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Zakh R, Churkin A, Totzeck F, Parr M, Tuller T, Etzion O, Dahari H, Roggendorf M, Frishman D, Barash D. A Mathematical Analysis of HDV Genotypes: From Molecules to Cells. MATHEMATICS (BASEL, SWITZERLAND) 2021; 9:2063. [PMID: 34540628 PMCID: PMC8445514 DOI: 10.3390/math9172063] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Hepatitis D virus (HDV) is classified according to eight genotypes. The various genotypes are included in the HDVdb database, where each HDV sequence is specified by its genotype. In this contribution, a mathematical analysis is performed on RNA sequences in HDVdb. The RNA folding predicted structures of the Genbank HDV genome sequences in HDVdb are classified according to their coarse-grain tree-graph representation. The analysis allows discarding in a simple and efficient way the vast majority of the sequences that exhibit a rod-like structure, which is important for the virus replication, to attempt to discover other biological functions by structure consideration. After the filtering, there remain only a small number of sequences that can be checked for their additional stem-loops besides the main one that is known to be responsible for virus replication. It is found that a few sequences contain an additional stem-loop that is responsible for RNA editing or other possible functions. These few sequences are grouped into two main classes, one that is well-known experimentally belonging to genotype 3 for patients from South America associated with RNA editing, and the other that is not known at present belonging to genotype 7 for patients from Cameroon. The possibility that another function besides virus replication reminiscent of the editing mechanism in HDV genotype 3 exists in HDV genotype 7 has not been explored before and is predicted by eigenvalue analysis. Finally, when comparing native and shuffled sequences, it is shown that HDV sequences belonging to all genotypes are accentuated in their mutational robustness and thermodynamic stability as compared to other viruses that were subjected to such an analysis.
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Affiliation(s)
- Rami Zakh
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Alexander Churkin
- Department of Software Engineering, Sami Shamoon College of Engineering, Beer-Sheva 8410501, Israel
| | - Franziska Totzeck
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Marina Parr
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Tel-Aviv 6997801, Israel
| | - Ohad Etzion
- Soroka University Medical Center, Ben-Gurion University, Beer-Sheva 8410501, Israel
| | - Harel Dahari
- Stritch School of Medicine, Loyola University Chicago, Maywood, IL 60153, USA
| | - Michael Roggendorf
- Institute of Virology, Technische Universität München, 81675 Munich, Germany
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, 85354 Freising, Germany
| | - Danny Barash
- Department of Computer Science, Ben-Gurion University, Beer-Sheva 8410501, Israel
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Zarai Y, Zafrir Z, Siridechadilok B, Suphatrakul A, Roopin M, Julander J, Tuller T. Evolutionary selection against short nucleotide sequences in viruses and their related hosts. DNA Res 2021; 27:5825729. [PMID: 32339222 PMCID: PMC7320823 DOI: 10.1093/dnares/dsaa008] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/02/2020] [Accepted: 04/20/2020] [Indexed: 11/13/2022] Open
Abstract
Viruses are under constant evolutionary pressure to effectively interact with the host intracellular factors, while evading its immune system. Understanding how viruses co-evolve with their hosts is a fundamental topic in molecular evolution and may also aid in developing novel viral based applications such as vaccines, oncologic therapies, and anti-bacterial treatments. Here, based on a novel statistical framework and a large-scale genomic analysis of 2,625 viruses from all classes infecting 439 host organisms from all kingdoms of life, we identify short nucleotide sequences that are under-represented in the coding regions of viruses and their hosts. These sequences cannot be explained by the coding regions’ amino acid content, codon, and dinucleotide frequencies. We specifically show that short homooligonucleotide and palindromic sequences tend to be under-represented in many viruses probably due to their effect on gene expression regulation and the interaction with the host immune system. In addition, we show that more sequences tend to be under-represented in dsDNA viruses than in other viral groups. Finally, we demonstrate, based on in vitro and in vivo experiments, how under-represented sequences can be used to attenuated Zika virus strains.
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Affiliation(s)
- Yoram Zarai
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel
| | - Zohar Zafrir
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | | | - Amporn Suphatrakul
- National Center for Genetic Engineering and Biotechnology, Pathumthani 12120, Thailand
| | - Modi Roopin
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
| | - Justin Julander
- Institute for Antiviral Research, Utah State University, Logan, UT, USA
| | - Tamir Tuller
- Biomedical Engineering Department, Tel Aviv University, Tel Aviv 69978, Israel.,SynVaccine Ltd., Ramat Hachayal, Tel Aviv, Israel
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3
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Kiening M, Ochsenreiter R, Hellinger HJ, Rattei T, Hofacker I, Frishman D. Conserved Secondary Structures in Viral mRNAs. Viruses 2019; 11:E401. [PMID: 31035717 PMCID: PMC6563262 DOI: 10.3390/v11050401] [Citation(s) in RCA: 17] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2019] [Revised: 04/23/2019] [Accepted: 04/26/2019] [Indexed: 12/29/2022] Open
Abstract
RNA secondary structure in untranslated and protein coding regions has been shown to play an important role in regulatory processes and the viral replication cycle. While structures in non-coding regions have been investigated extensively, a thorough overview of the structural repertoire of protein coding mRNAs, especially for viruses, is lacking. Secondary structure prediction of large molecules, such as long mRNAs remains a challenging task, as the contingent of structures a sequence can theoretically fold into grows exponentially with sequence length. We applied a structure prediction pipeline to Viral Orthologous Groups that first identifies the local boundaries of potentially structured regions and subsequently predicts their functional importance. Using this procedure, the orthologous groups were split into structurally homogenous subgroups, which we call subVOGs. This is the first compilation of potentially functional conserved RNA structures in viral coding regions, covering the complete RefSeq viral database. We were able to recover structural elements from previous studies and discovered a variety of novel structured regions. The subVOGs are available through our web resource RNASIV (RNA structure in viruses; http://rnasiv.bio.wzw.tum.de).
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Affiliation(s)
- Michael Kiening
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.
| | - Roman Ochsenreiter
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
| | - Hans-Jörg Hellinger
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Thomas Rattei
- Division of Computational Systems Biology, Department of Microbiology and Ecosystem Science, University of Vienna, Althanstraße 14, 1090 Vienna, Austria.
| | - Ivo Hofacker
- University of Vienna, Faculty of Computer Science, Research Group Bioinformatics and Computational Biology, Währingerstr. 29, 1090 Vienna, Austria.
- University of Vienna, Faculty of Chemistry, Department of Theoretical Chemistry, Währingerstrasse 17, 1090 Vienna, Austria.
| | - Dmitrij Frishman
- Department of Bioinformatics, Wissenschaftszentrum Weihenstephan, Technische Universität München, Maximus-von-Imhof-Forum 3, D-85354 Freising, Germany.
- St Petersburg State Polytechnic University, St Petersburg 195251, Russia.
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Abstract
Background Synthetic virology is an important multidisciplinary scientific field, with emerging applications in biotechnology and medicine, aiming at developing methods to generate and engineer synthetic viruses. In particular, many of the RNA viruses, including among others the Dengue and Zika, are widespread pathogens of significant importance to human health. The ability to design and synthesize such viruses may contribute to exploring novel approaches for developing vaccines and virus based therapies. Results Here we develop a full multidisciplinary pipeline for generation and analysis of synthetic RNA viruses and specifically apply it to Dengue virus serotype 2 (DENV-2). The major steps of the pipeline include comparative genomics of endogenous and synthetic viral strains. Specifically, we show that although the synthetic DENV-2 viruses were found to have lower nucleotide variability, their phenotype, as reflected in the study of the AG129 mouse model morbidity, RNA levels, and neutralization antibodies, is similar or even more pathogenic in comparison to the wildtype master strain. Additionally, the highly variable positions, identified in the analyzed DENV-2 population, were found to overlap with less conserved homologous positions in Zika virus and other Dengue serotypes. These results may suggest that synthetic DENV-2 could enhance virulence if the correct sequence is selected. Conclusions The approach reported in this study can be used to generate and analyze synthetic RNA viruses both on genotypic and on phenotypic level. It could be applied for understanding the functionality and the fitness effects of any set of mutations in viral RNA and for editing RNA viruses for various target applications. Electronic supplementary material The online version of this article (10.1186/s12859-018-2132-3) contains supplementary material, which is available to authorized users.
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Goz E, Mioduser O, Diament A, Tuller T. Evidence of translation efficiency adaptation of the coding regions of the bacteriophage lambda. DNA Res 2017; 24:333-342. [PMID: 28338832 PMCID: PMC5737525 DOI: 10.1093/dnares/dsx005] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2016] [Accepted: 02/01/2017] [Indexed: 11/15/2022] Open
Abstract
Deciphering the way gene expression regulatory aspects are encoded in viral genomes is a challenging mission with ramifications related to all biomedical disciplines. Here, we aimed to understand how the evolution shapes the bacteriophage lambda genes by performing a high resolution analysis of ribosomal profiling data and gene expression related synonymous/silent information encoded in bacteriophage coding regions. We demonstrated evidence of selection for distinct compositions of synonymous codons in early and late viral genes related to the adaptation of translation efficiency to different bacteriophage developmental stages. Specifically, we showed that evolution of viral coding regions is driven, among others, by selection for codons with higher decoding rates; during the initial/progressive stages of infection the decoding rates in early/late genes were found to be superior to those in late/early genes, respectively. Moreover, we argued that selection for translation efficiency could be partially explained by adaptation to Escherichia coli tRNA pool and the fact that it can change during the bacteriophage life cycle. An analysis of additional aspects related to the expression of viral genes, such as mRNA folding and more complex/longer regulatory signals in the coding regions, is also reported. The reported conclusions are likely to be relevant also to additional viruses.
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Affiliation(s)
- Eli Goz
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.,SynVaccine Ltd Ramat Hachayal, Tel Aviv 6971039, Israel
| | - Oriah Mioduser
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Alon Diament
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel
| | - Tamir Tuller
- Department of Biomedical Engineering, Tel-Aviv University, Ramat Aviv 69978, Israel.,SynVaccine Ltd Ramat Hachayal, Tel Aviv 6971039, Israel.,Sagol School of Neuroscience, Tel-Aviv University, Ramat Aviv 69978, Israel
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Faure G, Ogurtsov AY, Shabalina SA, Koonin EV. Adaptation of mRNA structure to control protein folding. RNA Biol 2017; 14:1649-1654. [PMID: 28722509 DOI: 10.1080/15476286.2017.1349047] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022] Open
Abstract
Comparison of mRNA and protein structures shows that highly structured mRNAs typically encode compact protein domains suggesting that mRNA structure controls protein folding. This function is apparently performed by distinct structural elements in the mRNA, which implies 'fine tuning' of mRNA structure under selection for optimal protein folding. We find that, during evolution, changes in the mRNA folding energy follow amino acid replacements, reinforcing the notion of an intimate connection between the structures of a mRNA and the protein it encodes, and the double encoding of protein sequence and folding in the mRNA.
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Affiliation(s)
- Guilhem Faure
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Aleksey Y Ogurtsov
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Svetlana A Shabalina
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
| | - Eugene V Koonin
- a National Center for Biotechnology Information, National Library of Medicine , National Institutes of Health , Bethesda , MD , USA
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Abstract
This paper reports on the various nuances of the origins of life on Earth and highlights the latest findings in that arena as reported at the Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT and LUCA) which was held from the 3–4th November 2016 at the Open University, UK. Although the answers to the question of the origin of life on Earth will not be fathomable anytime soon, a wide variety of subject matter was able to be covered, ranging from examining what constitutes a LUCA, looking at viral connections and “from RNA to DNA”, i.e., could DNA have been formed simultaneously with RNA, rather than RNA first and then describing the emergence of DNA from RNA. Also discussed are proteins and the origins of genomes as well as various ideas that purport to explain the origin of life here on Earth and potentially further afield elsewhere on other planets.
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Affiliation(s)
- Sohan Jheeta
- Network of Researchers on Horizontal Gene Transfer and the Last Universal Common Ancestor (NoR HGT & LUCA), Leeds LS7 3RB, UK.
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