1
|
Ballarino M, Pepe G, Helmer-Citterich M, Palma A. Exploring the landscape of tools and resources for the analysis of long non-coding RNAs. Comput Struct Biotechnol J 2023; 21:4706-4716. [PMID: 37841333 PMCID: PMC10568309 DOI: 10.1016/j.csbj.2023.09.041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2023] [Revised: 09/28/2023] [Accepted: 09/28/2023] [Indexed: 10/17/2023] Open
Abstract
In recent years, research on long non-coding RNAs (lncRNAs) has gained considerable attention due to the increasing number of newly identified transcripts. Several characteristics make their functional evaluation challenging, which called for the urgent need to combine molecular biology with other disciplines, including bioinformatics. Indeed, the recent development of computational pipelines and resources has greatly facilitated both the discovery and the mechanisms of action of lncRNAs. In this review, we present a curated collection of the most recent computational resources, which have been categorized into distinct groups: databases and annotation, identification and classification, interaction prediction, and structure prediction. As the repertoire of lncRNAs and their analysis tools continues to expand over the years, standardizing the computational pipelines and improving the existing annotation of lncRNAs will be crucial to facilitate functional genomics studies.
Collapse
Affiliation(s)
- Monica Ballarino
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00161 Rome, Italy
| | - Gerardo Pepe
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy
| | - Manuela Helmer-Citterich
- Department of Biology, University of Rome Tor Vergata, Via della Ricerca Scientifica, 1, 00133 Rome, Italy
| | - Alessandro Palma
- Department of Biology and Biotechnologies “Charles Darwin”, Sapienza University of Rome, Piazzale Aldo Moro 5, 00161 Rome, Italy
| |
Collapse
|
2
|
Web Services for RNA-RNA Interaction Prediction. Methods Mol Biol 2023; 2586:175-195. [PMID: 36705905 DOI: 10.1007/978-1-0716-2768-6_11] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/28/2023]
Abstract
Non-coding RNAs have various biological functions such as translational regulation, and RNA-RNA interactions play essential roles in the mechanisms of action of these RNAs. Therefore, RNA-RNA interaction prediction is an important problem in bioinformatics, and many tools have been developed for the computational prediction of RNA-RNA interactions. In addition to the development of novel algorithms with high accuracy, the development and maintenance of web services is essential for enhancing usability by experimental biologists. In this review, we survey web services for RNA-RNA interaction predictions and introduce how to use primary web services. We present various prediction tools, including general interaction prediction tools, prediction tools for specific RNA classes, and RNA-RNA interaction-based RNA design tools. Additionally, we discuss the future perspectives of the development of RNA-RNA interaction prediction tools and the sustainability of web services.
Collapse
|
3
|
Tummala H, Walne A, Buccafusca R, Alnajar J, Szabo A, Robinson P, McConkie-Rosell A, Wilson M, Crowley S, Kinsler V, Ewins AM, Madapura PM, Patel M, Pontikos N, Codd V, Vulliamy T, Dokal I. Germline thymidylate synthase deficiency impacts nucleotide metabolism and causes dyskeratosis congenita. Am J Hum Genet 2022; 109:1472-1483. [PMID: 35931051 PMCID: PMC9388389 DOI: 10.1016/j.ajhg.2022.06.014] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 06/23/2022] [Indexed: 11/19/2022] Open
Abstract
Dyskeratosis congenita (DC) is an inherited bone-marrow-failure disorder characterized by a triad of mucocutaneous features that include abnormal skin pigmentation, nail dystrophy, and oral leucoplakia. Despite the identification of several genetic variants that cause DC, a significant proportion of probands remain without a molecular diagnosis. In a cohort of eight independent DC-affected families, we have identified a remarkable series of heterozygous germline variants in the gene encoding thymidylate synthase (TYMS). Although the inheritance appeared to be autosomal recessive, one parent in each family had a wild-type TYMS coding sequence. Targeted genomic sequencing identified a specific haplotype and rare variants in the naturally occurring TYMS antisense regulator ENOSF1 (enolase super family 1) inherited from the other parent. Lymphoblastoid cells from affected probands have severe TYMS deficiency, altered cellular deoxyribonucleotide triphosphate pools, and hypersensitivity to the TYMS-specific inhibitor 5-fluorouracil. These defects in the nucleotide metabolism pathway resulted in genotoxic stress, defective transcription, and abnormal telomere maintenance. Gene-rescue studies in cells from affected probands revealed that post-transcriptional epistatic silencing of TYMS is occurring via elevated ENOSF1. These cell and molecular abnormalities generated by the combination of germline digenic variants at the TYMS-ENOSF1 locus represent a unique pathogenetic pathway for DC causation in these affected individuals, whereas the parents who are carriers of either of these variants in a singular fashion remain unaffected.
Collapse
Affiliation(s)
- Hemanth Tummala
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK.
| | - Amanda Walne
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Roberto Buccafusca
- School of Physical and Chemical Sciences, Queen Mary University of London, Mile End, London E1 4NS, UK
| | - Jenna Alnajar
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Anita Szabo
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, 11-43 Bath St, London EC1V 9EL, UK
| | - Peter Robinson
- The Jackson Laboratory for Genomic Medicine, 10 Discovery Dr., Farmington, CT 06032, USA
| | | | - Meredith Wilson
- Department of Clinical Genetics, The Children's Hospital at Westmead, Sydney, Australia
| | - Suzanne Crowley
- Department of Paediatrics, St George's Healthcare NHS Trust, London, UK
| | - Veronica Kinsler
- Department of Paediatric Dermatology, Great Ormond Street Hospital, The Francis Crick Institute, London, UK
| | - Anna-Maria Ewins
- Haematology/Oncology Department, Royal Hospital for Sick Children, Glasgow, UK
| | - Pradeepa M Madapura
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Manthan Patel
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Nikolas Pontikos
- Institute of Ophthalmology, Faculty of Brain Sciences, University College London, 11-43 Bath St, London EC1V 9EL, UK
| | - Veryan Codd
- Department of Cardiovascular Sciences, University of Leicester, Leicester, UK
| | - Tom Vulliamy
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK
| | - Inderjeet Dokal
- Genomics and Child Health, Blizard Institute, Queen Mary University of London, Newark Street, London E1 2AT, UK; Barts Health NHS Trust, London, UK
| |
Collapse
|
4
|
Yoshinaga N, Naito M, Tachihara Y, Boonstra E, Osada K, Cabral H, Uchida S. PEGylation of mRNA by Hybridization of Complementary PEG-RNA Oligonucleotides Stabilizes mRNA without Using Cationic Materials. Pharmaceutics 2021; 13:800. [PMID: 34071840 PMCID: PMC8227728 DOI: 10.3390/pharmaceutics13060800] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/10/2021] [Revised: 05/20/2021] [Accepted: 05/24/2021] [Indexed: 12/19/2022] Open
Abstract
Messenger RNA (mRNA) delivery strategies are required to protect biologically fragile mRNA from ribonuclease (RNase) attacks to achieve efficient therapeutic protein expression. To tackle this issue, most mRNA delivery systems have used cationic components, which form electrostatically driven complexes with mRNA and shield encapsulated mRNA strands. However, cationic materials interact with anionic biomacromolecules in physiological environments, which leads to unspecific reactions and toxicities. To circumvent this issue of cation-based approaches, herein, we propose a cation-free delivery strategy by hybridization of PEGylated RNA oligonucleotides with mRNA. The PEG strands on the mRNA sterically and electrostatically shielded the mRNA, improving mRNA nuclease stability 15-fold after serum incubation compared with unhybridized mRNA. Eventually, the PEGylated mRNA induced nearly 20-fold higher efficiency of reporter protein expression than unhybridized mRNA in cultured cells. This study provides a platform to establish a safe and efficient cation-free mRNA delivery system.
Collapse
Grants
- 20H04524 the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)
- 18K03529 the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)
- JP18K19901 the Ministry of Education, Culture, Sports, Science and Technology, Japan (MEXT)
- JP18ae0201009 Japan Agency for Medical Research and Development
Collapse
Affiliation(s)
- Naoto Yoshinaga
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (N.Y.); (Y.T.); (E.B.)
- RIKEN Center for Sustainable Resource Science, Wako 351-0198, Saitama, Japan
| | - Mitsuru Naito
- Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan;
| | - Yoshihiro Tachihara
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (N.Y.); (Y.T.); (E.B.)
| | - Eger Boonstra
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (N.Y.); (Y.T.); (E.B.)
| | - Kensuke Osada
- National Institute of Radiological Science, 4-9-1 Anagawa, Inage-ku, Chiba-shi 236-8555, Chiba, Japan;
| | - Horacio Cabral
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (N.Y.); (Y.T.); (E.B.)
| | - Satoshi Uchida
- Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; (N.Y.); (Y.T.); (E.B.)
- Graduate School of Medical Science, Kyoto Prefectural University of Medicine, Inamori Memorial Building, 1-5 Shimogamohangi-cho, Sakyo-ku, Kyoto 606-0823, Japan
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki 210-0821, Japan
| |
Collapse
|
5
|
Wang YJ, Li SC, Lin WC, Huang FC. Intracellular Microbiome Profiling of the Acanthamoeba Clinical Isolates from Lens Associated Keratitis. Pathogens 2021; 10:pathogens10030266. [PMID: 33669045 PMCID: PMC7996525 DOI: 10.3390/pathogens10030266] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2021] [Revised: 02/22/2021] [Accepted: 02/23/2021] [Indexed: 11/16/2022] Open
Abstract
Acanthamoeba act as hosts for various microorganisms and pathogens, causing Acanthamoeba Keratitis (AK). To investigate the association between endosymbionts and AK progression, we performed a metagenomics study to characterize the intracellular microbiome from five lenses associated with AK isolates and standard strains to characterize the role of ocular flora in AK progression. The used clinical isolates were axenic cultured from lenses associated with AK patients. AK isolates and standard controls such as 16S ribosomal RNA sequencing techniques were used for analysis. The microbiome compositions and relative abundance values were compared. The orders of Clostridiales and Bacteroidales presented major populations of intracellular microbes belonging to all isolates. Comparison of the different source isolates showed that most of the abundance in keratitis isolates came from Ruminococcus gnavus (121.0 folds), Eubacterium dolichum (54.15 folds), Roseburia faecis (24.51 folds), and Blautia producta (3.15 folds). Further analysis of the relative abundance data from keratitis isolates showed that Blautia producta was positively correlated with the disease course. In contrast, Bacteroides ovatus was found to be abundant in early-stage keratitis isolates. This study reveals the abundant anaerobic Gram-positive rods present in severe keratitis isolate and characterize the association between Acanthamoeba and ocular flora in AK progression.
Collapse
Affiliation(s)
- Yu-Jen Wang
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
| | - Sung-Chou Li
- Genomics and Proteomics Core Laboratory, Department of Medical Research, Kaohsiung Chang Gung Memorial Hospital and Chang Gung University College of Medicine, Kaohsiung 83325, Taiwan;
| | - Wei-Chen Lin
- Institute of Basic Medical Sciences, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan;
- Department of Parasitology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Department of Microbiology and Immunology, College of Medicine, National Cheng Kung University, Tainan 70101, Taiwan
- Correspondence: (W.-C.L.); (F.-C.H.); Tel.: +886-6-2353535 (ext. 5584) (W.-C.L.); +886-2353535 (ext. 5441) (F.-C.H.)
| | - Fu-Chin Huang
- Department of Ophthalmology, National Cheng Kung University Hospital, College of Medicine, National Cheng Kung University, Tainan 70403, Taiwan
- Correspondence: (W.-C.L.); (F.-C.H.); Tel.: +886-6-2353535 (ext. 5584) (W.-C.L.); +886-2353535 (ext. 5441) (F.-C.H.)
| |
Collapse
|
6
|
Cardoso AM, Morais CM, Rebelo O, Tão H, Barbosa M, Pedroso de Lima MC, Jurado AS. Downregulation of long non-protein coding RNA MVIH impairs glioblastoma cell proliferation and invasion through an miR-302a-dependent mechanism. Hum Mol Genet 2021; 30:46-64. [PMID: 33438023 DOI: 10.1093/hmg/ddab009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2020] [Revised: 12/18/2020] [Accepted: 01/05/2021] [Indexed: 02/07/2023] Open
Abstract
Glioblastoma (GB) is the most frequent and malignant type of brain tumor, for which no effective therapy exists. The high proliferative and invasive nature of GB, as well as its acquired resistance to chemotherapy, makes this type of cancer extremely lethal shortly after diagnosis. Long non-protein coding RNAs (lncRNA) are a class of regulatory RNAs whose levels can be dysregulated in the context of diseases, unbalancing several physiological processes. The lncRNA associated with microvascular invasion in hepatocellular carcinoma (lncRNA-MVIH), overexpressed in several cancers, was described to co-precipitate with phosphoglycerate kinase 1 (PGK1), preventing secretion of this enzyme to the extracellular environment and promoting cell migration and invasion. We hypothesized that, by silencing the expression of lncRNA-MVIH, the secretion of PGK1 would increase, reducing GB cell migration and invasion capabilities. We observed that lncRNA-MVIH silencing in human GB cells significantly decreased glycolysis, cell growth, migration, and invasion and sensitized GB cells to cediranib. However, no increase in extracellular PGK1 was observed as a consequence of lncRNA-MVIH silencing, and therefore, we investigated the possibility of a mechanism of miRNA sponge of lncRNA-MVIH being in place. We found that the levels of miR-302a loaded onto RISC increased in GB cells after lncRNA-MVIH silencing, with the consequent downregulation of several miR-302a molecular targets. Our findings suggest a new mechanism of action of lncRNA-MVIH as a sponge of miR-302a. We suggest that lncRNA-MVIH knockdown may be a promising strategy to address GB invasiveness and chemoresistance, holding potential towards its future application in a clinical context.
Collapse
Affiliation(s)
- Ana M Cardoso
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Catarina M Morais
- Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| | - Olinda Rebelo
- Neuropathology Laboratory, Neurology Service, University Hospital of Coimbra, 3004-561 Coimbra, Portugal
| | - Hermínio Tão
- Neurosurgery Service, University Hospital of Coimbra, 33004-561 Coimbra, Portugal
| | - Marcos Barbosa
- Neurosurgery Service, University Hospital of Coimbra, 33004-561 Coimbra, Portugal.,Faculty of Medicine, University of Coimbra, 3000-548 Coimbra, Portugal
| | - Maria C Pedroso de Lima
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal
| | - Amália S Jurado
- CNC - Center for Neuroscience and Cell Biology, CIBB - Centre for Innovative Biomedicine and Biotechnology, University of Coimbra, IIIUC - Institute for Interdisciplinary Research, Coimbra, Portugal.,Department of Life Sciences, University of Coimbra, Calçada Martim de Freitas, 3000-456 Coimbra, Portugal
| |
Collapse
|
7
|
Complex dynamics under tension in a high-efficiency frameshift stimulatory structure. Proc Natl Acad Sci U S A 2019; 116:19500-19505. [PMID: 31409714 DOI: 10.1073/pnas.1905258116] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
Specific structures in mRNA can stimulate programmed ribosomal frameshifting (PRF). PRF efficiency can vary enormously between different stimulatory structures, but the features that lead to efficient PRF stimulation remain uncertain. To address this question, we studied the structural dynamics of the frameshift signal from West Nile virus (WNV), which stimulates -1 PRF at very high levels and has been proposed to form several different structures, including mutually incompatible pseudoknots and a double hairpin. Using optical tweezers to apply tension to single mRNA molecules, mimicking the tension applied by the ribosome during PRF, we found that the WNV frameshift signal formed an unusually large number of different metastable structures, including all of those previously proposed. From force-extension curve measurements, we mapped 2 mutually exclusive pathways for the folding, each encompassing multiple intermediates. We identified the intermediates in each pathway from length changes and the effects of antisense oligomers blocking formation of specific contacts. Intriguingly, the number of transitions between the different conformers of the WNV frameshift signal was maximal in the range of forces applied by the ribosome during -1 PRF. Furthermore, the occupancy of the pseudoknotted conformations was far too low for static pseudoknots to account for the high levels of -1 PRF. These results support the hypothesis that conformational heterogeneity plays a key role in frameshifting and suggest that transitions between different conformers under tension are linked to efficient PRF stimulation.
Collapse
|
8
|
PEG-OligoRNA Hybridization of mRNA for Developing Sterically Stable Lipid Nanoparticles toward In Vivo Administration. Molecules 2019; 24:molecules24071303. [PMID: 30987102 PMCID: PMC6479949 DOI: 10.3390/molecules24071303] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/27/2019] [Revised: 03/22/2019] [Accepted: 04/02/2019] [Indexed: 02/07/2023] Open
Abstract
Lipid nanoparticles (LNPs) exhibit high potential as carriers of messenger RNA (mRNA). However, the arduous preparation process of mRNA-loaded LNPs remains a huge obstacle for their widespread clinical application. Herein, we tackled this issue by mRNA PEGylation through hybridization with polyethylene glycol (PEG)-conjugated RNA oligonucleotides (PEG-OligoRNAs). Importantly, mRNA translational activity was preserved even after hybridization of 20 PEG-OligoRNAs per mRNA. The straightforward mixing of the PEGylated mRNA with lipofectamine LTX, a commercial lipid-based carrier, just by pipetting in aqueous solution, allowed the successful preparation of mRNA-loaded LNPs with a diameter below 100 nm, whereas the use of non-PEGylated mRNA provided large aggregates above 100- and 1000-nm. In vivo, LNPs prepared from PEG-OligoRNA-hybridized mRNA exhibited high structural stability in biological milieu, without forming detectable aggregates in mouse blood after intravenous injection. In contrast, LNPs from non-PEGylated mRNA formed several micrometer-sized aggregates in blood, leading to rapid clearance from blood circulation and deposition of the aggregates in lung capillaries. Our strategy of mRNA PEGylation was also versatile to prevent aggregation of another type of mRNA-loaded LNP, DOTAP/Chol liposomes. Together, our approach provides a simple and robust preparation method to LNPs for in vivo application.
Collapse
|
9
|
Yoshinaga N, Uchida S, Naito M, Osada K, Cabral H, Kataoka K. Induced packaging of mRNA into polyplex micelles by regulated hybridization with a small number of cholesteryl RNA oligonucleotides directed enhanced in vivo transfection. Biomaterials 2019; 197:255-267. [PMID: 30669016 DOI: 10.1016/j.biomaterials.2019.01.023] [Citation(s) in RCA: 35] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2018] [Revised: 12/23/2018] [Accepted: 01/12/2019] [Indexed: 12/22/2022]
Abstract
There has been a progressive interest in the molecular design of polymers and lipids as synthetic carriers for targeting therapeutic mRNA in vivo with the ability to circumvent nuclease attack for treating intractable diseases. Herein, we developed a simple approach to attain one order of magnitude higher nuclease tolerability of mRNA through the formation of polyplex micelles (PMs) by combining ω-cholesteryl (ω-Chol)-poly (ethylene-glycol) (PEG)-polycation block copolymers with mRNA pre-hybridized with cholesterol (Chol)-tethered RNA oligonucleotides (Chol (+)-OligoRNA). Even one or a few short Chol (+)-OligoRNA anchors harboring along the 46-fold longer mRNA strand was sufficient to induce tight mRNA packaging in the PM core, as evidenced by Förster resonance energy transfer (FRET) measurement as well as by a longitudinal relaxation time (T1) measurement using NMR. These results suggest that Chol (+)-OligoRNA on mRNA strand serves as a node to attract ω-Chol moiety of the block copolymers to tighten the mRNA packaging in the PM core. These mRNA loaded PMs showed high tolerability against nuclease attack, and exerted appreciable protein translational activity in cultured cells without any inflammatory responses, achieved by shortening of the length of hybridizing Chol (+)-OligoRNAs to 17 nucleotides. Finally, the Chol (+)-OligoRNA-stabilized PM revealed efficient mRNA introduction into the mouse lungs via intratracheal administration, demonstrating in vivo utility of this formulation.
Collapse
Affiliation(s)
- Naoto Yoshinaga
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Satoshi Uchida
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan; Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan.
| | - Mitsuru Naito
- Center for Disease Biology and Integrative Medicine, Graduate School of Medicine, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan
| | - Kensuke Osada
- National Institute of Radiological Science, 4-9-1 Anagawa, Inage-ku, Chiba-shi, Chiba 263-8555, Japan
| | - Horacio Cabral
- Department of Bioengineering, Graduate School of Engineering, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-8656, Japan
| | - Kazunori Kataoka
- Innovation Center of NanoMedicine (iCONM), Kawasaki Institute of Industrial Promotion, 3-25-14 Tonomachi, Kawasaki-ku, Kawasaki, 210-0821, Japan; Policy Alternatives Research Institute, The University of Tokyo, 7-3-1 Hongo, Bunkyo-ku, Tokyo 113-0033, Japan.
| |
Collapse
|
10
|
Antunes D, Jorge NAN, Caffarena ER, Passetti F. Using RNA Sequence and Structure for the Prediction of Riboswitch Aptamer: A Comprehensive Review of Available Software and Tools. Front Genet 2018; 8:231. [PMID: 29403526 PMCID: PMC5780412 DOI: 10.3389/fgene.2017.00231] [Citation(s) in RCA: 25] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 12/21/2017] [Indexed: 12/14/2022] Open
Abstract
RNA molecules are essential players in many fundamental biological processes. Prokaryotes and eukaryotes have distinct RNA classes with specific structural features and functional roles. Computational prediction of protein structures is a research field in which high confidence three-dimensional protein models can be proposed based on the sequence alignment between target and templates. However, to date, only a few approaches have been developed for the computational prediction of RNA structures. Similar to proteins, RNA structures may be altered due to the interaction with various ligands, including proteins, other RNAs, and metabolites. A riboswitch is a molecular mechanism, found in the three kingdoms of life, in which the RNA structure is modified by the binding of a metabolite. It can regulate multiple gene expression mechanisms, such as transcription, translation initiation, and mRNA splicing and processing. Due to their nature, these entities also act on the regulation of gene expression and detection of small metabolites and have the potential to helping in the discovery of new classes of antimicrobial agents. In this review, we describe software and web servers currently available for riboswitch aptamer identification and secondary and tertiary structure prediction, including applications.
Collapse
Affiliation(s)
- Deborah Antunes
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Natasha A N Jorge
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| | - Ernesto R Caffarena
- Scientific Computing Program (PROCC), Computational Biophysics and Molecular Modeling Group, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil
| | - Fabio Passetti
- Laboratory of Functional Genomics and Bioinformatics, Oswaldo Cruz Institute, Fundação Oswaldo Cruz, Rio de Janeiro, Brazil.,Laboratory of Gene Expression Regulation, Carlos Chagas Institute, Fundação Oswaldo Cruz, Curitiba, Brazil
| |
Collapse
|
11
|
Yun SI, Song BH, Polejaeva IA, Davies CJ, White KL, Lee YM. Comparison of the live-attenuated Japanese encephalitis vaccine SA14-14-2 strain with its pre-attenuated virulent parent SA14 strain: similarities and differences in vitro and in vivo. J Gen Virol 2016; 97:2575-2591. [PMID: 27498826 DOI: 10.1099/jgv.0.000574] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023] Open
Abstract
Japanese encephalitis virus (JEV) is the main cause of acute viral encephalitis, primarily affecting children and young adults in the Asia-Pacific region. JEV is a vaccine-preventable pathogen, with four types of JE vaccine licensed in different regions of the world. To date, the most common JEV strain used in vaccine development and production is SA14-14-2, an attenuated strain derived from its wild-type parental strain SA14. In this study, we directly compared the phenotypic and genotypic characteristics of SA14 and SA14-14-2 to determine the biological and genetic properties associated with their differential virulence. In susceptible BHK-21 cells, SA14-14-2 grew slightly more slowly and formed smaller plaques than SA14, but unlike SA14, it showed almost no expression of the viral protein NS1', the product of a conserved predicted RNA pseudoknot-mediated ribosomal frameshift. In weanling ICR mice, SA14-14-2 was highly attenuated in terms of both neuroinvasiveness and neurovirulence, with its median lethal doses invariably over five logs higher than those of SA14 when inoculated intramuscularly and intracerebrally. Interestingly, the neurovirulence of SA14-14-2 was dependent on mouse age, with the 1- to 7-day-old mice being highly susceptible and the 14- to 21-day-old mice becoming resistant to intracerebral inoculation. At the genome level, SA14-14-2 differed from SA14 by 57 nucleotides, including one silent G-to-A substitution at position 3599 within the predicted RNA pseudoknot for NS1' synthesis; of the 57 differences, 25 resulted in amino acid substitutions. Our data pave the way for the development of new genetically modified JE vaccines.
Collapse
Affiliation(s)
- Sang-Im Yun
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| | - Byung-Hak Song
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| | - Irina A Polejaeva
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| | - Christopher J Davies
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| | - Kenneth L White
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| | - Young-Min Lee
- Department of Animal, Dairy, and Veterinary Sciences, Utah Science Technology and Research, College of Agriculture and Applied Sciences, Utah State University, 4815 Old Main Hill, Logan, UT 84322, USA
| |
Collapse
|
12
|
Vasilakis N, Guzman H, Firth C, Forrester NL, Widen SG, Wood TG, Rossi SL, Ghedin E, Popov V, Blasdell KR, Walker PJ, Tesh RB. Mesoniviruses are mosquito-specific viruses with extensive geographic distribution and host range. Virol J 2014; 11:97. [PMID: 24884700 PMCID: PMC4038087 DOI: 10.1186/1743-422x-11-97] [Citation(s) in RCA: 60] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2014] [Accepted: 05/05/2014] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The family Mesoniviridae (order Nidovirales) comprises of a group of positive-sense, single-stranded RNA ([+]ssRNA) viruses isolated from mosquitoes. FINDINGS Thirteen novel insect-specific virus isolates were obtained from mosquitoes collected in Indonesia, Thailand and the USA. By electron microscopy, the virions appeared as spherical particles with a diameter of ~50 nm. Their 20,129 nt to 20,777 nt genomes consist of positive-sense, single-stranded RNA with a poly-A tail. Four isolates from Houston, Texas, and one isolate from Java, Indonesia, were identified as variants of the species Alphamesonivirus-1 which also includes Nam Dinh virus (NDiV) from Vietnam and Cavally virus (CavV) from Côte d'Ivoire. The eight other isolates were identified as variants of three new mesoniviruses, based on genome organization and pairwise evolutionary distances: Karang Sari virus (KSaV) from Java, Bontag Baru virus (BBaV) from Java and Kalimantan, and Kamphaeng Phet virus (KPhV) from Thailand. In comparison with NDiV, the three new mesoniviruses each contained a long insertion (180 - 588 nt) of unknown function in the 5' region of ORF1a, which accounted for much of the difference in genome size. The insertions contained various short imperfect repeats and may have arisen by recombination or sequence duplication. CONCLUSIONS In summary, based on their genome organizations and phylogenetic relationships, thirteen new viruses were identified as members of the family Mesoniviridae, order Nidovirales. Species demarcation criteria employed previously for mesoniviruses would place five of these isolates in the same species as NDiV and CavV (Alphamesonivirus-1) and the other eight isolates would represent three new mesonivirus species (Alphamesonivirus-5, Alphamesonivirus-6 and Alphamesonivirus-7). The observed spatiotemporal distribution over widespread geographic regions and broad species host range in mosquitoes suggests that mesoniviruses may be common in mosquito populations worldwide.
Collapse
Affiliation(s)
- Nikos Vasilakis
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Hilda Guzman
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Cadhla Firth
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Naomi L Forrester
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| | - Steven G Widen
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555-1079, USA
| | - Thomas G Wood
- Department of Biochemistry and Molecular Biology, The University of Texas Medical Branch, Galveston, TX 77555-1079, USA
| | - Shannan L Rossi
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Elodie Ghedin
- Department of Computational Biology and Center for Vaccine Research, University of Pittsburgh, Pittsburgh, PA 15214, USA
- Current Address: NYU-Biology, Center for Genomics and Systems Biology, New York University, New York, NY 10032, USA
| | - Vsevolov Popov
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
| | - Kim R Blasdell
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Peter J Walker
- CSIRO Animal, Food and Health Sciences, Australian Animal Health Laboratory, Geelong, VIC 3220, Australia
| | - Robert B Tesh
- Department of Pathology and Center for Biodefense and Emerging Infectious Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Center for Tropical Diseases, University of Texas Medical Branch, Galveston, TX 77555-0609, USA
- Institute for Human Infection and Immunity, University of Texas Medical Branch, Galveston, TX 77555-0610, USA
| |
Collapse
|