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Sharma A, Chandrashekar CR, Krishna S, Sowdhamini R. Computational Analysis of the Accumulation of Mutations in Therapeutically Important RNA Viral Proteins During Pandemics with Special Emphasis on SARS-CoV-2. J Mol Biol 2024; 436:168716. [PMID: 39047897 DOI: 10.1016/j.jmb.2024.168716] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2024] [Revised: 07/06/2024] [Accepted: 07/18/2024] [Indexed: 07/27/2024]
Abstract
Single stranded RNA viruses are primary causative agents for pandemics, causing extensive morbidity and mortality worldwide. A pivotal question in pandemic preparedness and therapeutic intervention is what are the specific mutations which are more likely to emerge during such global health crises? This study aims to identify markers for mutations with the highest probability of emergence in these pandemics, focusing on the SARS-CoV-2 spike protein, an essential and therapeutically significant viral protein, starting from sequence information from the onset of the pandemic until July 2022. Quite consistently, we observed that emerged mutations tended to demonstrate a high genetic score, which reflects high similarity of the type of codon required for translation between an amino acid and to the mutated one. Further, this pattern is also observed in therapeutically significant proteins of other ssRNA pandemic viruses, including influenza (HA, NA), spike proteins of Ebola, envelope of Dengue and Chikungunya. We propose that the genetic score serves as an initial indicator, preceding the actual impact of the mutation on viral fitness. Finally, we developed a comprehensive computational pipeline to further explore and predict the subsequent effects of mutations on viral fitness. We believe that our pipeline can narrow down and predict future mutations in therapeutically important viral proteins during a pandemic.
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Affiliation(s)
- Abhishek Sharma
- National Centre for Biological Science, GKVK Campus, Bengaluru 560065, India
| | - C R Chandrashekar
- National Centre for Biological Science, GKVK Campus, Bengaluru 560065, India
| | - Sudhir Krishna
- National Centre for Biological Science, GKVK Campus, Bengaluru 560065, India
| | - Ramanathan Sowdhamini
- Molecular Biophysics Unit, Indian Institute of Science, Banagalore 560012, India; Institute of Bioinformatics and Applied Biotechnology, Bangalore, 560100, India.
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2
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Tawfeeq MT, Voordeckers K, van den Berg P, Govers SK, Michiels J, Verstrepen KJ. Mutational robustness and the role of buffer genes in evolvability. EMBO J 2024; 43:2294-2307. [PMID: 38719995 PMCID: PMC11183146 DOI: 10.1038/s44318-024-00109-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/08/2023] [Revised: 03/19/2024] [Accepted: 04/17/2024] [Indexed: 06/19/2024] Open
Abstract
Organisms rely on mutations to fuel adaptive evolution. However, many mutations impose a negative effect on fitness. Cells may have therefore evolved mechanisms that affect the phenotypic effects of mutations, thus conferring mutational robustness. Specifically, so-called buffer genes are hypothesized to interact directly or indirectly with genetic variation and reduce its effect on fitness. Environmental or genetic perturbations can change the interaction between buffer genes and genetic variation, thereby unmasking the genetic variation's phenotypic effects and thus providing a source of variation for natural selection to act on. This review provides an overview of our understanding of mutational robustness and buffer genes, with the chaperone gene HSP90 as a key example. It discusses whether buffer genes merely affect standing variation or also interact with de novo mutations, how mutational robustness could influence evolution, and whether mutational robustness might be an evolved trait or rather a mere side-effect of complex genetic interactions.
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Affiliation(s)
- Mohammed T Tawfeeq
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Karin Voordeckers
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Pieter van den Berg
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
- Department of Biology, KU Leuven, Leuven, Belgium
| | | | - Jan Michiels
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium
| | - Kevin J Verstrepen
- VIB-KU Leuven Center for Microbiology, Leuven, Belgium.
- Department of Microbial and Molecular Systems, KU Leuven, Leuven, Belgium.
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3
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Chan KWK, Bifani AM, Watanabe S, Choy MM, Ooi EE, Vasudevan SG. Tissue-specific expansion of Zika virus isogenic variants drive disease pathogenesis. EBioMedicine 2023; 91:104570. [PMID: 37068347 PMCID: PMC10130475 DOI: 10.1016/j.ebiom.2023.104570] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/23/2022] [Revised: 03/09/2023] [Accepted: 03/30/2023] [Indexed: 04/19/2023] Open
Abstract
BACKGROUND The Asian lineage Zika virus (ZIKV) emerged as a public health emergency in 2016 causing severe neurological pathologies with no apparent historical correlate to the mild, disease-causing innocuous member of the mosquito-borne flavivirus genus that was discovered in Africa in 1947. Replication error rate of RNA viruses combined with viral protein/RNA structural plasticity can lead to evolution of virus-induced pathogenicity that is critical to identify and validate. METHODS Infection studies in cells and A129 interferon alpha/beta receptor deficient mice with ZIKV French Polynesian H/PF/2013 clinical isolate, plaque-purified isogenic clone derivatives as well as infectious cDNA clone derived wild-type and site-specific mutant viruses, were employed together with Next-Generation Sequencing (NGS) to pin-point the contributions of specific viral variants in neurovirulence recapitulated in our ZIKV mouse model. FINDINGS NGS analysis of the low-passage inoculum virus as well as mouse serum, brain and testis derived virus, revealed specific enrichment in the mouse brain that were not found in the other tissues. Specifically, non-structural (NS) protein 2A variant at position 117 along with changes in NS1 and NS4B were uniquely associated with the mouse brain isolate. Mutational analysis of these variants in cDNA infectious clones identified the NS2A A117V as the lethal pathogenic determinant with potential epistatic contribution of NS1 and NS4B variants in ZIKV brain penetrance. INTERPRETATION Our findings confirm that viral subpopulations drive ZIKV neuropathogenicity and identify specific sequence variants that expand in the mouse brain that associates with this phenotype which can serve as predictors of severe epidemics. FUNDING Duke-NUS Khoo Post-doctoral Fellowship Award 2020 (KWKC) and National Medical Research Council of Singapore grants MOH-000524 (OFIRG) (SW) and MOH-OFIRG20nov-0002 (SGV).
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Affiliation(s)
- Kitti Wing Ki Chan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Amanda Makha Bifani
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Satoru Watanabe
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Milly M Choy
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore
| | - Eng Eong Ooi
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore.
| | - Subhash G Vasudevan
- Program in Emerging Infectious Disease, Duke-NUS Medical School, 8 College Road, 169857, Singapore; Department of Microbiology and Immunology, National University of Singapore, 5 Science Drive 2, 117545, Singapore; Institute for Glycomics, Griffith University, Gold Coast Campus, Southport, Queensland, 4222, Australia.
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4
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Wright LR, Wright DL, Weller SK. Viral Nucleases from Herpesviruses and Coronavirus in Recombination and Proofreading: Potential Targets for Antiviral Drug Discovery. Viruses 2022; 14:v14071557. [PMID: 35891537 PMCID: PMC9324378 DOI: 10.3390/v14071557] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2022] [Revised: 07/08/2022] [Accepted: 07/11/2022] [Indexed: 02/05/2023] Open
Abstract
In this review, we explore recombination in two very different virus families that have become major threats to human health. The Herpesviridae are a large family of pathogenic double-stranded DNA viruses involved in a range of diseases affecting both people and animals. Coronaviridae are positive-strand RNA viruses (CoVs) that have also become major threats to global health and economic stability, especially in the last two decades. Despite many differences, such as the make-up of their genetic material (DNA vs. RNA) and overall mechanisms of genome replication, both human herpes viruses (HHVs) and CoVs have evolved to rely heavily on recombination for viral genome replication, adaptation to new hosts and evasion of host immune regulation. In this review, we will focus on the roles of three viral exonucleases: two HHV exonucleases (alkaline nuclease and PolExo) and one CoV exonuclease (ExoN). We will review the roles of these three nucleases in their respective life cycles and discuss the state of drug discovery efforts against these targets.
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Affiliation(s)
- Lee R. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Dennis L. Wright
- Department of Pharmaceutical Sciences, University of Connecticut School of Pharmacy, Storrs, CT 06269, USA; (L.R.W.); (D.L.W.)
| | - Sandra K. Weller
- Department of Molecular Biology and Biophysics, University of Connecticut School of Medicine, 263 Farmington Ave., Farmington, CT 06030, USA
- Correspondence: ; Tel.: +1-(860)-679-2310; Fax: +1-(860)-679-1239
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5
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A BioID-Derived Proximity Interactome for SARS-CoV-2 Proteins. Viruses 2022; 14:v14030611. [PMID: 35337019 PMCID: PMC8951556 DOI: 10.3390/v14030611] [Citation(s) in RCA: 15] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/10/2022] [Revised: 03/09/2022] [Accepted: 03/12/2022] [Indexed: 12/11/2022] Open
Abstract
The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here, the cellular impact of expressing SARS-CoV-2 viral proteins was studied by global proteomic analysis, and proximity biotinylation (BioID) was used to map the SARS-CoV-2 virus–host interactome in human lung cancer-derived cells. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are associated with SARS-CoV-2 proteins. We have established a website to host the proteomic data to allow for public access and continued analysis of host–viral protein associations and whole-cell proteomes of cells expressing the viral–BioID fusion proteins. Furthermore, we identified 66 high-confidence interactions by comparing this study with previous reports, providing a strong foundation for future follow-up studies. Finally, we cross-referenced candidate interactors with the CLUE drug library to identify potential therapeutics for drug-repurposing efforts. Collectively, these studies provide a valuable resource to uncover novel SARS-CoV-2 biology and inform development of antivirals.
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6
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Gene Overlapping as a Modulator of Begomovirus Evolution. Microorganisms 2022; 10:microorganisms10020366. [PMID: 35208820 PMCID: PMC8875319 DOI: 10.3390/microorganisms10020366] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Revised: 02/01/2022] [Accepted: 02/01/2022] [Indexed: 02/06/2023] Open
Abstract
In RNA viruses, which have high mutation—and fast evolutionary— rates, gene overlapping (i.e., genomic regions that encode more than one protein) is a major factor controlling mutational load and therefore the virus evolvability. Although DNA viruses use host high-fidelity polymerases for their replication, and therefore should have lower mutation rates, it has been shown that some of them have evolutionary rates comparable to those of RNA viruses. Notably, these viruses have large proportions of their genes with at least one overlapping instance. Hence, gene overlapping could be a modulator of virus evolution beyond the RNA world. To test this hypothesis, we use the genus Begomovirus of plant viruses as a model. Through comparative genomic approaches, we show that terminal gene overlapping decreases the rate of virus evolution, which is associated with lower frequency of both synonymous and nonsynonymous mutations. In contrast, terminal overlapping has little effect on the pace of virus evolution. Overall, our analyses support a role for gene overlapping in the evolution of begomoviruses and provide novel information on the factors that shape their genetic diversity.
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Oberemok VV, Puzanova YV, Kubyshkin AV, Kamenetsky-Goldstein R. Top Three Strategies of ss(+)RNA Plant Viruses: Great Opportunists and Ecosystem Tuners with a Small Genome. Viruses 2021; 13:v13112304. [PMID: 34835110 PMCID: PMC8620770 DOI: 10.3390/v13112304] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2021] [Revised: 11/08/2021] [Accepted: 11/16/2021] [Indexed: 11/16/2022] Open
Abstract
ss(+)RNA viruses represent the dominant group of plant viruses. They owe their evolutionary superiority to the large number of mutations that occur during replication, courtesy of RNA-dependent RNA polymerase. Natural selection rewards successful viral subtypes, whose effective tuning of the ecosystem regulates the interactions between its participants. Thus, ss(+)RNA viruses act as shuttles for the functionally important genes of the participants in symbiotic relationships within the ecosystem, of which the most common ecological triad is “plant–virus–insect”. Due to their short life cycle and large number of offspring, RNA viruses act as skillful tuners of the ecosystem, which benefits both viruses and the system as a whole. A fundamental understanding of this aspect of the role played by viruses in the ecosystem makes it possible to apply this knowledge to the creation of DNA insecticides. In fact, since the genes that viruses are involved in transferring are functionally important for both insects and plants, silencing these genes (for example, in insects) can be used to regulate the pest population. RNA viruses are increasingly treated not as micropathogens but as necessary regulators of ecosystem balance.
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Affiliation(s)
- Volodymyr V. Oberemok
- Molecular Genetics and Biotechnologies Lab, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Russia;
- Laboratory of Entomology and Phytopathology, Nikitsky Botanical Garden, National Scientific Centre, Russian Academy of Sciences, Yalta 298648, Russia
| | - Yelizaveta V. Puzanova
- Molecular Genetics and Biotechnologies Lab, V.I. Vernadsky Crimean Federal University, Simferopol 295007, Russia;
- Correspondence: ; Tel.: +7-(978)-500-67-58
| | - Anatoly V. Kubyshkin
- Department of General and Clinical Pathophysiology, V.I. Vernadsky Crimean Federal University, Simferopol 295006, Russia;
| | - Rina Kamenetsky-Goldstein
- Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Rishon LeZion 7505101, Israel;
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Upadhyay V, Lucas A, Panja S, Miyauchi R, Mallela KMG. Receptor binding, immune escape, and protein stability direct the natural selection of SARS-CoV-2 variants. J Biol Chem 2021; 297:101208. [PMID: 34543625 PMCID: PMC8445900 DOI: 10.1016/j.jbc.2021.101208] [Citation(s) in RCA: 29] [Impact Index Per Article: 9.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 01/04/2023] Open
Abstract
Emergence of new severe acute respiratory syndrome coronavirus 2 variants has raised concerns related to the effectiveness of vaccines and antibody therapeutics developed against the unmutated wildtype virus. Here, we examined the effect of the 12 most commonly occurring mutations in the receptor-binding domain of the spike protein on its expression, stability, activity, and antibody escape potential. Stability was measured using thermal denaturation, and the activity and antibody escape potential were measured using isothermal titration calorimetry in terms of binding to the human angiotensin-converting enzyme 2 and to neutralizing human antibody CC12.1, respectively. Our results show that mutants differ in their expression levels. Of the eight best-expressed mutants, two (N501Y and K417T/E484K/N501Y) showed stronger affinity to angiotensin-converting enzyme 2 compared with the wildtype, whereas four (Y453F, S477N, T478I, and S494P) had similar affinity and two (K417N and E484K) had weaker affinity than the wildtype. Compared with the wildtype, four mutants (K417N, Y453F, N501Y, and K417T/E484K/N501Y) had weaker affinity for the CC12.1 antibody, whereas two (S477N and S494P) had similar affinity, and two (T478I and E484K) had stronger affinity than the wildtype. Mutants also differ in their thermal stability, with the two least stable mutants showing reduced expression. Taken together, these results indicate that multiple factors contribute toward the natural selection of variants, and all these factors need to be considered to understand the evolution of the virus. In addition, since not all variants can escape a given neutralizing antibody, antibodies to treat new variants can be chosen based on the specific mutations in that variant.
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Affiliation(s)
- Vaibhav Upadhyay
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Alexandra Lucas
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Sudipta Panja
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Ryuki Miyauchi
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA
| | - Krishna M G Mallela
- Department of Pharmaceutical Sciences, Skaggs School of Pharmacy and Pharmaceutical Sciences, University of Colorado Anschutz Medical Campus, Aurora, Colorado, USA.
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May DG, Martin-Sancho L, Anschau V, Liu S, Chrisopulos RJ, Scott KL, Halfmann CT, Peña RD, Pratt D, Campos AR, Roux KJ. A BioID-derived proximity interactome for SARS-CoV-2 proteins. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2021. [PMID: 34580671 PMCID: PMC8475972 DOI: 10.1101/2021.09.17.460814] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 01/10/2023]
Abstract
The novel coronavirus SARS-CoV-2 is responsible for the ongoing COVID-19 pandemic and has caused a major health and economic burden worldwide. Understanding how SARS-CoV-2 viral proteins behave in host cells can reveal underlying mechanisms of pathogenesis and assist in development of antiviral therapies. Here we use BioID to map the SARS-CoV-2 virus-host interactome using human lung cancer derived A549 cells expressing individual SARS-CoV-2 viral proteins. Functional enrichment analyses revealed previously reported and unreported cellular pathways that are in association with SARS-CoV-2 proteins. We have also established a website to host the proteomic data to allow for public access and continued analysis of host-viral protein associations and whole-cell proteomes of cells expressing the viral-BioID fusion proteins. Collectively, these studies provide a valuable resource to potentially uncover novel SARS-CoV-2 biology and inform development of antivirals.
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10
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Merleau NSC, Pénisson S, Gerrish PJ, Elena SF, Smerlak M. Why are viral genomes so fragile? The bottleneck hypothesis. PLoS Comput Biol 2021; 17:e1009128. [PMID: 34237053 PMCID: PMC8291636 DOI: 10.1371/journal.pcbi.1009128] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2021] [Revised: 07/20/2021] [Accepted: 05/28/2021] [Indexed: 11/29/2022] Open
Abstract
If they undergo new mutations at each replication cycle, why are RNA viral genomes so fragile, with most mutations being either strongly deleterious or lethal? Here we provide theoretical and numerical evidence for the hypothesis that genetic fragility is partly an evolutionary response to the multiple population bottlenecks experienced by viral populations at various stages of their life cycles. Modelling within-host viral populations as multi-type branching processes, we show that mutational fragility lowers the rate at which Muller’s ratchet clicks and increases the survival probability through multiple bottlenecks. In the context of a susceptible-exposed-infectious-recovered epidemiological model, we find that the attack rate of fragile viral strains can exceed that of more robust strains, particularly at low infectivities and high mutation rates. Our findings highlight the importance of demographic events such as transmission bottlenecks in shaping the genetic architecture of viral pathogens. Given that most mutations are deleterious, high mutation rates carry a significant evolutionary cost. To reduce this burden, an obvious evolutionary solution would be to reduce the fitness cost of mutations by becoming more robust; this solution is indeed selected in populations of constantly large size. Here, we show that when populations regularly experience bottlenecks, as viruses do upon transmission to a new host, a less obvious solution becomes more viable: namely, to increase the fitness cost of mutations so that unfit mutants are less likely to fix at each passage. This could explain why viruses—especially RNA viruses—do in fact have very fragile genomes.
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Affiliation(s)
| | - Sophie Pénisson
- Université Paris Est Créteil, CNRS, LAMA, Creteil, France
- Université Gustave Eiffel, LAMA, Marne-la-Vallée, France
| | - Philip J. Gerrish
- University of New Mexico, Albuquerque, New Mexico, United States of America
| | - Santiago F. Elena
- Instituto de Biología Integrativa de Sistemas (ISysBio), CSIC-Universitat de València, València, Spain
- Santa Fe Institute, Santa Fe, New Mexico, United States of America
| | - Matteo Smerlak
- Max Planck Institute for Mathematics in the Sciences, Leipzig, Germany
- * E-mail:
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Recovery of a Far-Eastern Strain of Tick-Borne Encephalitis Virus with a Full-Length Infectious cDNA Clone. Virol Sin 2021; 36:1375-1386. [PMID: 34191223 DOI: 10.1007/s12250-021-00396-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Accepted: 03/15/2021] [Indexed: 12/16/2022] Open
Abstract
Tick-borne encephalitis virus (TBEV) is a pathogenic virus known to cause central nervous system (CNS) diseases in humans, and has become an increasing public health threat nowadays. The rates of TBEV infection in the endemic countries are increasing. However, there is no effective antiviral against the disease. This underscores the urgent need for tools to study the emergence and pathogenesis of TBEV and to accelerate the development of vaccines and antivirals. In this study, we reported an infectious cDNA clone of TBEV that was isolated in China (the WH2012 strain). A beta-globin intron was inserted in the coding region of nonstructural protein 1 (NS1) gene to improve the stability of viral genome in bacteria. In mammalian cells, the inserted intron was excised and spliced precisely, which did not lead to the generation of inserted mutants. High titers of infectious progeny viruses were generated after the transfection of the infectious clone. The cDNA-derived TBEV replicated efficiently, and caused typical cytopathic effect (CPE) and plaques in BHK-21 cells. In addition, the CPE and growth curve of cDNA-derived virus were similar to that of its parental isolate in cells. Together, we have constructed the first infectious TBEV cDNA clone in China, and the clone can be used to investigate the genetic determinants of TBEV virulence and disease pathogenesis, and to develop countermeasures against the virus.
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Abstract
RNA viruses, such as hepatitis C virus (HCV), influenza virus, and SARS-CoV-2, are notorious for their ability to evolve rapidly under selection in novel environments. It is known that the high mutation rate of RNA viruses can generate huge genetic diversity to facilitate viral adaptation. However, less attention has been paid to the underlying fitness landscape that represents the selection forces on viral genomes, especially under different selection conditions. Here, we systematically quantified the distribution of fitness effects of about 1,600 single amino acid substitutions in the drug-targeted region of NS5A protein of HCV. We found that the majority of nonsynonymous substitutions incur large fitness costs, suggesting that NS5A protein is highly optimized. The replication fitness of viruses is correlated with the pattern of sequence conservation in nature, and viral evolution is constrained by the need to maintain protein stability. We characterized the adaptive potential of HCV by subjecting the mutant viruses to selection by the antiviral drug daclatasvir at multiple concentrations. Both the relative fitness values and the number of beneficial mutations were found to increase with the increasing concentrations of daclatasvir. The changes in the spectrum of beneficial mutations in NS5A protein can be explained by a pharmacodynamics model describing viral fitness as a function of drug concentration. Overall, our results show that the distribution of fitness effects of mutations is modulated by both the constraints on the biophysical properties of proteins (i.e., selection pressure for protein stability) and the level of environmental stress (i.e., selection pressure for drug resistance). IMPORTANCE Many viruses adapt rapidly to novel selection pressures, such as antiviral drugs. Understanding how pathogens evolve under drug selection is critical for the success of antiviral therapy against human pathogens. By combining deep sequencing with selection experiments in cell culture, we have quantified the distribution of fitness effects of mutations in hepatitis C virus (HCV) NS5A protein. Our results indicate that the majority of single amino acid substitutions in NS5A protein incur large fitness costs. Simulation of protein stability suggests viral evolution is constrained by the need to maintain protein stability. By subjecting the mutant viruses to selection under an antiviral drug, we find that the adaptive potential of viral proteins in a novel environment is modulated by the level of environmental stress, which can be explained by a pharmacodynamics model. Our comprehensive characterization of the fitness landscapes of NS5A can potentially guide the design of effective strategies to limit viral evolution.
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Heo JI, Yu J, Choi H, Kim KH. The Signatures of Natural Selection and Molecular Evolution in Fusarium graminearum Virus 1. Front Microbiol 2020; 11:600775. [PMID: 33281800 PMCID: PMC7688778 DOI: 10.3389/fmicb.2020.600775] [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: 08/31/2020] [Accepted: 10/27/2020] [Indexed: 11/21/2022] Open
Abstract
Fusarium graminearum virus 1 (FgV1) is a positive-sense ssRNA virus that confers hypovirulence in its fungal host, Fusarium graminearum. Like most mycoviruses, FgV1 exists in fungal cells, lacks an extracellular life cycle, and is therefore transmitted during sporulation or hyphal anastomosis. To understand FgV1 evolution and/or adaptation, we conducted mutation accumulation (MA) experiments by serial passage of FgV1 alone or with FgV2, 3, or 4 in F. graminearum. We expected that the effects of positive selection would be highly limited because of repeated bottleneck events. To determine whether selection on the virus was positive, negative, or neutral, we assessed both the phenotypic traits of the host fungus and the RNA sequences of FgV1. We inferred that there was positive selection on beneficial mutations in FgV1 based on the ratio of non-synonymous to synonymous substitutions (dN/dS), on the ratio of radical to conservation amino acid replacements (pNR/pNC), and by changes in the predicted protein structures. In support of this inference, we found evidence of positive selection only in the open reading frame 4 (ORF4) protein of DK21/FgV1 (MA line 1); mutations at amino acids 163A and 289H in the ORF4 of MA line 1 affected the entire structure of the protein predicted to be under positive selection. We also found, however, that deleterious mutations were a major driving force in viral evolution during serial passages. Linear relationships between changes in viral fitness and the number of mutations in each MA line demonstrated that some deleterious mutations resulted in fitness decline. Several mutations in MA line 1 were not shared with any of the other four MA lines (PH-1/FgV1, PH-1/FgV1 + 2, PH-1/FgV1 + 3, and PH-1/FgV1 + 4). This suggests that evolutionary pathways of the virus could differ with respect to hosts and also with respect to co-infecting viruses. The data also suggested that the differences among MA lines might also be explained by mutational robustness and other unidentified factors. Additional research is needed to clarify the effects of virus co-infection on the adaptation or evolution of FgV1 to its environments.
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Affiliation(s)
- Jeong-In Heo
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Jisuk Yu
- Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea
| | - Hoseong Choi
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
| | - Kook-Hyung Kim
- Department of Agricultural Biotechnology, College of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea.,Plant Genomics and Breeding Institute, Seoul National University, Seoul, South Korea.,Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul, South Korea
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14
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Satyam R, Jha NK, Kar R, Jha SK, Sharma A, Kumar D, Nand P, Ruokolainen J, Kesari KK, Kamal MA. Deciphering the SSR incidences across viral members of Coronaviridae family. Chem Biol Interact 2020; 331:109226. [PMID: 32971122 PMCID: PMC7505113 DOI: 10.1016/j.cbi.2020.109226] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2020] [Revised: 08/05/2020] [Accepted: 08/11/2020] [Indexed: 12/19/2022]
Abstract
Presence of Simple Sequence Repeats (SSRs), both in genic and intergenic regions, have been widely studied in eukaryotes, prokaryotes, and viruses. In the current study, we undertook a survey to analyze the frequency and distribution of microsatellites or SSRs in multiple genomes of Coronaviridae members. We successfully identified 919 SSRs with length ≥12 bp across 55 reference genomes majority of which (838 SSRs) were found abundant in genic regions. The in-silico analysis further identified the preferential abundance of hexameric SSRs than any other size-based motif class. Our analysis shows that the genome size and GC content of the genome had a weak influence on SSR frequency and density. However, we find a positive correlation of SSRs GC content with genomic GC content. We also report relatively low abundances of all theoretically possible 501 repeat motif classes in all the genomes of Coronaviridae. The majority of SSRs were AT-rich. Overall, we see an underrepresentation of SSRs across the genomes of Coronaviridae. Besides, our integrative study highlights the presence of SSRs in ORF1ab (nsp3, nsp4, nsp5A_3CLpro and nsp5B_3CLpro, nsp6, nsp10, nsp12, nsp13, & nsp15 domains), S, ORF3a, ORF7a, N & 3' UTR regions of SARS-CoV-2 and harbours multiple mutations (3'UTR and ORF1ab SSRs serving as major mutational hotspots). This indicates the genic SSRs are under selection pressure against mutations that might alter the reading frame and at the same time responsible for rapid protein evolution. Our preliminary results indicate the significance of the limited repertoire of SSRs in the genomes of Coronaviridae.
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Affiliation(s)
- Rohit Satyam
- Department of Biotechnology, Noida Institute of Engineering and Technology (NIET), Greater Noida, India
| | - Niraj Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, 201310, India.
| | - Rohan Kar
- Indian Institute of Management Ahmedabad (IIMA), Gujarat, 380015, India
| | - Saurabh Kumar Jha
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, 201310, India
| | - Ankur Sharma
- Department of Life Science, School of Basic Science & Research, Sharda University, Greater Noida, 201310, India
| | - Dhruv Kumar
- Amity Institute of Molecular Medicine and Stem Cell Research (AIMMSCR), Amity University Uttar Pradesh, Noida, 201313, India
| | - Parma Nand
- Department of Biotechnology, School of Engineering & Technology (SET), Sharda University, Greater Noida, 201310, India
| | | | | | - Mohammad Amjad Kamal
- King Fahd Medical Research Center, King Abdulaziz University, P. O. Box 80216, Jeddah, 21589, Saudi Arabia; Enzymoics, Novel Global Community Educational Foundation, 7 Peterlee Place, Hebersham, NSW, 2770, Australia
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15
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Butković A, González R, Cobo I, Elena SF. Adaptation of turnip mosaic potyvirus to a specific niche reduces its genetic and environmental robustness. Virus Evol 2020; 6:veaa041. [PMID: 32782826 PMCID: PMC7409916 DOI: 10.1093/ve/veaa041] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022] Open
Abstract
Robustness is the preservation of the phenotype in the face of genetic and environmental perturbations. It has been argued that robustness must be an essential fitness component of RNA viruses owed to their small and compacted genomes, high mutation rates and living in ever-changing environmental conditions. Given that genetic robustness might hamper possible beneficial mutations, it has been suggested that genetic robustness can only evolve as a side-effect of the evolution of robustness mechanisms specific to cope with environmental perturbations, a theory known as plastogenetic congruence. However, empirical evidences from different viral systems are contradictory. To test how adaptation to a particular environment affects both environmental and genetic robustness, we have used two strains of turnip mosaic potyvirus (TuMV) that differ in their degree of adaptation to Arabidopsis thaliana at a permissive temperature. We show that the highly adapted strain is strongly sensitive to the effect of random mutations and to changes in temperature conditions. In contrast, the non-adapted strain shows more robustness against both the accumulation of random mutations and drastic changes in temperature conditions. Together, these results are consistent with the predictions of the plastogenetic congruence theory, suggesting that genetic and environmental robustnesses may be two sides of the same coin for TuMV.
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Affiliation(s)
- Anamarija Butković
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980 Valencia, Spain
| | - Rubén González
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980 Valencia, Spain
| | - Inés Cobo
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980 Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas (I2SysBio), CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, 46980 Valencia, Spain.,The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
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16
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González R, Butković A, Elena SF. From foes to friends: Viral infections expand the limits of host phenotypic plasticity. Adv Virus Res 2020; 106:85-121. [PMID: 32327149 DOI: 10.1016/bs.aivir.2020.01.003] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023]
Abstract
Phenotypic plasticity enables organisms to survive in the face of unpredictable environmental stress. Intimately related to the notion of phenotypic plasticity is the concept of the reaction norm that places phenotypic plasticity in the context of a genotype-specific response to environmental gradients. Whether reaction norms themselves evolve and which factors might affect their shape has been the object of intense debates among evolutionary biologists along the years. Since their discovery, viruses have been considered as pathogens. However, new viromic techniques and a shift in conceptual paradigms are showing that viruses are mostly non-pathogenic ubiquitous entities. Recent studies have shown how viral infections can even be beneficial for their hosts. This may happen especially in the context of stressed hosts, where the virus infection can induce beneficial changes in the host's physiological homeostasis, hence changing the shape of the reaction norm. Despite the fact that underlying physiological mechanisms and evolutionary dynamics are still not well understood, such beneficial interactions are being discovered in a growing number of plant-virus systems. Here, we aim to review these disperse studies and place them into the context of phenotypic plasticity and the evolution of reaction norms. This is an emerging field that is posing many questions that still need to be properly answered. The answers would clearly interest virologists, plant pathologists and evolutionary biologists and likely they will suggest possible future biotechnological applications, including the development of crops with higher survival rates and yield under adverse environmental situations.
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Affiliation(s)
- Rubén González
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain.
| | - Anamarija Butković
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Valencia, Spain; The Santa Fe Institute, Santa Fe, NM, United States.
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17
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Franklin J, LaBar T, Adami C. Mapping the Peaks: Fitness Landscapes of the Fittest and the Flattest. ARTIFICIAL LIFE 2019; 25:250-262. [PMID: 31397601 DOI: 10.1162/artl_a_00296] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Populations exposed to a high mutation rate harbor abundant deleterious genetic variation, leading to depressed mean fitness. This reduction in mean fitness presents an opportunity for selection to restore fitness through the evolution of mutational robustness. In extreme cases, selection for mutational robustness can lead to flat genotypes (with low fitness but high robustness) outcompeting fit genotypes (with high fitness but low robustness)-a phenomenon known as survival of the flattest. While this effect was previously explored using the digital evolution system Avida, a complete analysis of the local fitness landscapes of fit and flat genotypes has been lacking, leading to uncertainty about the genetic basis of the survival-of-the-flattest effect. Here, we repeated the survival-of-the-flattest study and analyzed the mutational neighborhoods of fit and flat genotypes. We found that the flat genotypes, compared to the fit genotypes, had a reduced likelihood of deleterious mutations as well as an increased likelihood of neutral and, surprisingly, of lethal mutations. This trend holds for mutants one to four substitutions away from the wild-type sequence. We also found that flat genotypes have, on average, no epistasis between mutations, while fit genotypes have, on average, positive epistasis. Our results demonstrate that the genetic causes of mutational robustness on complex fitness landscapes are multifaceted. While the traditional idea of the survival of the flattest emphasized the evolution of increased neutrality, others have argued for increased mutational sensitivity in response to strong mutational loads. Our results show that both increased neutrality and increased lethality can lead to the evolution of mutational robustness. Furthermore, strong negative epistasis is not required for mutational sensitivity to lead to mutational robustness. Overall, these results suggest that mutational robustness is achieved by minimizing heritable deleterious variation.
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Affiliation(s)
- Joshua Franklin
- Michigan State University, Department of Microbiology and Molecular Genetics
| | - Thomas LaBar
- Harvard University, Department of Molecular and Cellular Biology.
- Michigan State University, BEACON Center for the Study of Evolution in Action
| | - Christoph Adami
- Michigan State University, Department of Microbiology and Molecular Genetics; Department of Ecology, Evolutionary Biology, and Behavior; BEACON Center for the Study of Evolution in Action
- Arizona State University, Department of Physics and Astronomy
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18
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Abstract
RNA viruses are diverse, abundant, and rapidly evolving. Genetic data have been generated from virus populations since the late 1970s and used to understand their evolution, emergence, and spread, culminating in the generation and analysis of many thousands of viral genome sequences. Despite this wealth of data, evolutionary genetics has played a surprisingly small role in our understanding of virus evolution. Instead, studies of RNA virus evolution have been dominated by two very different perspectives, the experimental and the comparative, that have largely been conducted independently and sometimes antagonistically. Here, we review the insights that these two approaches have provided over the last 40 years. We show that experimental approaches using in vitro and in vivo laboratory models are largely focused on short-term intrahost evolutionary mechanisms, and may not always be relevant to natural systems. In contrast, the comparative approach relies on the phylogenetic analysis of natural virus populations, usually considering data collected over multiple cycles of virus-host transmission, but is divorced from the causative evolutionary processes. To truly understand RNA virus evolution it is necessary to meld experimental and comparative approaches within a single evolutionary genetic framework, and to link viral evolution at the intrahost scale with that which occurs over both epidemiological and geological timescales. We suggest that the impetus for this new synthesis may come from methodological advances in next-generation sequencing and metagenomics.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales 2109, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, The University of Sydney, New South Wales 2006, Australia
- Charles Perkins Centre, The University of Sydney, New South Wales 2006, Australia
- School of Life and Environmental Sciences, The University of Sydney, New South Wales 2006, Australia
- Sydney Medical School, The University of Sydney, New South Wales 2006, Australia
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19
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Abstract
How virulence evolves after a virus jumps to a new host species is central to disease emergence. Our current understanding of virulence evolution is based on insights drawn from two perspectives that have developed largely independently: long-standing evolutionary theory based on limited real data examples that often lack a genomic basis, and experimental studies of virulence-determining mutations using cell culture or animal models. A more comprehensive understanding of virulence mutations and their evolution can be achieved by bridging the gap between these two research pathways through the phylogenomic analysis of virus genome sequence data as a guide to experimental study.
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Affiliation(s)
- Jemma L Geoghegan
- Department of Biological Sciences, Macquarie University, Sydney, New South Wales, Australia
| | - Edward C Holmes
- Marie Bashir Institute for Infectious Diseases and Biosecurity, Charles Perkins Centre, School of Life and Environmental Sciences and Sydney Medical School, The University of Sydney, Sydney, New South Wales, Australia.
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20
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Alves MP, Vielle NJ, Thiel V, Pfaender S. Research Models and Tools for the Identification of Antivirals and Therapeutics against Zika Virus Infection. Viruses 2018; 10:v10110593. [PMID: 30380760 PMCID: PMC6265910 DOI: 10.3390/v10110593] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2018] [Revised: 10/24/2018] [Accepted: 10/26/2018] [Indexed: 12/13/2022] Open
Abstract
Zika virus recently re-emerged and caused global outbreaks mainly in Central Africa, Southeast Asia, the Pacific Islands and in Central and South America. Even though there is a declining trend, the virus continues to spread throughout different geographical regions of the world. Since its re-emergence in 2015, massive advances have been made regarding our understanding of clinical manifestations, epidemiology, genetic diversity, genomic structure and potential therapeutic intervention strategies. Nevertheless, treatment remains a challenge as there is no licensed effective therapy available. This review focuses on the recent advances regarding research models, as well as available experimental tools that can be used for the identification and characterization of potential antiviral targets and therapeutic intervention strategies.
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Affiliation(s)
- Marco P Alves
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Nathalie J Vielle
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
- Graduate School for Cellular and Biomedical Sciences, University of Bern, 3012 Bern, Switzerland.
| | - Volker Thiel
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
| | - Stephanie Pfaender
- Institute of Virology and Immunology, 3012 Bern, Switzerland.
- Department of Infectious Diseases and Pathobiology, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland.
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21
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Fornés J, Tomás Lázaro J, Alarcón T, Elena SF, Sardanyés J. Viral replication modes in single-peak fitness landscapes: A dynamical systems analysis. J Theor Biol 2018; 460:170-183. [PMID: 30300648 DOI: 10.1016/j.jtbi.2018.10.007] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Revised: 08/30/2018] [Accepted: 10/02/2018] [Indexed: 12/11/2022]
Abstract
Positive-sense, single-stranded RNA viruses are important pathogens infecting almost all types of organisms. Experimental evidence from distributions of mutations and from viral RNA amplification suggest that these pathogens may follow different RNA replication modes, ranging from the stamping machine replication (SMR) to the geometric replication (GR) mode. Although previous theoretical work has focused on the evolutionary dynamics of RNA viruses amplifying their genomes with different strategies, little is known in terms of the bifurcations and transitions involving the so-called error threshold (mutation-induced dominance of mutants) and lethal mutagenesis (extinction of all sequences due to mutation accumulation and demographic stochasticity). Here we analyze a dynamical system describing the intracellular amplification of viral RNA genomes evolving on a single-peak fitness landscape focusing on three cases considering neutral, deleterious, and lethal mutants. We analytically derive the critical mutation rates causing lethal mutagenesis and error threshold, governed by transcritical bifurcations that depend on parameters α (parameter introducing the mode of replication), replicative fitness of mutants (k1), and on the spontaneous degradation rates of the sequences (ϵ). Our results relate the error catastrophe with lethal mutagenesis in a model with continuous populations of viral genomes. The former case involves dominance of the mutant sequences, while the latter, a deterministic extinction of the viral RNAs during replication due to increased mutation. For the lethal case the critical mutation rate involving lethal mutagenesis is μc=1-ɛ/α. Here, the SMR involves lower critical mutation rates, being the system more robust to lethal mutagenesis replicating closer to the GR mode. This result is also found for the neutral and deleterious cases, but for these later cases lethal mutagenesis can shift to the error threshold once the replication mode surpasses a threshold given by α=ϵ/k1.
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Affiliation(s)
- Joan Fornés
- Departament de Matemàtiques, Universitat Politècnica de Catalunya, Av Diagonal, 647, Barcelona 08028, Spain
| | - J Tomás Lázaro
- Departament de Matemàtiques, Universitat Politècnica de Catalunya, Av Diagonal, 647, Barcelona 08028, Spain; Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain
| | - Tomás Alarcón
- Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; ICREA, Pg. Lluis Companys 23, Barcelona 08010, Spain; Departament de Matemàtiques, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Santiago F Elena
- Instituto de Biología Integrativa de Sistemas, CSIC-Universitat de València, Parc Cientific UV, Catedrático Agustín Escardino 9, Paterna, València 46980, Spain; The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM 87501, USA
| | - Josep Sardanyés
- Centre de Recerca Matemàtica, Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain; Barcelona Graduate School of Mathematics (BGSMath) Campus de Bellaterra, Edifici C, Bellaterra, Barcelona 08193, Spain.
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22
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Dolan PT, Whitfield ZJ, Andino R. Mechanisms and Concepts in RNA Virus Population Dynamics and Evolution. Annu Rev Virol 2018; 5:69-92. [PMID: 30048219 DOI: 10.1146/annurev-virology-101416-041718] [Citation(s) in RCA: 78] [Impact Index Per Article: 13.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
RNA viruses are unique in their evolutionary capacity, exhibiting high mutation rates and frequent recombination. They rapidly adapt to environmental changes, such as shifts in immune pressure or pharmacological challenge. The evolution of RNA viruses has been brought into new focus with the recent developments of genetic and experimental tools to explore and manipulate the evolutionary dynamics of viral populations. These studies have uncovered new mechanisms that enable viruses to overcome evolutionary challenges in the environment and have emphasized the intimate relationship of viral populations with evolution. Here, we review some of the emerging viral and host mechanisms that underlie the evolution of RNA viruses. We also discuss new studies that demonstrate that the relationship between evolutionary dynamics and virus biology spans many spatial and temporal scales, affecting transmission dynamics within and between hosts as well as pathogenesis.
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Affiliation(s)
- Patrick T Dolan
- Department of Biology, Stanford University, Stanford, California 94305, USA.,Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Zachary J Whitfield
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
| | - Raul Andino
- Department of Microbiology and Immunology, University of California, San Francisco, California 94143, USA;
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23
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Du Y, Xin L, Shi Y, Zhang TH, Wu NC, Dai L, Gong D, Brar G, Shu S, Luo J, Reiley W, Tseng YW, Bai H, Wu TT, Wang J, Shu Y, Sun R. Genome-wide identification of interferon-sensitive mutations enables influenza vaccine design. Science 2018; 359:290-296. [PMID: 29348231 DOI: 10.1126/science.aan8806] [Citation(s) in RCA: 56] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2017] [Accepted: 11/15/2017] [Indexed: 12/11/2022]
Abstract
In conventional attenuated viral vaccines, immunogenicity is often suboptimal. Here we present a systematic approach for vaccine development that eliminates interferon (IFN)-modulating functions genome-wide while maintaining virus replication fitness. We applied a quantitative high-throughput genomics system to influenza A virus that simultaneously measured the replication fitness and IFN sensitivity of mutations across the entire genome. By incorporating eight IFN-sensitive mutations, we generated a hyper-interferon-sensitive (HIS) virus as a vaccine candidate. HIS virus is highly attenuated in IFN-competent hosts but able to induce transient IFN responses, elicits robust humoral and cellular immune responses, and provides protection against homologous and heterologous viral challenges. Our approach, which attenuates the virus and promotes immune responses concurrently, is broadly applicable for vaccine development against other pathogens.
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Affiliation(s)
- Yushen Du
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA. .,Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou 310058, China
| | - Li Xin
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China
| | - Yuan Shi
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Tian-Hao Zhang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Nicholas C Wu
- Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
| | - Lei Dai
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Danyang Gong
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Gurpreet Brar
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Sara Shu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Jiadi Luo
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA.,Department of Pathology, The Second Xiangya Hospital of Central South University, Changsha, Hunan 410005, China
| | | | - Yen-Wen Tseng
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Hongyan Bai
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China
| | - Ting-Ting Wu
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA
| | - Jieru Wang
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA.,Department of Pediatrics, University of Pittsburgh School of Medicine, Pittsburgh, PA 15224, USA
| | - Yuelong Shu
- National Institute for Viral Disease Control and Prevention, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, Chinese Center for Disease Control and Prevention, Key Laboratory for Medical Virology and Viral Diseases, Ministry of Health of the People's Republic of China, Beijing 102206, China.,School of Public Health (Shenzhen), Sun Yat-sen University, Guangdong 510275, China
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, University of California, Los Angeles, CA 90095, USA. .,Cancer Institute, Collaborative Innovation Center for Diagnosis and Treatment of Infectious Diseases, School of Medicine, Zhejiang University, Hangzhou 310058, China.,Molecular Biology Institute, University of California, Los Angeles, CA 90095, USA
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24
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Abstract
Influenza A virus (IAV) continues to pose an enormous and unpredictable global public health threat, largely due to the continual evolution of escape from preexisting immunity and the potential for zoonotic emergence. Understanding how the unique genetic makeup and structure of IAV populations influences their transmission and evolution is essential for developing more-effective vaccines, therapeutics, and surveillance capabilities. Owing to their mutation-prone replicase and unique genome organization, IAV populations exhibit enormous amounts of diversity both in terms of sequence and functional gene content. Here, I review what is currently known about the genetic and genomic diversity present within IAV populations and how this diversity may shape the replicative and evolutionary dynamics of these viruses.
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25
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LaBar T, Adami C. Evolution of drift robustness in small populations. Nat Commun 2017; 8:1012. [PMID: 29044114 PMCID: PMC5647343 DOI: 10.1038/s41467-017-01003-7] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 08/10/2017] [Indexed: 11/09/2022] Open
Abstract
Most mutations are deleterious and cause a reduction in population fitness known as the mutational load. In small populations, weakened selection against slightly-deleterious mutations results in an additional fitness reduction. Many studies have established that populations can evolve a reduced mutational load by evolving mutational robustness, but it is uncertain whether small populations can evolve a reduced susceptibility to drift-related fitness declines. Here, using mathematical modeling and digital experimental evolution, we show that small populations do evolve a reduced vulnerability to drift, or ‘drift robustness’. We find that, compared to genotypes from large populations, genotypes from small populations have a decreased likelihood of small-effect deleterious mutations, thus causing small-population genotypes to be drift-robust. We further show that drift robustness is not adaptive, but instead arises because small populations can only maintain fitness on drift-robust fitness peaks. These results have implications for genome evolution in organisms with small effective population sizes. Genetic drift can reduce fitness in small populations by counteracting selection against deleterious mutations. Here, LaBar and Adami demonstrate through a mathematical model and simulations that small populations tend to evolve to drift-robust fitness peaks, which have a low likelihood of slightly-deleterious mutations.
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Affiliation(s)
- Thomas LaBar
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA.,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA.,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA
| | - Christoph Adami
- Department of Microbiology & Molecular Genetics, Michigan State University, East Lansing, MI, 48824, USA. .,BEACON Center for the Study of Evolution in Action, Michigan State University, East Lansing, MI, 48824, USA. .,Program in Ecology, Evolutionary Biology, and Behavior, Michigan State University, East Lansing, MI, 48824, USA. .,Department of Physics and Astronomy, Michigan State University, East Lansing, MI, 48824, USA.
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26
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Minicka J, Elena SF, Borodynko-Filas N, Rubiś B, Hasiów-Jaroszewska B. Strain-dependent mutational effects for Pepino mosaic virus in a natural host. BMC Evol Biol 2017; 17:67. [PMID: 28264646 PMCID: PMC5339997 DOI: 10.1186/s12862-017-0920-4] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2016] [Accepted: 02/20/2017] [Indexed: 11/10/2022] Open
Abstract
Background Pepino mosaic virus (PepMV) is an emerging plant pathogen that infects tomatoes worldwide. Understanding the factors that influence its evolutionary success is essential for developing new control strategies that may be more robust against the evolution of new viral strains. One of these evolutionary factors is the distribution of mutational fitness effect (DMFE), that is, the fraction of mutations that are lethal, deleterious, neutral, and beneficial on a given viral strain and host species. The goal of this study was to characterize the DMFE of introduced nonsynonymous mutations on a mild isolate of PepMV from the Chilean 2 strain (PepMV-P22). Additionally, we also explored whether the fitness effect of a given mutation depends on the gene where it appears or on epistatic interactions with the genetic background. To address this latter possibility, a subset of mutations were also introduced in a mild isolate of the European strain (PepMV-P11) and the fitness of the resulting clones measured. Results A collection of 25 PepMV clones each containing a single nucleotide nonsynonymous substitution was created by site-directed mutagenesis and the fitness of each mutant was determined. PepMV-P22 genome showed a high degree of robustness against point mutations, with 80% of mutations being either neutral or even beneficial and only 20% being deleterious or lethal. We found that the effect of mutations strongly depended on the gene in which they were introduced. Mutations with the largest average beneficial effects were those affecting the RdRp gene, in contrast to mutations affecting TGB1 and CP genes, for which the average effects were deleterious. Moreover, significant epistatic interactions were observed between nonsynonymous mutations and the genetic background, meaning that the effect of a given nucleotide substitution on a particular genomic context cannot be predicted by knowing its effect in a different one. Conclusions Our results indicated that PepMV genome has a surprisingly high robustness against mutations. We also found that fitness consequences of a given mutation differ between the two strains analyzed. This discovery suggests that the strength of selection, and thus the rates of evolution, vary among PepMV strains.
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Affiliation(s)
- Julia Minicka
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain.,Instituto de Biología Integrativa y de Sistemas, Consejo Superior de Investigaciones Científicas-Universitat de València, València, Spain.,The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Natasza Borodynko-Filas
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland
| | - Błażej Rubiś
- Department of Clinical Chemistry and Molecular Diagnostics, Poznan University of Medical Sciences, Poznan, Poland
| | - Beata Hasiów-Jaroszewska
- Department of Virology and Bacteriology, Institute of Plant Protection-National Research Institute, Poznan, Poland.
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27
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Saha D, Podder S, Ghosh TC. Overlapping Regions in HIV-1 Genome Act as Potential Sites for Host-Virus Interaction. Front Microbiol 2016; 7:1735. [PMID: 27867372 PMCID: PMC5095123 DOI: 10.3389/fmicb.2016.01735] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 10/17/2016] [Indexed: 01/05/2023] Open
Abstract
More than a decade, overlapping genes in RNA viruses became a subject of research which has explored various effect of gene overlapping on the evolution and function of viral genomes like genome size compaction. Additionally, overlapping regions (OVRs) are also reported to encode elevated degree of protein intrinsic disorder (PID) in unspliced RNA viruses. With the aim to explore the roles of OVRs in HIV-1 pathogenesis, we have carried out an in-depth analysis on the association of gene overlapping with PID in 35 HIV1- M subtypes. Our study reveals an over representation of PID in OVR of HIV-1 genomes. These disordered residues endure several vital, structural features like short linear motifs (SLiMs) and protein phosphorylation (PP) sites which are previously shown to be involved in massive host–virus interaction. Moreover, SLiMs in OVRs are noticed to be more functionally potential as compared to that of non-overlapping region. Although, density of experimentally verified SLiMs, resided in 9 HIV-1 genes, involved in host–virus interaction do not show any bias toward clustering into OVR, tat and rev two important proteins mediates host–pathogen interaction by their experimentally verified SLiMs, which are mostly localized in OVR. Finally, our analysis suggests that the acquisition of SLiMs in OVR is mutually exclusive of the occurrence of disordered residues, while the enrichment of PPs in OVR is solely dependent on PID and not on overlapping coding frames. Thus, OVRs of HIV-1 genomes could be demarcated as potential molecular recognition sites during host–virus interaction.
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Affiliation(s)
- Deeya Saha
- Bioinformatics Centre, Bose Institute Kolkata, India
| | - Soumita Podder
- Department of Microbiology, Raiganj University Raiganj, India
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Willemsen A, Zwart MP, Higueras P, Sardanyés J, Elena SF. Predicting the Stability of Homologous Gene Duplications in a Plant RNA Virus. Genome Biol Evol 2016; 8:3065-3082. [PMID: 27604880 PMCID: PMC5633665 DOI: 10.1093/gbe/evw219] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/02/2016] [Indexed: 01/03/2023] Open
Abstract
One of the striking features of many eukaryotes is the apparent amount of redundancy in coding and non-coding elements of their genomes. Despite the possible evolutionary advantages, there are fewer examples of redundant sequences in viral genomes, particularly those with RNA genomes. The factors constraining the maintenance of redundant sequences in present-day RNA virus genomes are not well known. Here, we use Tobacco etch virus, a plant RNA virus, to investigate the stability of genetically redundant sequences by generating viruses with potentially beneficial gene duplications. Subsequently, we tested the viability of these viruses and performed experimental evolution. We found that all gene duplication events resulted in a loss of viability or in a significant reduction in viral fitness. Moreover, upon analyzing the genomes of the evolved viruses, we always observed the deletion of the duplicated gene copy and maintenance of the ancestral copy. Interestingly, there were clear differences in the deletion dynamics of the duplicated gene associated with the passage duration and the size and position of the duplicated copy. Based on the experimental data, we developed a mathematical model to characterize the stability of genetically redundant sequences, and showed that fitness effects are not enough to predict genomic stability. A context-dependent recombination rate is also required, with the context being the duplicated gene and its position. Our results therefore demonstrate experimentally the deleterious nature of gene duplications in RNA viruses. Beside previously described constraints on genome size, we identified additional factors that reduce the likelihood of the maintenance of duplicated genes.
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Affiliation(s)
- Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Present address: MIVEGEC (UMR CNRS 5290, IRD 224, UM), National Center for Scientific Research (CNRS), 911 Avenue Agropolis, BP 64501, 34394 Montpellier, Cedex 5, France
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Present address: Institute of Theoretical Physics, University of Cologne, Zülpicher Straße 77, 50937 Cologne, Germany
| | - Pablo Higueras
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain
| | - Josep Sardanyés
- ICREA Complex Systems Laboratory, Universitat Pompeu Fabra, Barcelona, Spain Institut de Biologia Evolutiva (Consejo Superior de Investigaciones Científicas-Universitat Pompeu Fabra), Barcelona, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas (IBMCP), Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, València, Spain Instituto de Biología Integrativa y de Sistems (I2SysBio), Consejo Superior de Investigaciones Científicas-Universitat de València, Parc Científic de la Universitat de València, Paterna, València, Spain The Santa Fe Institute, Santa Fe, New Mexico
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29
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Abstract
A virus’ mutational robustness is described in terms of the strength and distribution of the mutational fitness effects, or MFE. The distribution of MFE is central to many questions in evolutionary theory and is a key parameter in models of molecular evolution. Here we define the mutational fitness effects in influenza A virus by generating 128 viruses, each with a single nucleotide mutation. In contrast to mutational scanning approaches, this strategy allowed us to unambiguously assign fitness values to individual mutations. The presence of each desired mutation and the absence of additional mutations were verified by next generation sequencing of each stock. A mutation was considered lethal only after we failed to rescue virus in three independent transfections. We measured the fitness of each viable mutant relative to the wild type by quantitative RT-PCR following direct competition on A549 cells. We found that 31.6% of the mutations in the genome-wide dataset were lethal and that the lethal fraction did not differ appreciably between the HA- and NA-encoding segments and the rest of the genome. Of the viable mutants, the fitness mean and standard deviation were 0.80 and 0.22 in the genome-wide dataset and best modeled as a beta distribution. The fitness impact of mutation was marginally lower in the segments coding for HA and NA (0.88 ± 0.16) than in the other 6 segments (0.78 ± 0.24), and their respective beta distributions had slightly different shape parameters. The results for influenza A virus are remarkably similar to our own analysis of CirSeq-derived fitness values from poliovirus and previously published data from other small, single stranded DNA and RNA viruses. These data suggest that genome size, and not nucleic acid type or mode of replication, is the main determinant of viral mutational fitness effects. Like other RNA viruses, influenza virus has a very high mutation rate. While high mutation rates may increase the rate at which influenza virus will adapt to a new host, acquire a new route of transmission, or escape from host immune surveillance, data from model systems suggest that most new viral mutations are either lethal or highly detrimental. Mutational robustness refers to the ability of a virus to tolerate, or buffer, these mutations. The mutational robustness of a virus will determine which mutations are maintained in a population and may have a greater impact on viral evolution than mutation rate. We defined the mutational robustness of influenza A virus by measuring the fitness of a large number of viruses, each with a single point mutation. We found that the overall robustness of influenza was similar to that of poliovirus and other viruses of similar size. Interestingly, mutations appeared to be more easily accommodated in hemagglutinin and neuraminidase than elsewhere in the genome. This work will inform models of influenza evolution at the global and molecular scale.
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A Full-Length Infectious cDNA Clone of Zika Virus from the 2015 Epidemic in Brazil as a Genetic Platform for Studies of Virus-Host Interactions and Vaccine Development. mBio 2016; 7:mBio.01114-16. [PMID: 27555311 PMCID: PMC4999549 DOI: 10.1128/mbio.01114-16] [Citation(s) in RCA: 103] [Impact Index Per Article: 12.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023] Open
Abstract
UNLABELLED An arthropod-borne virus, Zika virus (ZIKV), has recently emerged as a major human pathogen. Associated with complications during perinatal development and Guillain-Barré syndrome in adults, ZIKV raises new challenges for understanding the molecular determinants of flavivirus pathogenesis. This underscores the necessity for the development of a reverse genetic system based on an epidemic ZIKV strain. Here, we describe the generation and characterization in cell cultures of an infectious cDNA clone of ZIKV isolated from the 2015 epidemic in Brazil. The cDNA-derived ZIKV replicated efficiently in a variety of cell lines, including those of both neuronal and placental origin. We observed that the growth of cDNA-derived virus was attenuated compared to the growth of the parental isolate in most cell lines, which correlates with substantial differences in sequence heterogeneity between these viruses that were determined by deep-sequencing analysis. Our findings support the role of genetic diversity in maintaining the replicative fitness of viral populations under changing conditions. Moreover, these results indicate that caution should be exercised when interpreting the results of reverse-genetics experiments in attempts to accurately predict the biology of natural viruses. Finally, a Vero cell-adapted cDNA clone of ZIKV was generated that can be used as a convenient platform for studies aimed at the development of ZIKV vaccines and therapeutics. IMPORTANCE The availability of genetic tools and laboratory models determines the progress in understanding mechanisms of virus emergence and pathogenesis. Recent large-scale outbreaks of Zika virus (ZIKV) that were linked to complications during perinatal development and Guillain-Barré syndrome in adults emphasize the urgency for the development of a reverse-genetics system based on an epidemic ZIKV strain. Here, we report a stable infectious cDNA clone for ZIKV isolated during the 2015 epidemic in Brazil, as well as a Vero cell-adapted version of it, which will be used for virus-host interaction studies and vaccine development.
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Abstract
Tobacco mosaic virus and other tobamoviruses have served as models for studying the mechanisms of viral RNA replication. In tobamoviruses, genomic RNA replication occurs via several steps: (a) synthesis of viral replication proteins by translation of the genomic RNA; (b) translation-coupled binding of the replication proteins to a 5'-terminal region of the genomic RNA; (c) recruitment of the genomic RNA by replication proteins onto membranes and formation of a complex with host proteins TOM1 and ARL8; (d) synthesis of complementary (negative-strand) RNA in the complex; and (e) synthesis of progeny genomic RNA. This article reviews current knowledge on tobamovirus RNA replication, particularly regarding how the genomic RNA is specifically selected as a replication template and how the replication proteins are activated. We also focus on the roles of the replication proteins in evading or suppressing host defense systems.
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Affiliation(s)
- Kazuhiro Ishibashi
- Plant and Microbial Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8602, Japan ,
| | - Masayuki Ishikawa
- Plant and Microbial Research Unit, Division of Plant and Microbial Sciences, Institute of Agrobiological Sciences, National Agriculture and Food Research Organization (NARO), Tsukuba 305-8602, Japan ,
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32
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Hillung J, Cuevas JM, Elena SF. Evaluating the within-host fitness effects of mutations fixed during virus adaptation to different ecotypes of a new host. Philos Trans R Soc Lond B Biol Sci 2016; 370:rstb.2014.0292. [PMID: 26150658 DOI: 10.1098/rstb.2014.0292] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
Abstract
The existence of genetic variation for resistance in host populations is assumed to be essential to the spread of an emerging virus. Models predict that the rate of spread slows down with the increasing frequency and higher diversity of resistance alleles in the host population. We have been using the experimental pathosystem Arabidopsis thaliana-tobacco etch potyvirus (TEV) to explore the interplay between genetic variation in host's susceptibility and virus diversity. We have recently shown that TEV populations evolving in A. thaliana ecotypes that differ in susceptibility to infection gained within-host fitness, virulence and infectivity in a manner compatible with a gene-for-gene model of host-parasite interactions: hard-to-infect ecotypes were infected by generalist viruses, whereas easy-to-infect ecotypes were infected by every virus. We characterized the genomes of the evolved viruses and found cases of host-driven convergent mutations. To gain further insights in the mechanistic basis of this gene-for-gene model, we have generated all viral mutations individually as well as in specific combinations and tested their within-host fitness effects across ecotypes. Most of these mutations were deleterious or neutral in their local ecotype and only a very reduced number had a host-specific beneficial effect. We conclude that most of the mutations fixed during the evolution experiment were so by drift or by selective sweeps along with the selected driver mutation. In addition, we evaluated the ruggedness of the underlying adaptive fitness landscape and found that mutational effects were mostly multiplicative, with few cases of significant epistasis.
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Affiliation(s)
- Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, València 46022, Spain The Santa Fe Institute, Santa Fe, NM 87501, USA
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33
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Bernet GP, Elena SF. Distribution of mutational fitness effects and of epistasis in the 5' untranslated region of a plant RNA virus. BMC Evol Biol 2015; 15:274. [PMID: 26643527 PMCID: PMC4672503 DOI: 10.1186/s12862-015-0555-2] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2015] [Accepted: 12/02/2015] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Understanding the causes and consequences of phenotypic variability is a central topic of evolutionary biology. Mutations within non-coding cis-regulatory regions are thought to be of major effect since they affect the expression of downstream genes. To address the evolutionary potential of mutations affecting such regions in RNA viruses, we explored the fitness properties of mutations affecting the 5'-untranslated region (UTR) of a prototypical member of the picorna-like superfamily, Tobacco etch virus (TEV). This 5' UTR acts as an internal ribosomal entry site (IRES) and is essential for expression of all viral genes. RESULTS We determined in vitro the folding of 5' UTR using the selective 2'-hydroxyl acylation analyzed by primer extension (SHAPE) technique. Then, we created a collection of single-nucleotide substitutions on this region and evaluated the statistical properties of their fitness effects in vivo. We found that, compared to random mutations affecting coding sequences, mutations at the 5' UTR were of weaker effect. We also created double mutants by combining pairs of these single mutations and found variation in the magnitude and sign of epistatic interactions, with an enrichment of cases of positive epistasis. A correlation exists between the magnitude of fitness effects and the size of the perturbation made in the RNA folding structure, suggesting that the larger the departure from the predicted fold, the more negative impact in viral fitness. CONCLUSIONS Evidence that mutational fitness effects on the short 5' UTR regulatory sequence of TEV are weaker than those affecting its coding sequences have been found. Epistasis among pairs of mutations on the 5' UTR ranged between the extreme cases of synthetic lethal and compensatory. A plausible hypothesis to explain all these observations is that the interaction between the 5' UTR and the host translational machinery was shaped by natural selection to be robust to mutations, thus ensuring the homeostatic expression of viral genes even at high mutation rates.
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Affiliation(s)
- Guillermo P Bernet
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-UPV, Campus UPV CPI 8E, Ingeniero Fausto Elio s/n, 46022, València, Spain.
- The Santa Fe Institute, 1399 Hyde Park Road, Santa Fe, NM, 87501, USA.
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34
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Peck KM, Burch CL, Heise MT, Baric RS. Coronavirus Host Range Expansion and Middle East Respiratory Syndrome Coronavirus Emergence: Biochemical Mechanisms and Evolutionary Perspectives. Annu Rev Virol 2015; 2:95-117. [PMID: 26958908 DOI: 10.1146/annurev-virology-100114-055029] [Citation(s) in RCA: 61] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Coronaviruses have frequently expanded their host range in recent history, with two events resulting in severe disease outbreaks in human populations. Severe acute respiratory syndrome coronavirus (SARS-CoV) emerged in 2003 in Southeast Asia and rapidly spread around the world before it was controlled by public health intervention strategies. The 2012 Middle East respiratory syndrome coronavirus (MERS-CoV) outbreak represents another prime example of virus emergence from a zoonotic reservoir. Here, we review the current knowledge of coronavirus cross-species transmission, with particular focus on MERS-CoV. MERS-CoV is still circulating in the human population, and the mechanisms governing its cross-species transmission have been only partially elucidated, highlighting a need for further investigation. We discuss biochemical determinants mediating MERS-CoV host cell permissivity, including virus spike interactions with the MERS-CoV cell surface receptor dipeptidyl peptidase 4 (DPP4), and evolutionary mechanisms that may facilitate host range expansion, including recombination, mutator alleles, and mutational robustness. Understanding these mechanisms can help us better recognize the threat of emergence for currently circulating zoonotic strains.
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Affiliation(s)
| | | | - Mark T Heise
- Genetics.,Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599;
| | - Ralph S Baric
- Epidemiology, and.,Microbiology and Immunology, University of North Carolina, Chapel Hill, North Carolina 27599;
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35
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Cuevas JM, Willemsen A, Hillung J, Zwart MP, Elena SF. Temporal dynamics of intrahost molecular evolution for a plant RNA virus. Mol Biol Evol 2015; 32:1132-47. [PMID: 25660377 DOI: 10.1093/molbev/msv028] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023] Open
Abstract
Populations of plant RNA viruses are highly polymorphic in infected plants, which may allow rapid within-host evolution. To understand tobacco etch potyvirus (TEV) evolution, longitudinal samples from experimentally evolved populations in the natural host tobacco and from the alternative host pepper were phenotypically characterized and genetically analyzed. Temporal and compartmental variabilities of TEV populations were quantified using high throughput Illumina sequencing and population genetic approaches. Of the two viral phenotypic traits measured, virulence increased in the novel host but decreased in the original one, and viral load decreased in both hosts, though to a lesser extent in the novel one. Dynamics of population genetic diversity were also markedly different among hosts. Population heterozygosity increased in the ancestral host, with a dominance of synonymous mutations fixed, whereas it did not change or even decreased in the new host, with an excess of nonsynonymous mutations. All together, these observations suggest that directional selection is the dominant evolutionary force in TEV populations evolving in a novel host whereas either diversifying selection or random genetic drift may play a fundamental role in the natural host. To better understand these evolutionary dynamics, we developed a computer simulation model that incorporates the effects of mutation, selection, and drift. Upon parameterization with empirical data from previous studies, model predictions matched the observed patterns, thus reinforcing our idea that the empirical patterns of mutation accumulation represent adaptive evolution.
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Affiliation(s)
- José M Cuevas
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Anouk Willemsen
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Julia Hillung
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Mark P Zwart
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain
| | - Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, Consejo Superior de Investigaciones Científicas-Universidad Politécnica de Valencia, València, Spain The Santa Fe Institute, Santa Fe, NM
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36
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Massey SE. Genetic code evolution reveals the neutral emergence of mutational robustness, and information as an evolutionary constraint. Life (Basel) 2015; 5:1301-32. [PMID: 25919033 PMCID: PMC4500140 DOI: 10.3390/life5021301] [Citation(s) in RCA: 26] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2015] [Revised: 04/02/2015] [Accepted: 04/03/2015] [Indexed: 01/09/2023] Open
Abstract
The standard genetic code (SGC) is central to molecular biology and its origin and evolution is a fundamental problem in evolutionary biology, the elucidation of which promises to reveal much about the origins of life. In addition, we propose that study of its origin can also reveal some fundamental and generalizable insights into mechanisms of molecular evolution, utilizing concepts from complexity theory. The first is that beneficial traits may arise by non-adaptive processes, via a process of "neutral emergence". The structure of the SGC is optimized for the property of error minimization, which reduces the deleterious impact of point mutations. Via simulation, it can be shown that genetic codes with error minimization superior to the SGC can emerge in a neutral fashion simply by a process of genetic code expansion via tRNA and aminoacyl-tRNA synthetase duplication, whereby similar amino acids are added to codons related to that of the parent amino acid. This process of neutral emergence has implications beyond that of the genetic code, as it suggests that not all beneficial traits have arisen by the direct action of natural selection; we term these "pseudaptations", and discuss a range of potential examples. Secondly, consideration of genetic code deviations (codon reassignments) reveals that these are mostly associated with a reduction in proteome size. This code malleability implies the existence of a proteomic constraint on the genetic code, proportional to the size of the proteome (P), and that its reduction in size leads to an "unfreezing" of the codon - amino acid mapping that defines the genetic code, consistent with Crick's Frozen Accident theory. The concept of a proteomic constraint may be extended to propose a general informational constraint on genetic fidelity, which may be used to explain variously, differences in mutation rates in genomes with differing proteome sizes, differences in DNA repair capacity and genome GC content between organisms, a selective pressure in the evolution of sexual reproduction, and differences in translational fidelity. Lastly, the utility of the concept of an informational constraint to other diverse fields of research is explored.
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Affiliation(s)
- Steven E Massey
- Biology Department, PO Box 23360, University of Puerto Rico-Rio Piedras, San Juan, PR 00931, USA.
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37
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The Road Less Traveled: HIV's Use of Alternative Routes through Cellular Pathways. J Virol 2015; 89:5204-12. [PMID: 25762730 DOI: 10.1128/jvi.03684-14] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Pathogens such as HIV-1, with their minimalist genomes, must navigate cellular networks and rely on hijacking and manipulating the host machinery for successful replication. Limited overlap of host factors identified as vital for pathogen replication may be explained by considering that pathogens target, rather than specific cellular factors, crucial cellular pathways by targeting different, functionally equivalent, protein-protein interactions within that pathway. The ability to utilize alternative routes through cellular pathways may be essential for pathogen survival when restricted and provide flexibility depending on the viral replication stage and the environment in the infected host. In this minireview, we evaluate evidence supporting this notion, discuss specific HIV-1 examples, and consider the molecular mechanisms which allow pathogens to flexibly exploit different routes.
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Cheung PPH, Rogozin IB, Choy KT, Ng HY, Peiris JSM, Yen HL. Comparative mutational analyses of influenza A viruses. RNA (NEW YORK, N.Y.) 2015; 21:36-47. [PMID: 25404565 PMCID: PMC4274636 DOI: 10.1261/rna.045369.114] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/12/2023]
Abstract
The error-prone RNA-dependent RNA polymerase (RdRP) and external selective pressures are the driving forces for RNA viral diversity. When confounded by selective pressures, it is difficult to assess if influenza A viruses (IAV) that have a wide host range possess comparable or distinct spontaneous mutational frequency in their RdRPs. We used in-depth bioinformatics analyses to assess the spontaneous mutational frequencies of two RdRPs derived from human seasonal (A/Wuhan/359/95; Wuhan) and H5N1 (A/Vietnam/1203/04; VN1203) viruses using the mini-genome system with a common firefly luciferase reporter serving as the template. High-fidelity reverse transcriptase was applied to generate high-quality mutational spectra which allowed us to assess and compare the mutational frequencies and mutable motifs along a target sequence of the two RdRPs of two different subtypes. We observed correlated mutational spectra (τ correlation P < 0.0001), comparable mutational frequencies (H3N2:5.8 ± 0.9; H5N1:6.0 ± 0.5), and discovered a highly mutable motif "(A)AAG" for both Wuhan and VN1203 RdRPs. Results were then confirmed with two recombinant A/Puerto Rico/8/34 (PR8) viruses that possess RdRP derived from Wuhan or VN1203 (RG-PR8×Wuhan(PB2, PB1, PA, NP) and RG-PR8×VN1203(PB2, PB1, PA, NP)). Applying novel bioinformatics analysis on influenza mutational spectra, we provide a platform for a comprehensive analysis of the spontaneous mutation spectra for an RNA virus.
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Affiliation(s)
- Peter Pak-Hang Cheung
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, Maryland 20894-6075, USA
| | - Ka-Tim Choy
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hoi Yee Ng
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Joseph Sriyal Malik Peiris
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
| | - Hui-Ling Yen
- School of Public Health, Li Ka Shing Faculty of Medicine, The University of Hong Kong, Pokfulam, Hong Kong
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39
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Capel E, Parera M, Martinez MA. Epistasis as a determinant of the HIV-1 protease's robustness to mutation. PLoS One 2014; 9:e116301. [PMID: 25551558 PMCID: PMC4281083 DOI: 10.1371/journal.pone.0116301] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2014] [Accepted: 12/08/2014] [Indexed: 12/05/2022] Open
Abstract
The robustness of phenotypes to mutation is critical to protein evolution; robustness may be an adaptive trait if it promotes evolution. We hypothesised that native proteins subjected to natural selection in vivo should be more robust than proteins generated in vitro in the absence of natural selection. We compared the mutational robustness of two human immunodeficiency virus type 1 (HIV-1) proteases with comparable catalytic efficiencies, one isolated from an infected individual and the second generated in vitro via random mutagenesis. Single mutations in the protease (82 and 60 in the wild-type and mutant backgrounds, respectively) were randomly generated in vitro and the catalytic efficiency of each mutant was determined. No differences were observed between these two protease variants when lethal, neutral, and deleterious mutations were compared (P = 0.8025, chi-squared test). Similarly, average catalytic efficiency (−72.6% and −64.5%, respectively) did not significantly differ between protease mutant libraries (P = 0.3414, Mann Whitney test). Overall, the two parental proteins displayed similar mutational robustness. Importantly, strong and widespread epistatic interactions were observed when the effect of the same mutation was compared in both proteases, suggesting that epistasis can be a key determinant of the robustness displayed by the in vitro generated protease.
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Affiliation(s)
- Elena Capel
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Mariona Parera
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Universitat Autònoma de Barcelona, Barcelona, Spain
| | - Miguel Angel Martinez
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Badalona, Universitat Autònoma de Barcelona, Barcelona, Spain
- * E-mail:
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40
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Abstract
Viruses are common agents of plant infectious diseases. During last decades, worldwide agriculture production has been compromised by a series of epidemics caused by new viruses that spilled over from reservoir species or by new variants of classic viruses that show new pathogenic and epidemiological properties. Virus emergence has been generally associated with ecological change or with intensive agronomical practices. However, the complete picture is much more complex since the viral populations constantly evolve and adapt to their new hosts and vectors. This chapter puts emergence of plant viruses into the framework of evolutionary ecology, genetics, and epidemiology. We will stress that viral emergence begins with the stochastic transmission of preexisting genetic variants from the reservoir to the new host, whose fate depends on their fitness on each hosts, followed by adaptation to new hosts or vectors, and finalizes with an efficient epidemiological spread.
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Affiliation(s)
- Santiago F Elena
- Instituto de Biología Molecular y Celular de Plantas, CSIC-UPV, Campus UPV, València, Spain; The Santa Fe Institute, Santa Fe, New Mexico, USA
| | - Aurora Fraile
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain
| | - Fernando García-Arenal
- Centro de Biotecnología y Genómica de Plantas, UPM-INIA, and ETSI Agrónomos, UPM, Campus de Montegancedo, Madrid, Spain.
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41
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Abstract
A central question in protein molecular evolution is whether an amino acid that occurs at a given site makes an independent contribution to fitness or whether its contribution depends on other amino acid sites in the protein sequence, a phenomenon known as intragenic epistasis. In the absence of intragenic epistasis, natural selection acts on a protein mutation independent of its genetic background, and the experimentally determined fitness for a mutation should be the same across all genetic backgrounds. We tested this hypothesis by using site-directed mutagenesis to introduce a well-characterized deleterious single amino acid substitution in 56 different hepatitis C virus NS3 protease variants. The catalytic efficiency of the mutated proteases was determined and compared with the corresponding wild-type protein. Fitness effects ranged from lethality to significantly beneficial. Although primarily deleterious and lethal effects were observed (41 and 5 out of 56 tested variants, respectively), deleterious effects ranged from near neutral (-26.7% reduction of fitness) to near lethal (-98.5%). Our findings demonstrate that the introduced amino acid substitution has different fitness effects in different protein variants and provide independent support for the relevant role of intragenic epistasis in protein evolution.
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Affiliation(s)
- Mariona Parera
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
| | - Miguel Angel Martinez
- Fundació irsiCaixa, Hospital Universitari Germans Trias i Pujol, Universitat Autònoma de Barcelona, Badalona, Spain
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42
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Donovan P, Cato K, Legaie R, Jayalath R, Olsson G, Hall B, Olson S, Boros S, Reynolds BA, Harding A. Hyperdiploid tumor cells increase phenotypic heterogeneity within Glioblastoma tumors. MOLECULAR BIOSYSTEMS 2014; 10:741-58. [PMID: 24448662 DOI: 10.1039/c3mb70484j] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/09/2023]
Abstract
Here we report the identification of a proliferative, viable, and hyperdiploid tumor cell subpopulation present within Glioblastoma (GB) patient tumors. Using xenograft tumor models, we demonstrate that hyperdiploid cell populations are maintained in xenograft tumors and that clonally expanded hyperdiploid cells support tumor formation and progression in vivo. In some patient tumorsphere lines, hyperdiploidy is maintained during long-term culture and in vivo within xenograft tumor models, suggesting that hyperdiploidy can be a stable cell state. In other patient lines hyperdiploid cells display genetic drift in vitro and in vivo, suggesting that in these patients hyperdiploidy is a transient cell state that generates novel phenotypes, potentially facilitating rapid tumor evolution. We show that the hyperdiploid cells are resistant to conventional therapy, in part due to infrequent cell division due to a delay in the G₀/G₁ phase of the cell cycle. Hyperdiploid tumor cells are significantly larger and more metabolically active than euploid cancer cells, and this correlates to an increased sensitivity to the effects of glycolysis inhibition. Together these data identify GB hyperdiploid tumor cells as a potentially important subpopulation of cells that are well positioned to contribute to tumor evolution and disease recurrence in adult brain cancer patients, and suggest tumor metabolism as a promising point of therapeutic intervention against this subpopulation.
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Affiliation(s)
- Prudence Donovan
- Ecole polytechnique fédérale de Lausanne EPFL, School of Life Sciences SV, Swiss Institute for Experimental Cancer Research ISREC, Switzerland.
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43
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Pagan RF, Massey SE. A nonadaptive origin of a beneficial trait: in silico selection for free energy of folding leads to the neutral emergence of mutational robustness in single domain proteins. J Mol Evol 2013; 78:130-9. [PMID: 24362542 DOI: 10.1007/s00239-013-9606-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2013] [Accepted: 12/04/2013] [Indexed: 10/25/2022]
Abstract
Proteins are regarded as being robust to the deleterious effects of mutations. Here, the neutral emergence of mutational robustness in a population of single domain proteins is explored using computer simulations. A pairwise contact model was used to calculate the ΔG of folding (ΔG folding) using the three dimensional protein structure of leech eglin C. A random amino acid sequence with low mutational robustness, defined as the average ΔΔG resulting from a point mutation (ΔΔG average), was threaded onto the structure. A population of 1,000 threaded sequences was evolved under selection for stability, using an upper and lower energy threshold. Under these conditions, mutational robustness increased over time in the most common sequence in the population. In contrast, when the wild type sequence was used it did not show an increase in robustness. This implies that the emergence of mutational robustness is sequence specific and that wild type sequences may be close to maximal robustness. In addition, an inverse relationship between ∆∆G average and protein stability is shown, resulting partly from a larger average effect of point mutations in more stable proteins. The emergence of mutational robustness was also observed in the Escherichia coli colE1 Rop and human CD59 proteins, implying that the property may be common in single domain proteins under certain simulation conditions. The results indicate that at least a portion of mutational robustness in small globular proteins might have arisen by a process of neutral emergence, and could be an example of a beneficial trait that has not been directly selected for, termed a "pseudaptation."
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Affiliation(s)
- Rafael F Pagan
- Physics Department, University of Puerto Rico - Rio Piedras, San Juan, PR, USA
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44
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Abstract
Soybean vein necrosis-associated virus has been linked to an emerging soybean disease in the United States and Canada. Virus distribution and population structure in major growing areas were evaluated. Data were employed to design and develop sensitive detection protocols, able to detect all virus isolates available in databases. The host range for the virus was assessed and several species were found to sustain virus replication, including ivyleaf morning glory, a common weed species in soybean-growing areas in the United States. Koch's postulates were fulfilled using soybean thrips and transmission efficiency was determined. This article provides significant insight into the biology of the most widespread soybean virus in the United States.
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Affiliation(s)
- Jing Zhou
- Department of Plant Pathology, Division of Agriculture, University of Arkansas System, Fayetteville 72701, USA
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45
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Simon-Loriere E, Holmes EC, Pagán I. The effect of gene overlapping on the rate of RNA virus evolution. Mol Biol Evol 2013; 30:1916-28. [PMID: 23686658 DOI: 10.1093/molbev/mst094] [Citation(s) in RCA: 38] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/19/2023] Open
Abstract
Gene overlapping is widely employed by RNA viruses to generate genetic novelty while retaining a small genome size. However, gene overlapping also increases the deleterious effect of mutations as they affect more than one gene, thereby reducing the evolutionary rate of RNA viruses and hence their adaptive capacity. Although there is general agreement on the benefits of gene overlapping as a mechanism of genomic compression for rapidly evolving organisms, its effect on the pace of RNA virus evolution remains a source of debate. To address this issue, we collected sequence data from 117 instances of gene overlapping across 19 families, 30 genera, and 55 species of RNA viruses. On these data, we analyzed how genetic distances, selective pressures, and the distribution of RNA secondary structures and conserved protein functional domains vary between overlapping (OV) and nonoverlapping (NOV) regions. We show that gene overlapping generally results in a decrease in the rate of RNA virus evolution through a reduction in the frequency of synonymous mutations. However, this effect is less pronounced in genes with a terminal rather than an internal gene overlap, which might result from a greater proportion of protein functional conserved domains in NOV than in OV regions, in turn reducing the number of nonsynonymous mutations in the former. Overall, our analyses clarify the role of gene overlapping as a modulator of the evolutionary rates exhibited by RNA viruses and shed light on the factors that shape the genetic diversity of this important group of pathogens.
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Affiliation(s)
- Etienne Simon-Loriere
- Institut Pasteur, Unité de Génétique Fonctionnelle des Maladies Infectieuses, Paris, France
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46
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Repeated exposure to 5D9, an inhibitor of 3D polymerase, effectively limits the replication of foot-and-mouth disease virus in host cells. Antiviral Res 2013; 98:380-5. [PMID: 23578728 DOI: 10.1016/j.antiviral.2013.03.022] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2013] [Revised: 03/11/2013] [Accepted: 03/28/2013] [Indexed: 11/21/2022]
Abstract
Foot-and-mouth disease (FMD) is a highly contagious disease of livestock caused by a highly variable RNA virus (FMDV) that has seven serotypes and more than sixty subtypes. Both prophylactic and post-infection means of controlling the disease outbreak, including universally applicable vaccines and emergency response measures such as therapeutic treatments, are on high demand. In this study, we analyzed the long-term exposure outcome to a previously identified inhibitor of 3D polymerase (FMDV 3Dpol) for controlling FMDV infection and for the selection of resistance mutants. The results showed that no escape mutant viruses were isolated from FMDV A24 Cruzeiro infections in cell culture treated with gradually increasing concentrations of the antiviral compound 5D9 (4-chloro-N'-thieno, [2,3-d]pyrimidin-4-ylbenzenesulfonohydrazide) over ten passages. Biochemical and plaque assays revealed that when 5D9 was used at concentrations within a non-toxic range in cells, it drove the virus to undetectable levels at passage eight to ten. This is in contrast with observations made on parallel control (untreated) passages exhibiting fully viable and stable virus progenies. Collectively, the results demonstrated that under the experimental conditions, treatment with 5D9 does not confer a resistant phenotype and the virus is unable to evade the antiviral effect of the inhibitor. Further efforts using quantitative structure-property relationship (QSPR) based modifications of the 5D9 compound may result in the successful development of an effective in vivo antiviral drug targeting FMDV.
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47
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Borucki MK, Allen JE, Chen-Harris H, Zemla A, Vanier G, Mabery S, Torres C, Hullinger P, Slezak T. The role of viral population diversity in adaptation of bovine coronavirus to new host environments. PLoS One 2013; 8:e52752. [PMID: 23308119 PMCID: PMC3538757 DOI: 10.1371/journal.pone.0052752] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Accepted: 11/21/2012] [Indexed: 12/04/2022] Open
Abstract
The high mutation rate of RNA viruses enables a diverse genetic population of viral genotypes to exist within a single infected host. In-host genetic diversity could better position the virus population to respond and adapt to a diverse array of selective pressures such as host-switching events. Multiple new coronaviruses, including SARS, have been identified in human samples just within the last ten years, demonstrating the potential of coronaviruses as emergent human pathogens. Deep sequencing was used to characterize genomic changes in coronavirus quasispecies during simulated host-switching. Three bovine nasal samples infected with bovine coronavirus were used to infect human and bovine macrophage and lung cell lines. The virus reproduced relatively well in macrophages, but the lung cell lines were not infected efficiently enough to allow passage of non lab-adapted samples. Approximately 12 kb of the genome was amplified before and after passage and sequenced at average coverages of nearly 950×(454 sequencing) and 38,000×(Illumina). The consensus sequence of many of the passaged samples had a 12 nucleotide insert in the consensus sequence of the spike gene, and multiple point mutations were associated with the presence of the insert. Deep sequencing revealed that the insert was present but very rare in the unpassaged samples and could quickly shift to dominate the population when placed in a different environment. The insert coded for three arginine residues, occurred in a region associated with fusion entry into host cells, and may allow infection of new cell types via heparin sulfate binding. Analysis of the deep sequencing data indicated that two distinct genotypes circulated at different frequency levels in each sample, and support the hypothesis that the mutations present in passaged strains were “selected” from a pre-existing pool rather than through de novo mutation and subsequent population fixation.
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48
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Alves C, Cunha C. Order and disorder in viral proteins: new insights into an old paradigm. Future Virol 2012. [DOI: 10.2217/fvl.12.114] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/28/2022]
Abstract
The conventional dogma stating that proteins must fold into a well-defined structure in order to display biological function is being challenged everyday as new data emerge on the relevance of disordered regions and intrinsically disordered proteins. Viral proteins in particular can benefit greatly from the conformational flexibility granted by partially folded or unfolded protein segments. It enables them to adapt to hostile and changing environmental conditions, interact with the required host machinery while evading host defence mechanisms and tolerate the high mutation rates viral genomes are prone to. In this review, we will summarize and discuss the importance of the recent research field of protein disorder that is proving vital to gain better understanding of the roles and functions of viral proteins.
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Affiliation(s)
- Carolina Alves
- Medical Microbiology Unit, Center for Malaria & Tropical Diseases, Institute of Hygiene & Tropical Medicine, Nova University, Lisbon, Portugal
| | - Celso Cunha
- Medical Microbiology Unit, Center for Malaria & Tropical Diseases, Institute of Hygiene & Tropical Medicine, Nova University, Lisbon, Portugal
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49
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Abstract
The WHO has set regional elimination goals for measles eradication to be achieved by 2020 or earlier. A major question is whether an opportunity for veterinary virus infection of humans may arise when measles is eradicated and if vaccination is discontinued. Lessons have been learned from animal to human virus transmission i.e., HIV and more recently from severe acute respiratory syndrome and avian influenza virus infections. We are therefore alerted to the risk of zoonosis from the veterinary morbilliviruses. In this review the evidence from viral genomics, animal studies and cell culture experiments will be explored to evaluate the possibility of cross-infection of humans with these viruses.
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Affiliation(s)
- S Louise Cosby
- Queen’s University, Belfast, School of Medicine, Dentistry & Biomedical Sciences, Centre for Infection & Immunity, 4th Floor, Medical Biology Centre, Lisburn Road, Belfast, BT9 7BL
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50
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The compensatory G88R change is essential in restoring the normal functions of influenza A/WSN/33 virus matrix protein 1 with a disrupted nuclear localization signal. J Virol 2012; 87:345-53. [PMID: 23077315 DOI: 10.1128/jvi.02024-12] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
G88R emerged as a compensatory mutation in matrix protein 1 (M1) of influenza virus A/WSN/33 when its nuclear localization signal (NLS) was disrupted by R101S and R105S substitutions. The resultant M1 triple mutant M(NLS-88R) regained replication efficiency in vitro while remaining attenuated in vivo with the potential of being a live vaccine candidate. To understand why G88R was favored by the virus as a compensatory change for the NLS loss and resultant replication deficiency, three more M1 triple mutants with an alternative G88K, G88V, or G88E change in addition to R101S and R105S substitutions in the NLS were generated. Unlike the other M1 triple mutants, M(NLS-88R) replicated more efficiently in vitro and in vivo. The G88R compensatory mutation not only restored normal functions of M1 in the presence of a disrupted NLS but also resulted in a strong association of M1 with viral ribonucleoprotein. Under a transmission electron microscope, only the M1 layer of the M(NLS-88R) virion exhibited discontinuous fingerprint-like patterns with average thicknesses close to that of wild-type A/WSN/33. Computational modeling suggested that the compensatory G88R change could reestablish the integrity of the M1 layer through new salt bridges between adjacent M1 subunits when the original interactions were interrupted by simultaneous R101S and R105S replacements in the NLS. Our results suggested that restoring the normal functions of M1 was crucial for efficient virus replication.
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