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Singh K, Mehta D, Dumka S, Chauhan AS, Kumar S. Quasispecies Nature of RNA Viruses: Lessons from the Past. Vaccines (Basel) 2023; 11:308. [PMID: 36851186 PMCID: PMC9963406 DOI: 10.3390/vaccines11020308] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2022] [Revised: 01/22/2023] [Accepted: 01/23/2023] [Indexed: 01/31/2023] Open
Abstract
Viral quasispecies are distinct but closely related mutants formed by the disparity in viral genomes due to recombination, mutations, competition, and selection pressure. Theoretical derivation for the origin of a quasispecies is owed to the error-prone replication by polymerase and mutants of RNA replicators. Here, we briefly addressed the theoretical and mathematical origin of quasispecies and their dynamics. The impact of quasispecies for major salient human pathogens is reviewed. In the current global scenario, rapid changes in geographical landscapes favor the origin and selection of mutants. It comes as no surprise that a cauldron of mutants poses a significant risk to public health, capable of causing pandemics. Mutation rates in RNA viruses are magnitudes higher than in DNA organisms, explaining their enhanced virulence and evolvability. RNA viruses cause the most devastating pandemics; for example, members of the Orthomyxoviridae family caused the great influenza pandemic (1918 flu or Spanish flu), the SARS (severe acute respiratory syndrome) and MERS (Middle East respiratory syndrome) outbreak, and the human immunodeficiency viruses (HIV), lentiviruses of the Retroviridae family, caused worldwide devastation. Rapidly evolving RNA virus populations are a daunting challenge for the designing of effective control measures like vaccines. Developing awareness of the evolutionary dispositions of RNA viral mutant spectra and what influences their adaptation and virulence will help curtail outbreaks of past and future pathogens.
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Affiliation(s)
| | | | | | | | - Sachin Kumar
- Department of Biosciences and Bioengineering, Indian Institute of Technology Guwahati, Guwahati 781039, India
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Functional benefit of structural disorder for the replication of measles, Nipah and Hendra viruses. Essays Biochem 2022; 66:915-934. [PMID: 36148633 DOI: 10.1042/ebc20220045] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Revised: 08/18/2022] [Accepted: 08/25/2022] [Indexed: 12/24/2022]
Abstract
Measles, Nipah and Hendra viruses are severe human pathogens within the Paramyxoviridae family. Their non-segmented, single-stranded, negative-sense RNA genome is encapsidated by the nucleoprotein (N) within a helical nucleocapsid that is the substrate used by the viral RNA-dependent-RNA-polymerase (RpRd) for transcription and replication. The RpRd is a complex made of the large protein (L) and of the phosphoprotein (P), the latter serving as an obligate polymerase cofactor and as a chaperon for N. Both the N and P proteins are enriched in intrinsically disordered regions (IDRs), i.e. regions devoid of stable secondary and tertiary structure. N possesses a C-terminal IDR (NTAIL), while P consists of a large, intrinsically disordered N-terminal domain (NTD) and a C-terminal domain (CTD) encompassing alternating disordered and ordered regions. The V and W proteins, two non-structural proteins that are encoded by the P gene via a mechanism of co-transcriptional edition of the P mRNA, are prevalently disordered too, sharing with P the disordered NTD. They are key players in the evasion of the host antiviral response and were shown to phase separate and to form amyloid-like fibrils in vitro. In this review, we summarize the available information on IDRs within the N, P, V and W proteins from these three model paramyxoviruses and describe their molecular partnership. We discuss the functional benefit of disorder to virus replication in light of the critical role of IDRs in affording promiscuity, multifunctionality, fine regulation of interaction strength, scaffolding functions and in promoting liquid-liquid phase separation and fibrillation.
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Douglas J, Drummond AJ, Kingston RL. Evolutionary history of cotranscriptional editing in the paramyxoviral phosphoprotein gene. Virus Evol 2021; 7:veab028. [PMID: 34141448 PMCID: PMC8204654 DOI: 10.1093/ve/veab028] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
The phosphoprotein gene of the paramyxoviruses encodes multiple protein products. The P, V, and W proteins are generated by transcriptional slippage. This process results in the insertion of non-templated guanosine nucleosides into the mRNA at a conserved edit site. The P protein is an essential component of the viral RNA polymerase and is encoded by a faithful copy of the gene in the majority of paramyxoviruses. However, in some cases, the non-essential V protein is encoded by default and guanosines must be inserted into the mRNA in order to encode P. The number of guanosines inserted into the P gene can be described by a probability distribution, which varies between viruses. In this article, we review the nature of these distributions, which can be inferred from mRNA sequencing data, and reconstruct the evolutionary history of cotranscriptional editing in the paramyxovirus family. Our model suggests that, throughout known history of the family, the system has switched from a P default to a V default mode four times; complete loss of the editing system has occurred twice, the canonical zinc finger domain of the V protein has been deleted or heavily mutated a further two times, and the W protein has independently evolved a novel function three times. Finally, we review the physical mechanisms of cotranscriptional editing via slippage of the viral RNA polymerase.
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Affiliation(s)
- Jordan Douglas
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
- School of Computer Science, University of Auckland, Auckland 1010, New Zealand
| | - Alexei J Drummond
- Centre for Computational Evolution, University of Auckland, Auckland 1010, New Zealand
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
| | - Richard L Kingston
- School of Biological Sciences, University of Auckland, Auckland 1010, New Zealand
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Zhao N, Grund C, Beer M, Harder TC. Engineered recombinant protein products of the avian paramyxovirus type-1 nucleocapsid and phosphoprotein genes for serological diagnosis. Virol J 2018; 15:8. [PMID: 29325564 PMCID: PMC5765633 DOI: 10.1186/s12985-018-0924-8] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/24/2017] [Accepted: 01/08/2018] [Indexed: 11/29/2022] Open
Abstract
Background Virulent Newcastle disease virus (NDV, avian Avulavirus-1, APMV-1) induces a highly contagious and lethal systemic disease in gallinaceous poultry. APMV-1 antibody detection is used for surveillance and to control vaccination, but is hampered by cross-reactivity to other subtypes of avian Avulaviruses. Data are lacking concerning the applicability of NDV V proteins as differential diagnostic marker to distinguish vaccinated from virus-infected birds (DIVA strategy). Methods Full length and C-terminally truncated nucleocapsid (NP) protein, and the unique C-terminal regions of the phospho- (P) and V proteins of the NDV LaSota strain were bacterially expressed as fusion proteins with the multimerization domain of the human C4 binding protein, and used as diagnostic antigens in indirect ELISA. Results When used as diagnostic antigen in indirect ELISAs, recombinant full-length proved to be a sensitive target to detect seroconversion in chickens after APMV-1 vaccination and infection, but revealed some degree of cross reactivity with sera raised against other APMV subtypes. Cross reactivity was abolished but also sensitivity decreased when employing a C-terminal fragment of the NP of NDV as diagnostic antigen. Antibodies to the NDV V protein were mounted in poultry following NDV infection but also, albeit at lower rates and titers, after vaccination with attenuated NDV vaccines. V-specific seroconversion within the flock was incomplete and titers in individual bird transient. Conclusions Indirect ELISA based on bacterially expressed recombinant full-length NP compared favorably with a commercial NDV ELISA based on whole virus antigen, but cross reactivity between the NP proteins of different APMV subtypes could compromise specificity. However, specificity increased when using a less conserved C-terminal fragment of NP instead. Moreover, a serological DIVA strategy built on the NDV V protein was not feasible due to reduced immunogenicity of the V protein and frequent use of live-attenuated NDV vaccines. Electronic supplementary material The online version of this article (10.1186/s12985-018-0924-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Na Zhao
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Christian Grund
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Martin Beer
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany
| | - Timm C Harder
- The Federal Research Institute for Animal Health, Friedrich-Loeffler-Institut, Institute of Diagnostic Virology, Suedufer 10, 17493, Greifswald, Germany.
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Longhi S, Bloyet LM, Gianni S, Gerlier D. How order and disorder within paramyxoviral nucleoproteins and phosphoproteins orchestrate the molecular interplay of transcription and replication. Cell Mol Life Sci 2017; 74:3091-3118. [PMID: 28600653 PMCID: PMC11107670 DOI: 10.1007/s00018-017-2556-3] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2017] [Accepted: 06/01/2017] [Indexed: 01/01/2023]
Abstract
In this review, we summarize computational and experimental data gathered so far showing that structural disorder is abundant within paramyxoviral nucleoproteins (N) and phosphoproteins (P). In particular, we focus on measles, Nipah, and Hendra viruses and highlight both commonalities and differences with respect to the closely related Sendai virus. The molecular mechanisms that control the disorder-to-order transition undergone by the intrinsically disordered C-terminal domain (NTAIL) of their N proteins upon binding to the C-terminal X domain (XD) of the homologous P proteins are described in detail. By having a significant residual disorder, NTAIL-XD complexes are illustrative examples of "fuzziness", whose possible functional significance is discussed. Finally, the relevance of N-P interactions as promising targets for innovative antiviral approaches is underscored, and the functional advantages of structural disorder for paramyxoviruses are pinpointed.
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Affiliation(s)
- Sonia Longhi
- Aix-Marseille Univ, AFMB UMR 7257, 163, avenue de Luminy, Case 932, 13288, Marseille Cedex 09, France.
- CNRS, AFMB UMR 7257, 13288, Marseille, France.
| | - Louis-Marie Bloyet
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
| | - Stefano Gianni
- Istituto Pasteur, Fondazione Cenci Bolognetti and Istituto di Biologia e Patologia Molecolari del CNR, Dipartimento di Scienze Biochimiche "A. Rossi Fanelli", Sapienza Università di Roma, 00185, Rome, Italy
| | - Denis Gerlier
- CIRI, International Center for Infectiology Research, Université de Lyon, Lyon, France
- INSERM, U1111, Lyon, France
- Ecole Normale Supérieure de Lyon, Lyon, France
- Université Claude Bernard Lyon 1, Centre International de Recherche en Infectiologie, Lyon, France
- CNRS, UMR5308, Lyon, France
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Habchi J, Longhi S. Structural Disorder within Paramyxoviral Nucleoproteins and Phosphoproteins in Their Free and Bound Forms: From Predictions to Experimental Assessment. Int J Mol Sci 2015; 16:15688-726. [PMID: 26184170 PMCID: PMC4519920 DOI: 10.3390/ijms160715688] [Citation(s) in RCA: 18] [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] [Received: 05/22/2015] [Revised: 06/26/2015] [Accepted: 06/29/2015] [Indexed: 01/10/2023] Open
Abstract
We herein review available computational and experimental data pointing to the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed molecular description of the mechanisms governing the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (PXD) of the homologous P proteins. We also show that NTAIL-PXD complexes are "fuzzy", i.e., they possess a significant residual disorder, and discuss the possible functional significance of this fuzziness. Finally, we emphasize the relevance of N-P interactions involving intrinsically disordered proteins as promising targets for new antiviral approaches, and end up summarizing the general functional advantages of disorder for viruses.
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
| | - Sonia Longhi
- Aix-Marseille Université, Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
- Centre National pour la Recherche Scientifique (CNRS), AFMB UMR 7257, 163, Avenue de Luminy, Case 932, 13288 Marseille, France.
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Order and Disorder in the Replicative Complex of Paramyxoviruses. ADVANCES IN EXPERIMENTAL MEDICINE AND BIOLOGY 2015; 870:351-81. [PMID: 26387109 DOI: 10.1007/978-3-319-20164-1_12] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
In this review we summarize available data showing the abundance of structural disorder within the nucleoprotein (N) and phosphoprotein (P) from three paramyxoviruses, namely the measles (MeV), Nipah (NiV) and Hendra (HeV) viruses. We provide a detailed description of the molecular mechanisms that govern the disorder-to-order transition that the intrinsically disordered C-terminal domain (NTAIL) of their N proteins undergoes upon binding to the C-terminal X domain (XD) of the homologous P proteins. We also show that a significant flexibility persists within NTAIL-XD complexes, which therefore provide illustrative examples of "fuzziness". The functional implications of structural disorder for viral transcription and replication are discussed in light of the ability of disordered regions to establish a complex molecular partnership and to confer a considerable reach to the elements of the replicative machinery.
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Shukla A, Hilgenfeld R. Acquisition of new protein domains by coronaviruses: analysis of overlapping genes coding for proteins N and 9b in SARS coronavirus. Virus Genes 2014; 50:29-38. [PMID: 25410051 PMCID: PMC7089080 DOI: 10.1007/s11262-014-1139-8] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2014] [Accepted: 10/25/2014] [Indexed: 12/02/2022]
Abstract
Acquisition of new proteins by viruses usually occurs through horizontal gene transfer or through gene duplication, but another, less common mechanism is the usage of completely or partially overlapping reading frames. A case of acquisition of a completely new protein through introduction of a start codon in an alternative reading frame is the protein encoded by open reading frame (orf) 9b of SARS coronavirus. This gene completely overlaps with the nucleocapsid (N) gene (orf9a). Our findings indicate that the orf9b gene features a discordant codon-usage pattern. We analyzed the evolution of orf9b in concert with orf9a using sequence data of betacoronavirus-lineage b and found that orf9b, which encodes the overprinting protein, evolved largely independent of the overprinted orf9a. We also examined the protein products of these genomic sequences for their structural flexibility and found that it is not necessary for a newly acquired, overlapping protein product to be intrinsically disordered, in contrast to earlier suggestions. Our findings contribute to characterizing sequence properties of newly acquired genes making use of overlapping reading frames.
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Affiliation(s)
- Aditi Shukla
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- Graduate School for Computing in Medicine & Life Sciences, University of Lübeck, Lübeck, Germany
| | - Rolf Hilgenfeld
- Institute of Biochemistry, Center for Structural and Cell Biology in Medicine, University of Lübeck, Ratzeburger Allee 160, 23538 Lübeck, Germany
- German Center for Infection Research (DZIF), University of Lübeck, Lübeck, Germany
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Affiliation(s)
- Johnny Habchi
- Aix-Marseille Université , Architecture et Fonction des Macromolécules Biologiques (AFMB), UMR 7257, 13288, Marseille, France
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Xue B, Blocquel D, Habchi J, Uversky AV, Kurgan L, Uversky VN, Longhi S. Structural disorder in viral proteins. Chem Rev 2014; 114:6880-911. [PMID: 24823319 DOI: 10.1021/cr4005692] [Citation(s) in RCA: 140] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/07/2023]
Affiliation(s)
- Bin Xue
- Department of Cell Biology, Microbiology and Molecular Biology, College of Fine Arts and Sciences, and ‡Department of Molecular Medicine and USF Health Byrd Alzheimer's Research Institute, Morsani College of Medicine, University of South Florida , Tampa, Florida 33620, United States
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Lo MK, Søgaard TM, Karlin DG. Evolution and structural organization of the C proteins of paramyxovirinae. PLoS One 2014; 9:e90003. [PMID: 24587180 PMCID: PMC3934983 DOI: 10.1371/journal.pone.0090003] [Citation(s) in RCA: 25] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2013] [Accepted: 01/24/2014] [Indexed: 12/21/2022] Open
Abstract
The phosphoprotein (P) gene of most Paramyxovirinae encodes several proteins in overlapping frames: P and V, which share a common N-terminus (PNT), and C, which overlaps PNT. Overlapping genes are of particular interest because they encode proteins originated de novo, some of which have unknown structural folds, challenging the notion that nature utilizes only a limited, well-mapped area of fold space. The C proteins cluster in three groups, comprising measles, Nipah, and Sendai virus. We predicted that all C proteins have a similar organization: a variable, disordered N-terminus and a conserved, α-helical C-terminus. We confirmed this predicted organization by biophysically characterizing recombinant C proteins from Tupaia paramyxovirus (measles group) and human parainfluenza virus 1 (Sendai group). We also found that the C of the measles and Nipah groups have statistically significant sequence similarity, indicating a common origin. Although the C of the Sendai group lack sequence similarity with them, we speculate that they also have a common origin, given their similar genomic location and structural organization. Since C is dispensable for viral replication, unlike PNT, we hypothesize that C may have originated de novo by overprinting PNT in the ancestor of Paramyxovirinae. Intriguingly, in measles virus and Nipah virus, PNT encodes STAT1-binding sites that overlap different regions of the C-terminus of C, indicating they have probably originated independently. This arrangement, in which the same genetic region encodes simultaneously a crucial functional motif (a STAT1-binding site) and a highly constrained region (the C-terminus of C), seems paradoxical, since it should severely reduce the ability of the virus to adapt. The fact that it originated twice suggests that it must be balanced by an evolutionary advantage, perhaps from reducing the size of the genetic region vulnerable to mutations.
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Affiliation(s)
- Michael K. Lo
- Centers for Disease Control and Prevention, Viral Special Pathogens Branch, Atlanta, Georgia, United States of America
| | - Teit Max Søgaard
- Division of Structural Biology, Oxford University, Oxford, United Kingdom
| | - David G. Karlin
- Division of Structural Biology, Oxford University, Oxford, United Kingdom
- Department of Zoology, University of Oxford, Oxford, United Kingdom
- * E-mail:
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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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Yoshida A, Sakaguchi T, Irie T. Passage of a Sendai virus recombinant in embryonated chicken eggs leads to markedly rapid accumulation of U-to-C transitions in a limited region of the viral genome. PLoS One 2012. [PMID: 23185501 PMCID: PMC3503868 DOI: 10.1371/journal.pone.0049968] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/03/2022] Open
Abstract
The P gene of paramyxoviruses is unique in producing not only P but also “accessory” C and/or V proteins. Successful generation of C- or V-deficient recombinant viruses using a reverse genetics technique has been revealing their importance in viral pathogenesis as well as replication. As for Sendai virus (SeV), the C proteins, a nested set of four polypeptides C’, C, Y1, and Y2, have been shown to exert multiple functions in escaping from the host innate immunity, inhibiting virus-induced apoptosis, promoting virus assembly and budding, and regulating viral RNA synthesis. In this study, we subjected the 4C(-) recombinant lacking expression of all four C proteins to serial passages through eggs, and found the rapid emergence of a C-recovered revertant virus. Unlike the SeV strains or the recombinants reported previously or tested in this study, this was caused by an exceptionally quick accumulation of U-to-C transitions in a limited region of the 4C(-) genome causing recovery of the C protein expression. These results suggest that a lack of C proteins could lead unexpectedly to strong selective pressures, and that the C proteins might play more critical roles in SeV replication than ever reported.
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Affiliation(s)
- Asuka Yoshida
- Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takemasa Sakaguchi
- Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
| | - Takashi Irie
- Department of Virology, Institute of Biomedical and Health Sciences, Hiroshima University, Hiroshima, Japan
- * E-mail:
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Sabath N, Wagner A, Karlin D. Evolution of viral proteins originated de novo by overprinting. Mol Biol Evol 2012; 29:3767-80. [PMID: 22821011 PMCID: PMC3494269 DOI: 10.1093/molbev/mss179] [Citation(s) in RCA: 104] [Impact Index Per Article: 8.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
New protein-coding genes can originate either through modification of existing genes or de novo. Recently, the importance of de novo origination has been recognized in eukaryotes, although eukaryotic genes originated de novo are relatively rare and difficult to identify. In contrast, viruses contain many de novo genes, namely those in which an existing gene has been “overprinted” by a new open reading frame, a process that generates a new protein-coding gene overlapping the ancestral gene. We analyzed the evolution of 12 experimentally validated viral genes that originated de novo and estimated their relative ages. We found that young de novo genes have a different codon usage from the rest of the genome. They evolve rapidly and are under positive or weak purifying selection. Thus, young de novo genes might have strain-specific functions, or no function, and would be difficult to detect using current genome annotation methods that rely on the sequence signature of purifying selection. In contrast to young de novo genes, older de novo genes have a codon usage that is similar to the rest of the genome. They evolve slowly and are under stronger purifying selection. Some of the oldest de novo genes evolve under stronger selection pressure than the ancestral gene they overlap, suggesting an evolutionary tug of war between the ancestral and the de novo gene.
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Affiliation(s)
- Niv Sabath
- Institute of Evolutionary Biology and Environmental Studies, University of Zurich, Zurich, Switzerland.
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Munir M, Abbas M, Khan MT, Zohari S, Berg M. Genomic and biological characterization of a velogenic Newcastle disease virus isolated from a healthy backyard poultry flock in 2010. Virol J 2012; 9:46. [PMID: 22340092 PMCID: PMC3295720 DOI: 10.1186/1743-422x-9-46] [Citation(s) in RCA: 37] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2011] [Accepted: 02/16/2012] [Indexed: 01/08/2023] Open
Abstract
BACKGROUND Newcastle disease virus (NDV) causes severe and economically important disease in poultry around the globe. None of NDV strains in Pakistan have been completely characterized and the role of rural poultry in harbouring NDV is unclear. Since they have a very important role for long-term circulation of the virus, samples were collected from apparently healthy backyard poultry (BYP) flocks. These samples were biologically analyzed using mean death time (MDT) and intracerebral pathogenicity index (ICPI), whereas genotypically characterized by the real-time PCRs coupled with sequencing of the complete genome. FINDINGS Despite of being non-pathogenic for BYP, the isolate exhibited MDT of 49.6 h in embryonated chicken eggs and an ICPI value of 1.5. The F gene based real-time PCR was positive, whereas M-gene based was negative due to substantial changes in the probe-binding site. The entire genome of the isolate was found to be 15192 nucleotides long and encodes for six genes with an order of 3'-NP-P-M-F-HN-L-5'. The F protein cleavage site, an indicative of pathogenicity, was 112RRQKRF117. Complete genome comparison indicated that the RNA dependent RNA polymerase gene was the most and the phosphoprotein was least conserved gene, among all the genes. The isolate showed an Y526Q substitution in the HN protein, which determines neuraminidase receptor binding and fusion activity of NDV. Phylogenetic analysis, based on F and HN genes, classified this isolate into genotype VII, a predominant genotype responsible for ND outbreaks in Asian countries. However, it clustered well apart from other isolates in this genotype to be considered a new subgenotype (VII-f). CONCLUSIONS These results revealed that this isolate was similar to virulent strains of NDV and was avirulent in BYP either due to resistance of local breeds or due to other factors such as substantial mutations in the HN protein. Furthermore, we have characterized the first isolate of NDV, which could act as domestic reference strain and could help in development and selection of appropriate strain of NDV for vaccine in the country.
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Affiliation(s)
- Muhammad Munir
- Division of Virology, Department of Biomedical Sciences and Veterinary Public Health, Swedish University of Agricultural Sciences, SLU, Ulls väg 2B, 751 89 Uppsala, Sweden.
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Level of gene expression is a major determinant of protein evolution in the viral order Mononegavirales. J Virol 2012; 86:5253-63. [PMID: 22345453 DOI: 10.1128/jvi.06050-11] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022] Open
Abstract
Although the rate at which proteins change is a key parameter in molecular evolution, its determinants are poorly understood in viruses. A variety of factors, including gene length, codon usage bias, protein abundance, protein function, and gene expression level, have been shown to affect the rate of protein evolution in a diverse array of organisms. However, the role of these factors in viral evolution has yet to be addressed. The polar 3'-5' stepwise attenuation of transcription in the Mononegavirales, a group of single-strand negative-sense RNA viruses, provides a unique system to explore the determinants of protein evolution in viruses. We analyzed the relative importance of a variety of factors in shaping patterns of sequence variation in full-length genomes from 13 Mononegavirales species. Our analysis suggests that the level of gene expression, and by extension the relative genomic position of each gene, is a key determinant of the protein evolution in these viruses. This appears to be the consequence of selection for translational robustness, but not for translational accuracy, in highly expressed genes. The small genome size and number of proteins encoded by these viruses allowed us to identify other protein-specific factors that may also play a role in virus evolution, such as host-virus interactions and functional constraints. Finally, we explored the evolutionary pressures acting on noncoding regions in Mononegavirales genomes and observed that, despite being less constrained than coding regions, their evolutionary rates are also associated with genomic position.
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Habchi J, Longhi S. Structural disorder within paramyxovirus nucleoproteins and phosphoproteins. ACTA ACUST UNITED AC 2012; 8:69-81. [DOI: 10.1039/c1mb05204g] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/20/2023]
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18
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Ma MR, Ha XQ, Ling H, Wang ML, Zhang FX, Zhang SD, Li G, Yan W. The characteristics of the synonymous codon usage in hepatitis B virus and the effects of host on the virus in codon usage pattern. Virol J 2011; 8:544. [PMID: 22171933 PMCID: PMC3287100 DOI: 10.1186/1743-422x-8-544] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2011] [Accepted: 12/15/2011] [Indexed: 12/18/2022] Open
Abstract
BACKGROUND Hepatitis B virus (HBV) infection is one of the main human health problem and causes a large-scale of patients chronic infection worldwide.. As the replication of HBV depends on its host cell system, codon usage pattern for the viral gene might be susceptible to two main selections, namely mutation pressure and translation selection. In this case, a deeper investigation between HBV evolution and host adaptive response might assist control this disease. RESULT Relative synonymous codon usage (RSCU) values for the whole HBV coding sequence were studied by Principal component analysis (PCA). The characteristics of the synonymous codon usage patterns, nucleotide contents and the comparison between ENC values of the whole HBV coding sequence indicated that the interaction between virus mutation pressure and host translation selection exists in the processes of HBV evolution. The synonymous codon usage pattern of HBV is a mixture of coincidence and antagonism to that of host cell. But the difference of genetic characteristic of HBV failed to be observed to its different epidemic areas or subtypes, suggesting that geographic factor is limited to influence the evolution of this virus, while genetic characteristic based on HBV genotypes could be divided into three groups, namely (i) genotyps A and E, (ii) genotype B, (iii) genotypes C, D and G. CONCLUSION Codon usage patterns from PCA for identification of evolutionary trends in HBV provide an alternative approach to understand the evolution of HBV. Further more, a combined selection of mutation pressure with translation selection on codon usage might shed a light on understanding the evolutionary trends of HBV genotypes.
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Affiliation(s)
- Ming-ren Ma
- Experimental Center of Medicine, Lanzhou General Hospital, Lanzhou Military Area Command, Lanzhou 730000, China.
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Habchi J, Mamelli L, Darbon H, Longhi S. Structural disorder within Henipavirus nucleoprotein and phosphoprotein: from predictions to experimental assessment. PLoS One 2010; 5:e11684. [PMID: 20657787 PMCID: PMC2908138 DOI: 10.1371/journal.pone.0011684] [Citation(s) in RCA: 71] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2010] [Accepted: 06/21/2010] [Indexed: 12/30/2022] Open
Abstract
Henipaviruses are newly emerged viruses within the Paramyxoviridae family. Their negative-strand RNA genome is packaged by the nucleoprotein (N) within alpha-helical nucleocapsid that recruits the polymerase complex made of the L protein and the phosphoprotein (P). To date structural data on Henipaviruses are scarce, and their N and P proteins have never been characterized so far. Using both computational and experimental approaches we herein show that Henipaviruses N and P proteins possess large intrinsically disordered regions. By combining several disorder prediction methods, we show that the N-terminal domain of P (PNT) and the C-terminal domain of N (NTAIL) are both mostly disordered, although they contain short order-prone segments. We then report the cloning, the bacterial expression, purification and characterization of Henipavirus PNT and NTAIL domains. By combining gel filtration, dynamic light scattering, circular dichroism and nuclear magnetic resonance, we show that both NTAIL and PNT belong to the premolten globule sub-family within the class of intrinsically disordered proteins. This study is the first reported experimental characterization of Henipavirus P and N proteins. The evidence that their respective N-terminal and C-terminal domains are highly disordered under native conditions is expected to be invaluable for future structural studies by helping to delineate N and P protein domains amenable to crystallization. In addition, following previous hints establishing a relationship between structural disorder and protein interactivity, the present results suggest that Henipavirus PNT and NTAIL domains could be involved in manifold protein-protein interactions.
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Affiliation(s)
- Johnny Habchi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Laurent Mamelli
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Hervé Darbon
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
| | - Sonia Longhi
- Architecture et Fonction des Macromolécules Biologiques, UMR 6098 CNRS et Universités Aix-Marseille I et II, Campus de Luminy, Marseille, France
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20
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Pagán I, Holmes EC. Long-term evolution of the Luteoviridae: time scale and mode of virus speciation. J Virol 2010; 84:6177-87. [PMID: 20375155 PMCID: PMC2876656 DOI: 10.1128/jvi.02160-09] [Citation(s) in RCA: 87] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2009] [Accepted: 03/31/2010] [Indexed: 12/20/2022] Open
Abstract
Despite their importance as agents of emerging disease, the time scale and evolutionary processes that shape the appearance of new viral species are largely unknown. To address these issues, we analyzed intra- and interspecific evolutionary processes in the Luteoviridae family of plant RNA viruses. Using the coat protein gene of 12 members of the family, we determined their phylogenetic relationships, rates of nucleotide substitution, times to common ancestry, and patterns of speciation. An associated multigene analysis enabled us to infer the nature of selection pressures and the genomic distribution of recombination events. Although rates of evolutionary change and selection pressures varied among genes and species and were lower in some overlapping gene regions, all fell within the range of those seen in animal RNA viruses. Recombination breakpoints were commonly observed at gene boundaries but less so within genes. Our molecular clock analysis suggested that the origin of the currently circulating Luteoviridae species occurred within the last 4 millennia, with intraspecific genetic diversity arising within the last few hundred years. Speciation within the Luteoviridae may therefore be associated with the expansion of agricultural systems. Finally, our phylogenetic analysis suggested that viral speciation events tended to occur within the same plant host species and country of origin, as expected if speciation is largely sympatric, rather than allopatric, in nature.
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Affiliation(s)
- Israel Pagán
- Center for Infectious Disease Dynamics, Department of Biology, The Pennsylvania State University, University Park, PA 16802, USA.
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21
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Firth AE, Atkins JF. Candidates in Astroviruses, Seadornaviruses, Cytorhabdoviruses and Coronaviruses for +1 frame overlapping genes accessed by leaky scanning. Virol J 2010; 7:17. [PMID: 20100346 PMCID: PMC2832772 DOI: 10.1186/1743-422x-7-17] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2009] [Accepted: 01/25/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Overlapping genes are common in RNA viruses where they serve as a mechanism to optimize the coding potential of compact genomes. However, annotation of overlapping genes can be difficult using conventional gene-finding software. Recently we have been using a number of complementary approaches to systematically identify previously undetected overlapping genes in RNA virus genomes. In this article we gather together a number of promising candidate new overlapping genes that may be of interest to the community. RESULTS Overlapping gene predictions are presented for the astroviruses, seadornaviruses, cytorhabdoviruses and coronaviruses (families Astroviridae, Reoviridae, Rhabdoviridae and Coronaviridae, respectively).
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Affiliation(s)
- Andrew E Firth
- BioSciences Institute, University College Cork, Cork, Ireland.
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22
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Zhang D, Chen J, Deng L, Mao Q, Zheng J, Wu J, Zeng C, Li Y. Evolutionary selection associated with the multi-function of overlapping genes in the hepatitis B virus. INFECTION GENETICS AND EVOLUTION 2010; 10:84-8. [DOI: 10.1016/j.meegid.2009.10.006] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/01/2009] [Revised: 10/10/2009] [Accepted: 10/20/2009] [Indexed: 11/16/2022]
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23
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Liang JW, Tian FL, Lan ZR, Huang B, Zhuang WZ. Selection characterization on overlapping reading frame of multiple-protein-encoding P gene in Newcastle disease virus. Vet Microbiol 2009; 144:257-63. [PMID: 20079581 DOI: 10.1016/j.vetmic.2009.12.029] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2009] [Accepted: 12/21/2009] [Indexed: 01/08/2023]
Abstract
The aim of this study was to characterize the molecular evolution of P and V protein genes of the Newcastle disease virus (NDV). The P gene sequences of 55 NDV isolates, representing different chronological and geographic origins, were obtained from GenBank. In this paper, the evolution of the specific regions of the NDV P gene, encoding the P and V proteins, was analyzed. The nucleotides from the shared P/V region encoded the co-amino terminus of the two proteins, while the P-V/V-P region was respectively encoded by the nucleotides within the P ORF or the V ORF in the common sequence (after the mRNA editing site). As well, the P-cut region exclusively encoded the P protein. Finally, the P-V and V-P regions were further broken down into P1 and P2 fragments with the corresponding V1 and V2 fragments. In the P gene, the P-cut portion corresponding to the C-terminal of the P protein was the most highly conserved, while the P-V region was the most variable. This was interpreted as a lower constraint for function in the common sequence than in the unique P sequence that is known to contain an important function. Interestingly, in the common P-V/V-P function, variability of V1 was compensated by a higher conservation of the corresponding P1, and conversely for the P2/V2, which suggested that the flexibility of one ORF with less function served the purpose of allowing positive selection in the other overlapping ORF that exhibited more function.
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Affiliation(s)
- Jun-Wen Liang
- College of Life Science, Shandong Normal University, Wenhua East Road, Shandong Province, Jinan 250014, China
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24
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McCarthy AJ, Goodman SJ. Reassessing conflicting evolutionary histories of the Paramyxoviridae and the origins of respiroviruses with Bayesian multigene phylogenies. INFECTION GENETICS AND EVOLUTION 2009; 10:97-107. [PMID: 19900582 DOI: 10.1016/j.meegid.2009.11.002] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/17/2009] [Revised: 10/26/2009] [Accepted: 11/03/2009] [Indexed: 10/20/2022]
Abstract
The evolution of paramyxoviruses is still poorly understood since past phylogenetic studies have revealed conflicting evolutionary signals among genes, and used varying methods and datasets. Using Bayesian phylogenetic analysis of full length single and concatenated sequences for the 6 genes shared among paramyxovirus genera, we reassess the ambiguous evolutionary relationships within the family, and examine causes of varying phylogenetic signals among different genes. Relative to a pneumovirus outgroup, the concatenated gene phylogeny, splits the Paramyxovirinae into two lineages, one comprising the avulaviruses and rubulaviruses, and a second containing the respiroviruses basal to the henipaviruses, and morbilliviruses. Phylogenies for the matrix (M), RNA dependent RNA polymerase (L) and the fusion (F) glycoprotein genes, are concordant with the topology from the concatenated dataset. In phylogenies derived from the nucleocapsid (N) and phosphoprotein (P) genes, the respiroviruses form the most basal genus of the Paramyxovirinae subfamily, with the avulaviruses and rubulaviruses in one lineage, and the henipaviruses, and morbilliviruses in a second. The phylogeny of the hemagglutinin (H) gene places the respiroviruses basal to the avula-rubulavirus group, but the relationship of this lineage with henipa and morbillviruses is not resolved. Different genes may be under varying evolutionary pressures giving rise to these conflicting signals. Given the level of conservation in the M and L genes, we suggest that together with F gene, these or concatenated datasets for all six genes are likely to reveal the most reliable phylogenies at a family level, and should be used for future phylogenetic studies in this group. Split decomposition analysis suggests that recombination within genera, may have a contributed to the emergence of dolphin morbillivirus, and several species within respiroviruses. A partial L gene alignment, resolves the relationship of 25 unclassified paramxyoviruses into 4 clades (Chiopteran-, Salmon-, Rodentian- and Ophidian paramyxoviruses) which group with rubula-, respiro-, morbilliviruses, and within the paramxyovirinae respectively.
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Affiliation(s)
- Alex J McCarthy
- Institute of Integrative & Comparative Biology, Faculty of Biological Sciences, University of Leeds, LS2 9JT, UK
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25
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Overlapping genes produce proteins with unusual sequence properties and offer insight into de novo protein creation. J Virol 2009; 83:10719-36. [PMID: 19640978 DOI: 10.1128/jvi.00595-09] [Citation(s) in RCA: 141] [Impact Index Per Article: 9.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
It is widely assumed that new proteins are created by duplication, fusion, or fission of existing coding sequences. Another mechanism of protein birth is provided by overlapping genes. They are created de novo by mutations within a coding sequence that lead to the expression of a novel protein in another reading frame, a process called "overprinting." To investigate this mechanism, we have analyzed the sequences of the protein products of manually curated overlapping genes from 43 genera of unspliced RNA viruses infecting eukaryotes. Overlapping proteins have a sequence composition globally biased toward disorder-promoting amino acids and are predicted to contain significantly more structural disorder than nonoverlapping proteins. By analyzing the phylogenetic distribution of overlapping proteins, we were able to confirm that 17 of these had been created de novo and to study them individually. Most proteins created de novo are orphans (i.e., restricted to one species or genus). Almost all are accessory proteins that play a role in viral pathogenicity or spread, rather than proteins central to viral replication or structure. Most proteins created de novo are predicted to be fully disordered and have a highly unusual sequence composition. This suggests that some viral overlapping reading frames encoding hypothetical proteins with highly biased composition, often discarded as noncoding, might in fact encode proteins. Some proteins created de novo are predicted to be ordered, however, and whenever a three-dimensional structure of such a protein has been solved, it corresponds to a fold previously unobserved, suggesting that the study of these proteins could enhance our knowledge of protein space.
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26
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Boxer EL, Nanda SK, Baron MD. The rinderpest virus non-structural C protein blocks the induction of type 1 interferon. Virology 2008; 385:134-42. [PMID: 19108859 DOI: 10.1016/j.virol.2008.11.022] [Citation(s) in RCA: 33] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2008] [Revised: 09/12/2008] [Accepted: 11/11/2008] [Indexed: 12/25/2022]
Abstract
The innate immune response, in particular the production of type 1 interferons, is an essential part of the mammalian host response to viral infection. We have previously shown that rinderpest virus, a morbillivirus closely related to the human pathogen measles virus, blocks the actions of type 1 and type 2 interferons. We show here that this virus can also block the induction of type 1 interferon. The viral non-structural C protein appears to be the active agent, since expressing this protein in cells makes them resistant to activation of the interferon-beta promoter while recombinant virus that does not express the C protein activates this promoter much more than virus expressing the C protein. In addition, differences in activation of the interferon-beta promoter by different strains of rinderpest virus are reflected in differing abilities of their respective C proteins to block activation of the promoter by dsRNA. The C protein blocks the activation of this promoter induced by either cytoplasmic dsRNA or by Newcastle disease virus (NDV) infection, as well as activation induced by overexpression of several elements of the signalling pathway, including mda-5, RIG-I and IRF-3. The RPV C protein also blocks transcription from promoters responsive individually to the three transcription factors that make up the interferon-beta promoter enhanceosome, although it does not appear to block the activation of IRF-3.
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Affiliation(s)
- Emma L Boxer
- Institute for Animal Health, Pirbright, Surrey, UK
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27
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Characterization of the genome sequence of an oncolytic Newcastle disease virus strain Italien. Virus Res 2008; 135:312-9. [PMID: 18420299 DOI: 10.1016/j.virusres.2008.03.003] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2007] [Revised: 03/04/2008] [Accepted: 03/06/2008] [Indexed: 11/22/2022]
Abstract
We determined the complete genome sequence of strain Italien, a virulent and oncolytic strain of Newcastle disease virus (NDV) by direct nucleotide sequencing of RT-PCR products, a size of 15,186 nucleotides (nt). Comparison of six coding genes and non-coding regions of Italien with those of the other 25 sequenced strains revealed NDV Herts/33 was the most similar strain with Italien. The gene encoding the RNA dependent RNA polymerase was the most highly conserved, while the gene encoding phosphoprotein was the most highly variable. The HN and F proteins of Italien have been modeled on the crystal structure in order to study the structural characteristics. Interaction between the HN protein and the heptad repeat B (HRB) region of F protein was analyzed in silico by molecular docking predicted five critical residues I133, V142, D143, R480, and K567 on HN protein. Identification of amino acid residues that could be crucial for this interaction provides working hypotheses for subsequent studies.
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28
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Szklarczyk R, Heringa J, Pond SK, Nekrutenko A. Rapid asymmetric evolution of a dual-coding tumor suppressor INK4a/ARF locus contradicts its function. Proc Natl Acad Sci U S A 2007; 104:12807-12. [PMID: 17652172 PMCID: PMC1937548 DOI: 10.1073/pnas.0703238104] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
INK4a/ARF tumor suppressor locus encodes two protein products, INK4a and ARF, essential for controlling tumorigenesis and mutated in more than half of human cancers. There is no resemblance between the two proteins: their coding regions are assembled by alternative splicing of two mutually exclusive 5' exons into a constitutive one containing overlapping out-of-phase reading frames. We show that the dual-coding arrangement conflicts with the high cost of mutations within INK4a/ARF. Unexpectedly, the locus evolves rapidly and asymmetrically, with ARF accumulating the majority of amino acid replacements. Rapid evolution drives both INK4a and ARF proteins out of sync with other members of the RB and p53 tumor suppressor pathways, both of which are controlled by the locus. Yet, the asymmetric behavior may be an intrinsic property of dual-coding exons: INK4a/ARF closely mimics the evolution of 90 newly identified genes with similar dual-coding structure. Thus, the strong link between mutations in INK4a/ARF and cancer may be a direct consequence of the architecture of the locus.
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Affiliation(s)
- Radek Szklarczyk
- *Centre for Integrative Bioinformatics, Vrije University, De Boelelaan 1081a, 1081HV, Amsterdam, The Netherlands
| | - Jaap Heringa
- *Centre for Integrative Bioinformatics, Vrije University, De Boelelaan 1081a, 1081HV, Amsterdam, The Netherlands
| | | | - Anton Nekrutenko
- Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16803
- To whom correspondence should be addressed at:
505 Wartik Laboratory, Center for Comparative Genomics and Bioinformatics, Pennsylvania State University, University Park, PA 16802. E-mail:
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29
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Abstract
The possibility of creating novel genes from pre-existing sequences, known as overprinting, is a widespread phenomenon in small viruses. Here, the origin and evolution of gene overlap in the bacteriophages belonging to the family Microviridae have been investigated. The distinction between ancestral and derived frames was carried out by comparing the patterns of codon usage in overlapping and non-overlapping genes. By this approach, a gradual increase in complexity of the phage genome--from an ancestral state lacking gene overlap to a derived state with a high density of genetic information--was inferred. Genes encoding less-essential proteins, yet playing a role in phage growth and diffusion, were predicted to be novel genes that originated by overprinting. Evaluation of the rates of synonymous and non-synonymous substitution yielded evidence for overlapping genes under positive selection in one frame and purifying selection in the alternative frame.
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Affiliation(s)
- Angelo Pavesi
- Department of Genetics, Anthropology and Evolution, University of Parma, Parco Area delle Scienze 11/A, I-43100 Parma, Italy
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30
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Huang Z, Krishnamurthy S, Panda A, Samal SK. Newcastle disease virus V protein is associated with viral pathogenesis and functions as an alpha interferon antagonist. J Virol 2003; 77:8676-85. [PMID: 12885886 PMCID: PMC167241 DOI: 10.1128/jvi.77.16.8676-8685.2003] [Citation(s) in RCA: 164] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/02/2023] Open
Abstract
Newcastle disease virus (NDV) edits its P gene by inserting one or two G residues at the conserved editing site (UUUUUCCC, genome sense) and transcribes the P mRNA (unedited), the V mRNA (with a +1 frameshift), and the W mRNA (with a +2 frameshift). All three proteins are amino coterminal but vary at their carboxyl terminus in length and amino acid composition. Little is known about the role of the V and W proteins in NDV replication and pathogenesis. We have constructed and recovered two recombinant viruses in which the expression of the V or both the V and W proteins has been abolished. Compared to the parental virus, the mutant viruses showed impaired growth in cell cultures, except in Vero cells. However, transient expression of the carboxyl-terminal portion of the V protein enhanced the growth of the mutant viruses. In embryonated chicken eggs, the parental virus grew to high titers in embryos of different gestational ages, whereas the mutant viruses showed an age-dependent phenomenon, growing to lower titer in more-developed embryos. An interferon (IFN) sensitivity assay showed that the parental virus was more resistant to the antiviral effect of IFN than the mutant viruses. Moreover, infection with the parental virus resulted in STAT1 protein degradation, but not with the mutant viruses. These findings indicate that the V protein of NDV possesses the ability to inhibit alpha IFN and that the IFN inhibitory function lies in the carboxyl-terminal domain. Pathogenicity studies showed that the V protein of NDV significantly contributes to the virus virulence.
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Affiliation(s)
- Zhuhui Huang
- Virginia-Maryland Regional College of Veterinary Medicine, University of Maryland, College Park, Maryland 20742, USA
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31
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Novella IS. Contributions of vesicular stomatitis virus to the understanding of RNA virus evolution. Curr Opin Microbiol 2003; 6:399-405. [PMID: 12941412 DOI: 10.1016/s1369-5274(03)00084-5] [Citation(s) in RCA: 45] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Vesicular stomatitis virus has been a preferred system to study evolution for several decades. New approaches to antiviral treatment, such as lethal mutagenesis, stem from investigations done with VSV. Recent work has shed new light in the way we view neutrality, a fundamental concept to understand the evolutionary history of RNA viruses.
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Affiliation(s)
- Isabel S Novella
- Department of Microbiology and Immunology, Medical College of Ohio, 3055 Arlington Ave., Toledo 43614, OH, USA.
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32
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Guyader S, Ducray DG. Sequence analysis of Potato leafroll virus isolates reveals genetic stability, major evolutionary events and differential selection pressure between overlapping reading frame products. J Gen Virol 2002; 83:1799-1807. [PMID: 12075102 DOI: 10.1099/0022-1317-83-7-1799] [Citation(s) in RCA: 58] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to investigate the genetic diversity of Potato leafroll virus (PLRV), seven new complete genomic sequences of isolates collected worldwide were compared with the five sequences available in GenBank. Then, a restricted polymorphic region of the genome was chosen to further analyse new sequences. The sequences of PLRV open reading frames (ORFs) 3 and 4 were also compared with those of two other poleroviruses and the non-synonymous to synonymous substitution ratio distribution was analysed in overlapping and non-overlapping regions of the genome using maximum-likelihood models. Results confirmed that PLRV sequences from around the world are very closely related and showed that the region encoding protein P0 allowed the detection of three groups of isolates. When compared to other poleroviruses, PLRV was the most conserved in both ORFs 3 and 4. However, the results suggest that important events, such as deletion, mutation at a stop codon and intraspecific homologous recombination events, have occurred during the evolution of PLRV. Finally, it was shown that the translation products of ORFs 0 and 3 are significantly more conserved than those of the overlapping ORFs 1 and 4, respectively. All together, the results allow the proposal of new hypotheses to explain the apparent genetic stability of PLRV and its evolution.
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Affiliation(s)
- Sébastien Guyader
- INRA - UMR BiO3P, Domaine de la Motte, BP 35327, 35653 Le Rheu Cedex, France1
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33
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Rogozin IB, Spiridonov AN, Sorokin AV, Wolf YI, Jordan IK, Tatusov RL, Koonin EV. Purifying and directional selection in overlapping prokaryotic genes. Trends Genet 2002; 18:228-32. [PMID: 12047938 DOI: 10.1016/s0168-9525(02)02649-5] [Citation(s) in RCA: 94] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
In overlapping genes, the same DNA sequence codes for two proteins using different reading frames. Analysis of overlapping genes can help in understanding the mode of evolution of a coding region from noncoding DNA. We identified 71 pairs of convergent genes, with overlapping 3' ends longer than 15 nucleotides, that are conserved in at least two prokaryotic genomes. Among the overlap regions, we observed a statistically significant bias towards the 123:132 phase (i.e. the second codon base in one gene facing the degenerate third position in the second gene). This phase ensures the least mutual constraint on nonconservative amino acid replacements in both overlapping coding sequences. The excess of this phase is compatible with directional (positive) selection acting on the overlapping coding regions. This could be a general evolutionary mode for genes emerging from noncoding sequences, in which the protein sequence has not been subject to selection.
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Affiliation(s)
- Igor B Rogozin
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
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34
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Chua KB, Wang LF, Lam SK, Crameri G, Yu M, Wise T, Boyle D, Hyatt AD, Eaton BT. Tioman virus, a novel paramyxovirus isolated from fruit bats in Malaysia. Virology 2001; 283:215-29. [PMID: 11336547 DOI: 10.1006/viro.2000.0882] [Citation(s) in RCA: 114] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
A search for the natural host of Nipah virus has led to the isolation of a previously unknown member of the family Paramyxoviridae. Tioman virus (TiV) was isolated from the urine of fruit bats (Pteropus hypomelanus) found on the island of the same name off the eastern coast of peninsular Malaysia. An electron microscopic study of TiV-infected cells revealed spherical and pleomorphic-enveloped viral particles (100--500 nm in size) with a single fringe of embedded peplomers. Virus morphogenesis occurred at the plasma membrane of infected cells and morphological features of negative-stained ribonucleoprotein complexes were compatible with that of viruses in the family Paramyxoviridae. Serological studies revealed no cross-reactivity with antibodies against a number of known Paramyxoviridae members except for the newly described Menangle virus (MenV), isolated in Australia in 1997. Failure of PCR amplification using MenV-specific primers suggested that this new virus is related to but different from MenV. For molecular characterization of the virus, a cDNA subtraction strategy was employed to isolate virus-specific cDNA from virus-infected cells. Complete gene sequences for the nucleocapsid protein (N) and phosphoprotein (P/V) have been determined and recombinant N and V proteins produced in baculovirus. The recombinant N and V proteins reacted with porcine anti-MenV sera in Western blot, confirming the serological cross-reactivity observed during initial virus characterization. The lack of a C protein-coding region in the P/V gene, the creation of P mRNA by insertion of 2-G residues, and the results of phylogenetic analyses all indicated that TiV is a novel member of the genus Rubulavirus.
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Affiliation(s)
- K B Chua
- Department of Medical Microbiology, University of Malaya Medical Center, 50603 Kuala Lumpur, Malaysia
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Sweetman DA, Miskin J, Baron MD. Rinderpest virus C and V proteins interact with the major (L) component of the viral polymerase. Virology 2001; 281:193-204. [PMID: 11277692 DOI: 10.1006/viro.2000.0805] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
Rinderpest virus, like other Morbilliviruses, expresses three proteins from the single P gene. In addition to the P protein, which interacts both with the viral polymerase (L) and the nucleocapsid (N) protein, the virus expresses a C and a V protein from the same gene. The functions of these two proteins in the viral life cycle are not clear. Although both C and V proteins are dispensable, in that viable viruses can be made that express neither, each seems to play a role in optimum viral replication. We have used the yeast-two hybrid system, binding to coexpressed fusions of C and V to glutathione-S-transferase, and studies of the native size of these proteins to investigate interactions of the rinderpest virus C and V proteins with other virus-encoded proteins. The V protein was found to interact with both the N and L proteins, while the C protein was found to bind to the L protein, and to self-associate in high-molecular-weight aggregates.
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Affiliation(s)
- D A Sweetman
- Institute for Animal Health, Ash Road, Surrey, Pirbright, GU24 0NF, United Kingdom
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36
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Locke DP, Sellers HS, Crawford JM, Schultz-Cherry S, King DJ, Meinersmann RJ, Seal BS. Newcastle disease virus phosphoprotein gene analysis and transcriptional editing in avian cells. Virus Res 2000; 69:55-68. [PMID: 10989186 DOI: 10.1016/s0168-1702(00)00175-1] [Citation(s) in RCA: 36] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Nucleotide sequence was determined for the phosphoprotein (P) gene from 23 Newcastle disease virus (NDV) isolates representing all defined pathotypes with different chronological and geographic origins. Sequence variation, with synonymous substitutions dominating, occurred throughout the P gene. An exception was a conserved central region containing the transcriptional editing site. Four G nucleotide additions were detected in NDV P gene mRNA potentially creating alternative open reading frames. However, only one in-frame stop codon exists with a single G addition among all isolates that would allow for a potential V protein. A second potential stop codon does not exist in the P gene consensus sequence among all isolates with more than one G nucleotide addition at the editing site. This precludes a possible W protein in these isolates. A second potential alternative in-frame start site exists among all isolates that could encode a predicted X protein for NDV. Comparison of the P gene editing sites among the Paramyxovirinae and predicted P gene usage demonstrates that NDV more closely resembles the respiroviruses and morbilliviruses. Phylogenetic analysis of P gene sequences among NDV isolates demonstrates there are two clades of these viruses. One group includes viruses isolated in the US prior to 1970, while a second cluster includes virulent viruses circulating worldwide.
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Affiliation(s)
- D P Locke
- Southeast Poultry Research Laboratory, Agricultural Research Service, US Department of Agriculture, 934 College Station Road, Athens, GA 30605, USA
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