures of three vRNA7 fragment constructs - comprising independently folded subdomains - were determined. Much of the proposed vRNA7 structure is preserved between IAV strains, suggesting their importance in the influenza replication cycle. Possible structure rearrangements, which allow or preclude long-range RNA interactions, are also proposed.
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Lenartowicz E, Kesy J, Ruszkowska A, Soszynska-Jozwiak M, Michalak P, Moss WN, Turner DH, Kierzek R, Kierzek E. Self-Folding of Naked Segment 8 Genomic RNA of Influenza A Virus. PLoS One 2016; 11:e0148281. [PMID: 26848969 PMCID: PMC4743857 DOI: 10.1371/journal.pone.0148281] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2015] [Accepted: 01/15/2016] [Indexed: 01/10/2023] Open
Abstract
Influenza A is a negative sense RNA virus that kills hundreds of thousands of humans each year. Base pairing in RNA is very favorable, but possibilities for RNA secondary structure of the influenza genomic RNA have not been investigated. This work presents the first experimentally-derived exploration of potential secondary structure in an influenza A naked (protein-free) genomic segment. Favorable folding regions are revealed by in vitro chemical structure mapping, thermodynamics, bioinformatics, and binding to isoenergetic microarrays of an entire natural sequence of the 875 nt segment 8 vRNA and of a smaller fragment. Segment 8 has thermodynamically stable and evolutionarily conserved RNA structure and encodes essential viral proteins NEP and NS1. This suggests that vRNA self-folding may generate helixes and loops that are important at one or more stages of the influenza life cycle.
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Affiliation(s)
- Elzbieta Lenartowicz
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Julita Kesy
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Agnieszka Ruszkowska
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Marta Soszynska-Jozwiak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Paula Michalak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Walter N. Moss
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Douglas H. Turner
- Department of Chemistry, University of Rochester, Rochester, New York, 14627, United States of America
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61–704 Poznan, Poland
- * E-mail:
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Lisowiec J, Magner D, Kierzek E, Lenartowicz E, Kierzek R. Structural determinants for alternative splicing regulation of the MAPT pre-mRNA. RNA Biol 2015; 12:330-42. [PMID: 25826665 DOI: 10.1080/15476286.2015.1017214] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/09/2023] Open
Abstract
Alternative splicing at the MAPT gene exon 10 yields similar levels of the 3R and 4R tau protein isoforms. (1) The presence of mutations, particularly in exon 10 and intron 10-11, changes the quantity of tau isoforms. Domination each of the isoform yields tau protein aggregation and frontotemporal dementia and Parkinsonism linked to chromosome 17 (FTDP-17). Here, we report for the first time the secondary structure of the 194/195 nucleotide region for the wild type (WT) and 10 mutants of the MAPT gene pre-mRNA determined using both chemical and microarray mapping. Thermodynamic analyses indicate that single nucleotide mutations in the splicing regulatory element (SRE) that form a hairpin affect its stability by up to 4 and 7 kcal/mol. Moreover, binding the regulatory hairpin of small molecule ligands (neomycin, kanamycin, tobramycin and mitoxantrone) enhance its stability depending on the nature of the ligands and the RNA mutations. Experiments using the cos-7 cell line indicate that the presence of ligands and modified antisense oligonucleotides affect the quantity of 3R and 4R isoforms. This finding correlates with the thermodynamic stability of the regulatory hairpin. An alternative splicing regulation mechanism for exon 10 is postulated based on our experimental data and on published data.
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Key Words
- AD, Alzheimer disease
- DMS, dimethyl sulfide
- ESE, exonic splicing enhancer
- ESS, exonic splicing silencer
- FTD, frontotemporal dementia
- FTDP-17, frontotemporal dementia and Parkinsonism linked to chromosome 17
- ISM, intronic splicing modulator
- ISS, intronic splicing silencer
- MAPT, microtubule-associated protein tau
- NMIA, N-methylisotoic anhydride
- NMR, nuclear magnetic resonance
- PPE, polypurine enhancer
- RNA structure
- RNA thermodynamics
- RT-PCR, reverse transcription polymerase chain reaction
- SHAPE, selective 2′-hydroxyl acylation analyzed by primer extension
- SMA, spinal muscular atrophy
- SRE, splicing regulatory element
- U1 snRNP, U1 small nuclear ribonucleoprotein
- WT, wild type
- alternative splicing regulation
- antisense oligonucleotides
- neurodegradation
- pre-mRNA, pre-messenger RNA
- small molecule binding
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Affiliation(s)
- Jolanta Lisowiec
- a Institute of Bioorganic Chemistry; Polish Academy of Sciences ; Noskowskiego, Poland
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Fajardo T, Sung PY, Roy P. Disruption of Specific RNA-RNA Interactions in a Double-Stranded RNA Virus Inhibits Genome Packaging and Virus Infectivity. PLoS Pathog 2015; 11:e1005321. [PMID: 26646790 PMCID: PMC4672896 DOI: 10.1371/journal.ppat.1005321] [Citation(s) in RCA: 33] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2015] [Accepted: 11/11/2015] [Indexed: 11/18/2022] Open
Abstract
Bluetongue virus (BTV) causes hemorrhagic disease in economically important livestock. The BTV genome is organized into ten discrete double-stranded RNA molecules (S1-S10) which have been suggested to follow a sequential packaging pathway from smallest to largest segment during virus capsid assembly. To substantiate and extend these studies, we have investigated the RNA sorting and packaging mechanisms with a new experimental approach using inhibitory oligonucleotides. Putative packaging signals present in the 3’untranslated regions of BTV segments were targeted by a number of nuclease resistant oligoribonucleotides (ORNs) and their effects on virus replication in cell culture were assessed. ORNs complementary to the 3’ UTR of BTV RNAs significantly inhibited virus replication without affecting protein synthesis. Same ORNs were found to inhibit complex formation when added to a novel RNA-RNA interaction assay which measured the formation of supramolecular complexes between and among different RNA segments. ORNs targeting the 3’UTR of BTV segment 10, the smallest RNA segment, were shown to be the most potent and deletions or substitution mutations of the targeted sequences diminished the RNA complexes and abolished the recovery of viable viruses using reverse genetics. Cell-free capsid assembly/RNA packaging assay also confirmed that the inhibitory ORNs could interfere with RNA packaging and further substitution mutations within the putative RNA packaging sequence have identified the recognition sequence concerned. Exchange of 3’UTR between segments have further demonstrated that RNA recognition was segment specific, most likely acting as part of the secondary structure of the entire genomic segment. Our data confirm that genome packaging in this segmented dsRNA virus occurs via the formation of supramolecular complexes formed by the interaction of specific sequences located in the 3’ UTRs. Additionally, the inhibition of packaging in-trans with inhibitory ORNs suggests this that interaction is a bona fide target for the design of compounds with antiviral activity. Bluetongue virus (BTV) is an economically important pathogen of ruminants that belongs to a group of viruses whose genome consists of multiple segments of double-stranded RNA. In order for the virus to synthesize viable and infectious progeny, a precise set of the 10 newly replicated BTV segments must be selected for packaging into each new virus particle. How the virus is able to select its own genomic strands from the vast array of cellular RNAs is not clearly understood. One possibility is that that BTV segments harbours an interaction signal that allows them to be sorted and packaged as a set. Correct identification of these signals has basic and applied implications for a possible target of antiviral therapeutics through inhibition of genome sorting and packaging process. Here we showed that a series of short oligonucleotides (ORNs) complementary to multiple sites on the BTV RNA prevented the growth of viable virus in infected cells. ORNs positive for inhibition in virus growth also prevented the genomic RNA to be packaged in an in vitro packaging assay. Moreover, when these same targeted sequences were deleted or mutated in viral genome, viable virus recovery was abolished. Exchanging the terminal sequences between segments failed to recover virus confirming that such changes are deleterious to virus viability. These studies have identified specific regions and sequences key to genome packaging in dsRNA viruses and viability. The specific genome packaging sequences targeted by inhibitory activities of ORNs are bona fide drug target which, as a mechanism common amongst all serotypes, may represent an Achilles’ heel for the development of virus therapeutics.
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Affiliation(s)
- Teodoro Fajardo
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Po-Yu Sung
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
| | - Polly Roy
- Department of Pathogen Molecular Biology, Faculty of Infectious and Tropical Diseases, London School of Hygiene and Tropical Medicine, London, United Kingdom
- * E-mail:
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9
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Chen JL, Bellaousov S, Tubbs JD, Kennedy SD, Lopez MJ, Mathews DH, Turner DH. Nuclear Magnetic Resonance-Assisted Prediction of Secondary Structure for RNA: Incorporation of Direction-Dependent Chemical Shift Constraints. Biochemistry 2015; 54:6769-82. [PMID: 26451676 PMCID: PMC4666457 DOI: 10.1021/acs.biochem.5b00833] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
![]()
Knowledge
of RNA
structure is necessary to determine structure–function relationships
and to facilitate design of potential therapeutics.
RNA secondary structure prediction can be improved by applying constraints
from nuclear magnetic resonance (NMR) experiments to a dynamic programming
algorithm. Imino proton walks from NOESY spectra reveal double-stranded
regions. Chemical shifts of protons in GH1, UH3, and UH5 of GU pairs,
UH3, UH5, and AH2 of AU pairs, and GH1 of GC pairs were analyzed to
identify constraints for the 5′ to 3′ directionality
of base pairs in helices. The 5′ to 3′ directionality
constraints were incorporated into an NMR-assisted prediction of secondary
structure (NAPSS-CS) program. When it was tested on 18 structures,
including nine pseudoknots, the sensitivity and positive predictive
value were improved relative to those of three unrestrained programs.
The prediction accuracy for the pseudoknots improved the most. The
program also facilitates assignment of chemical shifts to individual
nucleotides, a necessary step for determining three-dimensional structure.
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Affiliation(s)
- Jonathan L Chen
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Stanislav Bellaousov
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Jason D Tubbs
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - Scott D Kennedy
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States
| | - Michael J Lopez
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States
| | - David H Mathews
- Department of Biochemistry and Biophysics, University of Rochester School of Medicine and Dentistry , Rochester, New York 14642, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
| | - Douglas H Turner
- Department of Chemistry, University of Rochester , Rochester, New York 14627, United States.,Center for RNA Biology, University of Rochester , Rochester, New York 14642, United States
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A Conserved Secondary Structural Element in the Coding Region of the Influenza A Virus Nucleoprotein (NP) mRNA Is Important for the Regulation of Viral Proliferation. PLoS One 2015; 10:e0141132. [PMID: 26488402 PMCID: PMC4619443 DOI: 10.1371/journal.pone.0141132] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2015] [Accepted: 10/05/2015] [Indexed: 11/22/2022] Open
Abstract
Influenza A virus is a threat to humans due to seasonal epidemics and infrequent, but dangerous, pandemics that lead to widespread infection and death. Eight segments of RNA constitute the genome of this virus and they encode greater than eight proteins via alternative splicing of coding (+)RNAs generated from the genomic (-)RNA template strand. RNA is essential in its life cycle. A bioinformatics analysis of segment 5, which encodes nucleoprotein, revealed a conserved structural motif in the (+)RNA. The secondary structure proposed by energy minimization and comparative analysis agrees with structure predicted based on experimental data using a 121 nucleotide in vitro RNA construct comprising an influenza A virus consensus sequence and also an entire segment 5 (+)RNA (strain A/VietNam/1203/2004 (H5N1)). The conserved motif consists of three hairpins with one being especially thermodynamically stable. The biological importance of this conserved secondary structure is supported in experiments using antisense oligonucleotides in cell line, which found that disruption of this motif led to inhibition of viral fitness. These results suggest that this conserved motif in the segment 5 (+)RNA might be a candidate for oligonucleotide-based antiviral therapy.
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11
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Le Grice SFJ. Targeting the HIV RNA genome: high-hanging fruit only needs a longer ladder. Curr Top Microbiol Immunol 2015; 389:147-69. [PMID: 25735922 PMCID: PMC7120518 DOI: 10.1007/82_2015_434] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/17/2023]
Abstract
Small molecules targeting the enzymes responsible for human immunodeficiency virus (HIV) maturation, DNA synthesis and its subsequent chromosomal integration as ribonucleotide-free double-stranded DNA remain the mainstay of combination antiretroviral therapy. For infected individuals harboring drug-susceptible virus, this approach has afforded complete or near-complete viral suppression. However, in the absence of a curative strategy, the predictable emergence of drug-resistant variants requires continued development of improved antiviral strategies, inherent to which is the necessity of identifying novel targets. Regulatory elements that mediate transcription, translation, nucleocytoplasmic transport, dimerization, packaging and reverse transcription of the (+) strand RNA genome should now be considered viable targets for small molecule, peptide- and oligonucleotide-based therapeutics. Where target specificity and cellular penetration and toxicity have been the primary obstacle to successful “macromolecule therapeutics”, this chapter summarizes (a) novel approaches targeting RNA motifs whose three-dimensional structure is critical for biological function and consequently may be less prone to resistance-conferring mutations and (b) improved methods for delivery.
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Affiliation(s)
- Stuart F J Le Grice
- RT Biochemistry Section, Basic Research Laboratory, National Cancer Institute, Frederick, MD, 21702, USA,
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12
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Kierzek R, Turner DH, Kierzek E. Microarrays for identifying binding sites and probing structure of RNAs. Nucleic Acids Res 2014; 43:1-12. [PMID: 25505162 PMCID: PMC4288193 DOI: 10.1093/nar/gku1303] [Citation(s) in RCA: 75] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Oligonucleotide microarrays are widely used in various biological studies. In this review, application of oligonucleotide microarrays for identifying binding sites and probing structure of RNAs is described. Deep sequencing allows fast determination of DNA and RNA sequence. High-throughput methods for determination of secondary structures of RNAs have also been developed. Those methods, however, do not reveal binding sites for oligonucleotides. In contrast, microarrays directly determine binding sites while also providing structural insights. Microarray mapping can be used over a wide range of experimental conditions, including temperature, pH, various cations at different concentrations and the presence of other molecules. Moreover, it is possible to make universal microarrays suitable for investigations of many different RNAs, and readout of results is rapid. Thus, microarrays are used to provide insight into oligonucleotide sequences potentially able to interfere with biological function. Better understanding of structure-function relationships of RNA can be facilitated by using microarrays to find RNA regions capable to bind oligonucleotides. That information is extremely important to design optimal sequences for antisense oligonucleotides and siRNA because both bind to single-stranded regions of target RNAs.
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Affiliation(s)
- Ryszard Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
| | - Douglas H Turner
- Department of Chemistry, University of Rochester, Rochester, NY 14627, USA
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry Polish Academy of Sciences, 61-704 Poznan, Noskowskiego 12/14, Poland
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13
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Dela-Moss LI, Moss WN, Turner DH. Identification of conserved RNA secondary structures at influenza B and C splice sites reveals similarities and differences between influenza A, B, and C. BMC Res Notes 2014; 7:22. [PMID: 24405943 PMCID: PMC3895672 DOI: 10.1186/1756-0500-7-22] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2013] [Accepted: 01/02/2014] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Influenza B and C are single-stranded RNA viruses that cause yearly epidemics and infections. Knowledge of RNA secondary structure generated by influenza B and C will be helpful in further understanding the role of RNA structure in the progression of influenza infection. FINDINGS All available protein-coding sequences for influenza B and C were analyzed for regions with high potential for functional RNA secondary structure. On the basis of conserved RNA secondary structure with predicted high thermodynamic stability, putative structures were identified that contain splice sites in segment 8 of influenza B and segments 6 and 7 of influenza C. The sequence in segment 6 also contains three unused AUG start codon sites that are sequestered within a hairpin structure. CONCLUSIONS When added to previous studies on influenza A, the results suggest that influenza splicing may share common structural strategies for regulation of splicing. In particular, influenza 3' splice sites are predicted to form secondary structures that can switch conformation to regulate splicing. Thus, these RNA structures present attractive targets for therapeutics aimed at targeting one or the other conformation.
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Affiliation(s)
- Lumbini I Dela-Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
| | - Douglas H Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York 14627-0216, USA
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Priore SF, Kierzek E, Kierzek R, Baman JR, Moss WN, Dela-Moss LI, Turner DH. Secondary structure of a conserved domain in the intron of influenza A NS1 mRNA. PLoS One 2013; 8:e70615. [PMID: 24023714 PMCID: PMC3759394 DOI: 10.1371/journal.pone.0070615] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2013] [Accepted: 06/22/2013] [Indexed: 12/04/2022] Open
Abstract
Influenza A virus is a segmented single-stranded (−)RNA virus that causes substantial annual morbidity and mortality. The transcriptome of influenza A is predicted to have extensive RNA secondary structure. The smallest genome segment, segment 8, encodes two proteins, NS1 and NEP, via alternative splicing. A conserved RNA domain in the intron of segment 8 may be important for regulating production of NS1. Two different multi-branch loop structures have been proposed for this region. A combination of in vitro chemical mapping and isoenergetic microarray techniques demonstrate that the consensus sequence for this region folds into a hairpin conformation. These results provide an alternative folding for this region and a foundation for designing experiments to probe its functional role in the influenza life cycle.
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Affiliation(s)
- Salvatore F. Priore
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Poland
| | - Jayson R. Baman
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Walter N. Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry and Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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15
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Moss WN, Dela-Moss LI, Priore SF, Turner DH. The influenza A segment 7 mRNA 3' splice site pseudoknot/hairpin family. RNA Biol 2012; 9:1305-10. [PMID: 23064116 PMCID: PMC3597570 DOI: 10.4161/rna.22343] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022] Open
Abstract
The 3′ splice site of the influenza A segment 7 transcript is utilized to produce mRNA for the critical M2 ion-channel protein. In solution a 63 nt fragment that includes this region can adopt two conformations: a pseudoknot and a hairpin. In each conformation, the splice site, a binding site for the SF2/ASF exonic splicing enhancer and a polypyrimidine tract, each exists in a different structural context. The most dramatic difference occurs for the splice site. In the hairpin the splice site is between two residues that are involved in a 2 by 2 nucleotide internal loop. In the pseudoknot, however, these bases are canonically paired within one of the pseudoknotted helices. The conformational switching observed in this region has implications for the regulation of splicing of the segment 7 mRNA. A measure of stability of the structures also shows interesting trends with respect to host specificity: avian strains tend to be the most stable, followed by swine and then human.
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Affiliation(s)
- Walter N Moss
- Department of Chemistry and Center for RNA Biology, University of Rochester; Rochester, NY, USA
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16
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Moss WN, Dela-Moss LI, Kierzek E, Kierzek R, Priore SF, Turner DH. The 3' splice site of influenza A segment 7 mRNA can exist in two conformations: a pseudoknot and a hairpin. PLoS One 2012; 7:e38323. [PMID: 22685560 PMCID: PMC3369869 DOI: 10.1371/journal.pone.0038323] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/22/2012] [Accepted: 05/03/2012] [Indexed: 12/29/2022] Open
Abstract
The 3′ splice site of influenza A segment 7 is used to produce mRNA for the M2 ion-channel protein, which is critical to the formation of viable influenza virions. Native gel analysis, enzymatic/chemical structure probing, and oligonucleotide binding studies of a 63 nt fragment, containing the 3′ splice site, key residues of an SF2/ASF splicing factor binding site, and a polypyrimidine tract, provide evidence for an equilibrium between pseudoknot and hairpin structures. This equilibrium is sensitive to multivalent cations, and can be forced towards the pseudoknot by addition of 5 mM cobalt hexammine. In the two conformations, the splice site and other functional elements exist in very different structural environments. In particular, the splice site is sequestered in the middle of a double helix in the pseudoknot conformation, while in the hairpin it resides in a two-by-two nucleotide internal loop. The results suggest that segment 7 mRNA splicing can be controlled by a conformational switch that exposes or hides the splice site.
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Affiliation(s)
- Walter N. Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Lumbini I. Dela-Moss
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Elzbieta Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Ryszard Kierzek
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Poznan, Noskowskiego, Poland
| | - Salvatore F. Priore
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
| | - Douglas H. Turner
- Department of Chemistry, Center for RNA Biology, University of Rochester, Rochester, New York, United States of America
- * E-mail:
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17
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Gude L, Berkovitch SS, Santos WL, Kutchukian PS, Pawloski AR, Kuimelis R, McGall G, Verdine GL. Mapping targetable sites on human telomerase RNA pseudoknot/template domain using 2'-OMe RNA-interacting polynucleotide (RIPtide) microarrays. J Biol Chem 2012; 287:18843-53. [PMID: 22451672 DOI: 10.1074/jbc.m111.316596] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Abstract
Most cellular RNAs engage in intrastrand base-pairing that gives rise to complex three-dimensional folds. This self-pairing presents an impediment toward binding of the RNA by nucleic acid-based ligands. An important step in the discovery of RNA-targeting ligands is therefore to identify those regions in a folded RNA that are accessible toward the nucleic acid-based ligand. Because the folding of RNA targets can involve interactions between nonadjacent regions and employ both Watson-Crick and non-Watson-Crick base-pairing, screening of candidate binder ensembles is typically necessary. Microarray-based screening approaches have shown great promise in this regard and have suggested that achieving complete sequence coverage would be a valuable attribute of a next generation system. Here, we report a custom microarray displaying a library of RNA-interacting polynucleotides comprising all possible 2'-OMe RNA sequences from 4- to 8-nucleotides in length. We demonstrate the utility of this array in identifying RNA-interacting polynucleotides that bind tightly and specifically to the highly conserved, functionally essential template/pseudoknot domain of human telomerase RNA and that inhibit telomerase function in vitro.
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Affiliation(s)
- Lourdes Gude
- Departmens of Chemistry and Chemical Biology, Harvard University, Cambridge, Massachusetts 02138, USA
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18
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Owczarzy R, You Y, Groth CL, Tataurov AV. Stability and mismatch discrimination of locked nucleic acid-DNA duplexes. Biochemistry 2011; 50:9352-67. [PMID: 21928795 PMCID: PMC3201676 DOI: 10.1021/bi200904e] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
Abstract
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Locked nucleic acids (LNA; symbols of bases, +A, +C,
+G, and +T) are introduced into chemically synthesized oligonucleotides
to increase duplex stability and specificity. To understand these
effects, we have determined thermodynamic parameters of consecutive
LNA nucleotides. We present guidelines for the design of LNA oligonucleotides
and introduce free online software that predicts the stability of
any LNA duplex oligomer. Thermodynamic analysis shows that the single
strand–duplex transition is characterized by a favorable enthalpic
change and by an unfavorable loss of entropy. A single LNA modification
confines the local conformation of nucleotides, causing a smaller,
less unfavorable entropic loss when the single strand is restricted
to the rigid duplex structure. Additional LNAs adjacent to the initial
modification appear to enhance stacking and H-bonding interactions
because they increase the enthalpic contributions to duplex stabilization.
New nearest-neighbor parameters correctly forecast the positive and
negative effects of LNAs on mismatch discrimination. Specificity is
enhanced in a majority of sequences and is dependent on mismatch type
and adjacent base pairs; the largest discriminatory boost occurs for
the central +C·C mismatch within the +T+C+C sequence and the
+A·G mismatch within the +T+A+G sequence. LNAs do not affect
specificity in some sequences and even impair it for many +G·T
and +C·A mismatches. The level of mismatch discrimination decreases
the most for the central +G·T mismatch within the +G+G+C sequence
and the +C·A mismatch within the +G+C+G sequence. We hypothesize
that these discrimination changes are not unique features of LNAs
but originate from the shift of the duplex conformation from B-form
to A-form.
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Affiliation(s)
- Richard Owczarzy
- Department of Molecular Genetics and Biophysics, Integrated DNA Technologies, Coralville, Iowa 52241, United States.
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19
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Fratczak A, Kierzek R, Kierzek E. Isoenergetic microarrays to study the structure and interactions of DsrA and OxyS RNAs in two- and three-component complexes. Biochemistry 2011; 50:7647-65. [PMID: 21793590 DOI: 10.1021/bi200463p] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022]
Abstract
Information on the secondary structure and interactions of RNA is important to understand the biological function of RNA as well as in applying RNA as a tool for therapeutic purposes. Recently, the isoenergetic microarray mapping method was developed to improve the prediction of RNA secondary structure. Herein, for the first time, isoenergetic microarrays were used to study the binding of RNA to protein or other RNAs as well as the interactions of two different RNAs and protein in a three-component complex. The RNAs used as models were the regulatory DsrA and OxyS RNAs from Escherichia coli, the fragments of their target mRNAs (fhlA and rpoS), and their complexes with Hfq protein. The collected results showed the advantages and some limitations of microarray mapping.
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Affiliation(s)
- Agata Fratczak
- Institute of Bioorganic Chemistry, Polish Academy of Sciences, Noskowskiego 12/14, 61-704 Poznan, Poland
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20
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Fernández N, García-Sacristán A, Ramajo J, Briones C, Martínez-Salas E. Structural analysis provides insights into the modular organization of picornavirus IRES. Virology 2010; 409:251-61. [PMID: 21056890 DOI: 10.1016/j.virol.2010.10.013] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2010] [Revised: 09/12/2010] [Accepted: 10/08/2010] [Indexed: 10/18/2022]
Abstract
Picornavirus RNA translation is driven by the internal ribosome entry site (IRES) element. The impact of RNA structure on the foot-and-mouth disease virus (FMDV) IRES activity has been analyzed using Selective 2'Hydroxyl Acylation analyzed by Primer Extension (SHAPE) and high throughput analysis of RNA conformation by antisense oligonucleotides printed on microarrays. SHAPE reactivity revealed the self-folding capacity of domain 3 and evidenced a change of RNA structure in a defective GNRA mutant. A modified RNA conformation of this mutant was also evidenced by RNA accessibility to oligonucleotides. Interestingly, comparison of nucleotide reactivity with RNA accessibility revealed that SHAPE reactive nucleotides corresponding to the GNRA motif were not accessible to their respective target oligonucleotides. The differential response was observed both in domain 3 and the entire IRES. Our results demonstrate distant effects of the GNRA motif in the domain 3 RNA conformation, and highlight the modular organization of a picornavirus IRES.
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Affiliation(s)
- Noemí Fernández
- Centro de Biología Molecular Severo Ochoa, Consejo Superior de Investigaciones Científicas, Universidad Autónoma de Madrid, Cantoblanco 28049 Madrid, Spain
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21
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Mathews DH, Moss WN, Turner DH. Folding and finding RNA secondary structure. Cold Spring Harb Perspect Biol 2010; 2:a003665. [PMID: 20685845 DOI: 10.1101/cshperspect.a003665] [Citation(s) in RCA: 106] [Impact Index Per Article: 7.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Optimal exploitation of the expanding database of sequences requires rapid finding and folding of RNAs. Methods are reviewed that automate folding and discovery of RNAs with algorithms that couple thermodynamics with chemical mapping, NMR, and/or sequence comparison. New functional noncoding RNAs in genome sequences can be found by combining sequence comparison with the assumption that functional noncoding RNAs will have more favorable folding free energies than other RNAs. When a new RNA is discovered, experiments and sequence comparison can restrict folding space so that secondary structure can be rapidly determined with the help of predicted free energies. In turn, secondary structure restricts folding in three dimensions, which allows modeling of three-dimensional structure. An example from a domain of a retrotransposon is described. Discovery of new RNAs and their structures will provide insights into evolution, biology, and design of therapeutics. Applications to studies of evolution are also reviewed.
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Affiliation(s)
- David H Mathews
- Department of Biochemistry and Biophysics and Center for RNA Biology, University of Rochester School of Medicine and Dentistry, Rochester, New York 14642, USA
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