1
|
Li Y, Liu T, Zhang Y, Duan X, Liu F. RNA recombination: non-negligible factor for preventing emergence or reemergence of Senecavirus A. Front Vet Sci 2024; 11:1357179. [PMID: 38328259 PMCID: PMC10847583 DOI: 10.3389/fvets.2024.1357179] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2023] [Accepted: 01/15/2024] [Indexed: 02/09/2024] Open
Affiliation(s)
- Yan Li
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Tianyu Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| | - Youming Zhang
- State Key Laboratory of Microbial Technology, Shandong University, Qingdao, China
| | - Xiaoxiao Duan
- Qingdao Center for Animal Disease Control and Prevention, Qingdao, China
| | - Fuxiao Liu
- College of Veterinary Medicine, Qingdao Agricultural University, Qingdao, China
| |
Collapse
|
2
|
Dexheimer S, Shrestha N, Chapagain BS, Bujarski JJ, Yin Y. Characterization of Variant RNAs Encapsidated during Bromovirus Infection by High-Throughput Sequencing. Pathogens 2024; 13:96. [PMID: 38276169 PMCID: PMC10819421 DOI: 10.3390/pathogens13010096] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2023] [Revised: 01/13/2024] [Accepted: 01/16/2024] [Indexed: 01/27/2024] Open
Abstract
Previously, we described the RNA recombinants accumulating in tissues infected with the bromoviruses BMV (Brome mosaic virus) and CCMV (Cowpea chlorotic mottle virus). In this work, we characterize the recombinants encapsidated inside the purified virion particles of BMV and CCMV. By using a tool called the Viral Recombination Mapper (ViReMa) that detects recombination junctions, we analyzed a high number of high-throughput sequencing (HTS) short RNA sequence reads. Over 28% of BMV or CCMV RNA reads did not perfectly map to the viral genomes. ViReMa identified 1.40% and 1.83% of these unmapped reads as the RNA recombinants, respectively, in BMV and CCMV. Intra-segmental crosses were more frequent than the inter-segmental ones. Most intra-segmental junctions carried short insertions/deletions (indels) and caused frameshift mutations. The mutation hotspots clustered mainly within the open reading frames. Substitutions of various lengths were also identified, whereas a small fraction of crosses occurred between viral and their host RNAs. Our data reveal that the virions can package detectable amounts of multivariate recombinant RNAs, contributing to the flexible nature of the viral genomes.
Collapse
Affiliation(s)
- Sarah Dexheimer
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Nipin Shrestha
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Bandana Sharma Chapagain
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Jozef J. Bujarski
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
| | - Yanbin Yin
- Department of Biological Sciences, Plant Molecular and Bioinformatics Center, Northern Illinois University, DeKalb, IL 60115, USA; (S.D.); (N.S.); (B.S.C.)
- Nebraska Food for Health Center, Department of Food Science and Technology, University of Nebraska—Lincoln, Lincoln, NE 68588, USA
| |
Collapse
|
3
|
Hassanin A, Rambaud O, Klein D. Genomic Bootstrap Barcodes and Their Application to Study the Evolution of Sarbecoviruses. Viruses 2022; 14:v14020440. [PMID: 35216033 PMCID: PMC8879460 DOI: 10.3390/v14020440] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2022] [Revised: 02/07/2022] [Accepted: 02/18/2022] [Indexed: 01/22/2023] Open
Abstract
Recombination creates mosaic genomes containing regions with mixed ancestry, and the accumulation of such events over time can complicate greatly many aspects of evolutionary inference. Here, we developed a sliding window bootstrap (SWB) method to generate genomic bootstrap (GB) barcodes to highlight the regions supporting phylogenetic relationships. The method was applied to an alignment of 56 sarbecoviruses, including SARS-CoV and SARS-CoV-2, responsible for the SARS epidemic and COVID-19 pandemic, respectively. The SWB analyses were also used to construct a consensus tree showing the most reliable relationships and better interpret hidden phylogenetic signals. Our results revealed that most relationships were supported by just a few genomic regions and confirmed that three divergent lineages could be found in bats from Yunnan: SCoVrC, which groups SARS-CoV related coronaviruses from China; SCoV2rC, which includes SARS-CoV-2 related coronaviruses from Southeast Asia and Yunnan; and YunSar, which contains a few highly divergent viruses recently described in Yunnan. The GB barcodes showed evidence for ancient recombination between SCoV2rC and YunSar genomes, as well as more recent recombination events between SCoVrC and SCoV2rC genomes. The recombination and phylogeographic patterns suggest a strong host-dependent selection of the viral RNA-dependent RNA polymerase. In addition, SARS-CoV-2 appears as a mosaic genome composed of regions sharing recent ancestry with three bat SCoV2rCs from Yunnan (RmYN02, RpYN06, and RaTG13) or related to more ancient ancestors in bats from Yunnan and Southeast Asia. Finally, our results suggest that viral circular RNAs may be key molecules for the mechanism of recombination.
Collapse
|
4
|
Tocchini-Valentini GD, Tocchini-Valentini GP. Archaeal tRNA-Splicing Endonuclease as an Effector for RNA Recombination and Novel Trans-Splicing Pathways in Eukaryotes. J Fungi (Basel) 2021; 7:jof7121069. [PMID: 34947051 PMCID: PMC8707768 DOI: 10.3390/jof7121069] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2021] [Revised: 12/09/2021] [Accepted: 12/09/2021] [Indexed: 11/16/2022] Open
Abstract
We have characterized a homodimeric tRNA endonuclease from the euryarchaeota Ferroplasma acidarmanus (FERAC), a facultative anaerobe which can grow at temperatures ranging from 35 to 42 °C. This enzyme, contrary to the eukaryal tRNA endonucleases and the homotetrameric Methanocaldococcus jannaschii (METJA) homologs, is able to cleave minimal BHB (bulge–helix–bulge) substrates at 30 °C. The expression of this enzyme in Schizosaccharomyces pombe (SCHPO) enables the use of its properties as effectors by inserting BHB motif introns into hairpin loops normally seen in mRNA transcripts. In addition, the FERAC endonuclease can create proteins with new functionalities through the recombination of protein domains.
Collapse
Affiliation(s)
- Giuseppe D. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
- Correspondence:
| | - Glauco P. Tocchini-Valentini
- Istituto di Biochimica e Biologia Cellulare, Campus Internazionale “A. Buzzati-Traverso”, Dipartimento Scienze Biomediche, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy;
- Dipartimento Scienze Biomediche, European Mouse Mutant Archive (EMMA), INFRAFRONTIER-IMPC, Monterotondo Mouse Clinic, Campus Internazionale “A. Buzzati-Traverso”, Consiglio Nazionale delle Ricerche, via Ramarini 32, 00015 Monterotondo, Rome, Italy
| |
Collapse
|
5
|
Tahir M. Coronavirus genomic nsp14-ExoN, structure, role, mechanism, and potential application as a drug target. J Med Virol 2021; 93:4258-4264. [PMID: 33837972 PMCID: PMC8250946 DOI: 10.1002/jmv.27009] [Citation(s) in RCA: 35] [Impact Index Per Article: 11.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2021] [Revised: 04/07/2021] [Accepted: 04/08/2021] [Indexed: 12/20/2022]
Abstract
The recent coronavirus disease 2019 (COVID-19), causing a global pandemic with devastating effects on healthcare and social-economic systems, has no special antiviral therapies available for human coronaviruses (CoVs). The severe acute respiratory syndrome coronavirus 2 (SARS-Cov-2) possesses a nonstructural protein (nsp14), with amino-terminal domain coding for proofreading exoribonuclease (ExoN) that is required for high-fidelity replication. The ability of CoVs during genome replication and transcription to proofread and exclude mismatched nucleotides has long hindered the development of anti-CoV drugs. The resistance of SARS-CoV-2 to antivirals, especially nucleoside analogs (NAs), shows the need to identify new CoV inhibition targets. Therefore, this review highlights the importance of nsp14-ExoN as a target for inhibition. Also, nucleoside analogs could be used in combination with existing anti-CoV therapeutics to target the proofreading mechanism.
Collapse
Affiliation(s)
- Mohammed Tahir
- Department of BiologyUniversity of SulaimaniSulaimanyahKurdistanIraq
| |
Collapse
|
6
|
Gultyaev AP, Spronken MI, Funk M, Fouchier RAM, Richard M. Insertions of codons encoding basic amino acids in H7 hemagglutinins of influenza A viruses occur by recombination with RNA at hotspots near snoRNA binding sites. RNA 2021; 27:123-132. [PMID: 33188057 PMCID: PMC7812872 DOI: 10.1261/rna.077495.120] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/27/2020] [Accepted: 11/06/2020] [Indexed: 06/11/2023]
Abstract
The presence of multiple basic amino acids in the protease cleavage site of the hemagglutinin (HA) protein is the main molecular determinant of virulence of highly pathogenic avian influenza (HPAI) viruses. Recombination of HA RNA with other RNA molecules of host or virus origin is a dominant mechanism of multibasic cleavage site (MBCS) acquisition for H7 subtype HA. Using alignments of HA RNA sequences from documented cases of MBCS insertion due to recombination, we show that such recombination with host RNAs is most likely to occur at particular hotspots in ribosomal RNAs (rRNAs), transfer RNAs (tRNAs), and viral RNAs. The locations of these hotspots in highly abundant RNAs indicate that RNA recombination is facilitated by the binding of small nucleolar RNA (snoRNA) near the recombination points.
Collapse
MESH Headings
- Amino Acids, Basic/genetics
- Amino Acids, Basic/metabolism
- Animals
- Base Pairing
- Base Sequence
- Chickens/virology
- Codon
- Gene Expression Regulation
- Hemagglutinin Glycoproteins, Influenza Virus/genetics
- Hemagglutinin Glycoproteins, Influenza Virus/metabolism
- Host-Pathogen Interactions/genetics
- Humans
- Influenza A virus/genetics
- Influenza A virus/metabolism
- Influenza A virus/pathogenicity
- Influenza in Birds/virology
- Influenza, Human/virology
- Mutagenesis, Insertional
- RNA, Small Nucleolar/chemistry
- RNA, Small Nucleolar/genetics
- RNA, Small Nucleolar/metabolism
- RNA, Viral/chemistry
- RNA, Viral/genetics
- RNA, Viral/metabolism
- Recombination, Genetic
- Sequence Alignment
- Virulence
Collapse
Affiliation(s)
- Alexander P Gultyaev
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
- Group Imaging and Bioinformatics, Leiden Institute of Advanced Computer Science (LIACS), Leiden University, 2300 RA Leiden, the Netherlands
| | - Monique I Spronken
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathis Funk
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Ron A M Fouchier
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| | - Mathilde Richard
- Department of Viroscience, Erasmus Medical Center, 3000 CA Rotterdam, the Netherlands
| |
Collapse
|
7
|
Meers C, Keskin H, Banyai G, Mazina O, Yang T, Gombolay AL, Mukherjee K, Kaparos EI, Newnam G, Mazin A, Storici F. Genetic Characterization of Three Distinct Mechanisms Supporting RNA-Driven DNA Repair and Modification Reveals Major Role of DNA Polymerase ζ. Mol Cell 2020; 79:1037-1050.e5. [PMID: 32882183 DOI: 10.1016/j.molcel.2020.08.011] [Citation(s) in RCA: 26] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2019] [Revised: 06/30/2020] [Accepted: 08/12/2020] [Indexed: 01/08/2023]
Abstract
DNA double-stranded breaks (DSBs) are dangerous lesions threatening genomic stability. Fidelity of DSB repair is best achieved by recombination with a homologous template sequence. In yeast, transcript RNA was shown to template DSB repair of DNA. However, molecular pathways of RNA-driven repair processes remain obscure. Utilizing assays of RNA-DNA recombination with and without an induced DSB in yeast DNA, we characterize three forms of RNA-mediated genomic modifications: RNA- and cDNA-templated DSB repair (R-TDR and c-TDR) using an RNA transcript or a DNA copy of the RNA transcript for DSB repair, respectively, and a new mechanism of RNA-templated DNA modification (R-TDM) induced by spontaneous or mutagen-induced breaks. While c-TDR requires reverse transcriptase, translesion DNA polymerase ζ (Pol ζ) plays a major role in R-TDR, and it is essential for R-TDM. This study characterizes mechanisms of RNA-DNA recombination, uncovering a role of Pol ζ in transferring genetic information from transcript RNA to DNA.
Collapse
Affiliation(s)
- Chance Meers
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Havva Keskin
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gabor Banyai
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Olga Mazina
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Taehwan Yang
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alli L Gombolay
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Kuntal Mukherjee
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Efiyenia I Kaparos
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Gary Newnam
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA
| | - Alexander Mazin
- Department of Biochemistry and Molecular Biology, Drexel University College of Medicine, Philadelphia, PA 19102, USA
| | - Francesca Storici
- School of Biological Sciences, Georgia Institute of Technology, Atlanta, GA 30332, USA.
| |
Collapse
|
8
|
Chetverin AB, Ugarov VI, Chetverina HV. [Unsolved Puzzles of Qβ Replicase]. Mol Biol (Mosk) 2020; 53:899-910. [PMID: 31876271 DOI: 10.1134/s0026898419060041] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2019] [Accepted: 06/01/2019] [Indexed: 11/23/2022]
Abstract
Qβ phage replicase has been the first RNA-directed RNA polymerase purified to homogeneity and intensively studied in vitro. In the mid-sixties, papers on Qβ and related replicases appeared in nearly every issue of the PNAS journal. By 1968, the mechanism of its action seemed to be almost completely understood. However, even now, a half of century later, a number of fundamental questions remains unanswered. How does the replicase manage to prevent the template and its complementary copy from annealing during the entire replication round? How does it recognize its templates? What is the function of the translation factors present in the replicase molecule? What is the mechanism the replicase uses to join (recombine) separate RNA molecules? Even the determination of the crystal structure of Qβ replicase did not help much. Certainly, there remains a lot to discover in the replication of Qβ phage, one of the smallest viruses known.
Collapse
Affiliation(s)
- A B Chetverin
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia.,
| | - V I Ugarov
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| | - H V Chetverina
- Institute of Protein Research of the Russian Academy of Sciences, Pushchino, Moscow oblast, 142290 Russia
| |
Collapse
|
9
|
Kovalev N, Pogany J, Nagy PD. Interviral Recombination between Plant, Insect, and Fungal RNA Viruses: Role of the Intracellular Ca 2+/Mn 2+ Pump. J Virol 2019; 94:e01015-19. [PMID: 31597780 PMCID: PMC6912095 DOI: 10.1128/jvi.01015-19] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2019] [Accepted: 10/07/2019] [Indexed: 01/18/2023] Open
Abstract
Recombination is one of the driving forces of viral evolution. RNA recombination events among similar RNA viruses are frequent, although RNA recombination could also take place among unrelated viruses. In this paper, we have established efficient interviral recombination systems based on yeast and plants. We show that diverse RNA viruses, including the plant viruses tomato bushy stunt virus, carnation Italian ringspot virus, and turnip crinkle virus-associated RNA; the insect plus-strand RNA [(+)RNA] viruses Flock House virus and Nodamura virus; and the double-stranded L-A virus of yeast, are involved in interviral recombination events. Most interviral recombinants are minus-strand recombinant RNAs, and the junction sites are not randomly distributed, but there are certain hot spot regions. Formation of interviral recombinants in yeast and plants is accelerated by depletion of the cellular SERCA-like Pmr1 ATPase-driven Ca2+/Mn2+ pump, regulating intracellular Ca2+ and Mn2+ influx into the Golgi apparatus from the cytosol. The interviral recombinants are generated by a template-switching mechanism during RNA replication by the viral replicase. Replication studies revealed that a group of interviral recombinants is replication competent in cell-free extracts, in yeast, and in the plant Nicotiana benthamiana We propose that there are major differences among the viral replicases to generate and maintain interviral recombinants. Altogether, the obtained data promote the model that host factors greatly contribute to the formation of recombinants among related and unrelated viruses. This is the first time that a host factor's role in affecting interviral recombination is established.IMPORTANCE Viruses with RNA genomes are abundant, and their genomic sequences show astonishing variation. Genetic recombination in RNA viruses is a major force behind their rapid evolution, enhanced pathogenesis, and adaptation to their hosts. We utilized a previously identified intracellular Ca2+/Mn2+ pump-deficient yeast to search for interviral recombinants. Noninfectious viral replication systems were used to avoid generating unwanted infectious interviral recombinants. Altogether, interviral RNA recombinants were observed between plant and insect viruses, and between a fungal double-stranded RNA (dsRNA) virus and an insect virus, in the yeast host. In addition, interviral recombinants between two plant virus replicon RNAs were identified in N. benthamiana plants, in which the intracellular Ca2+/Mn2+ pump was depleted. These findings underline the crucial role of the host in promoting RNA recombination among unrelated viruses.
Collapse
Affiliation(s)
- Nikolay Kovalev
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Judit Pogany
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| | - Peter D Nagy
- Department of Plant Pathology, University of Kentucky, Lexington, Kentucky, USA
| |
Collapse
|
10
|
Kempf BJ, Watkins CL, Peersen OB, Barton DJ. Picornavirus RNA Recombination Counteracts Error Catastrophe. J Virol 2019; 93:e00652-19. [PMID: 31068422 PMCID: PMC6600191 DOI: 10.1128/jvi.00652-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/18/2019] [Accepted: 04/25/2019] [Indexed: 01/24/2023] Open
Abstract
Template-dependent RNA replication mechanisms render picornaviruses susceptible to error catastrophe, an overwhelming accumulation of mutations incompatible with viability. Viral RNA recombination, in theory, provides a mechanism for viruses to counteract error catastrophe. We tested this theory by exploiting well-defined mutations in the poliovirus RNA-dependent RNA polymerase (RDRP), namely, a G64S mutation and an L420A mutation. Our data reveal two distinct mechanisms by which picornaviral RDRPs influence error catastrophe: fidelity of RNA synthesis and RNA recombination. A G64S mutation increased the fidelity of the viral polymerase and rendered the virus resistant to ribavirin-induced error catastrophe, but only when RNA recombination was at wild-type levels. An L420A mutation in the viral polymerase inhibited RNA recombination and exacerbated ribavirin-induced error catastrophe. Furthermore, when RNA recombination was substantially reduced by an L420A mutation, a high-fidelity G64S polymerase failed to make the virus resistant to ribavirin. These data indicate that viral RNA recombination is required for poliovirus to evade ribavirin-induced error catastrophe. The conserved nature of L420 within RDRPs suggests that RNA recombination is a common mechanism for picornaviruses to counteract and avoid error catastrophe.IMPORTANCE Positive-strand RNA viruses produce vast amounts of progeny in very short periods of time via template-dependent RNA replication mechanisms. Template-dependent RNA replication, while efficient, can be disadvantageous due to error-prone viral polymerases. The accumulation of mutations in viral RNA genomes leads to error catastrophe. In this study, we substantiate long-held theories regarding the advantages and disadvantages of asexual and sexual replication strategies among RNA viruses. In particular, we show that picornavirus RNA recombination counteracts the negative consequences of asexual template-dependent RNA replication mechanisms, namely, error catastrophe.
Collapse
Affiliation(s)
- Brian J Kempf
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| | - Colleen L Watkins
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - Olve B Peersen
- Department of Biochemistry and Molecular Biology, Colorado State University, Fort Collins, Colorado, USA
| | - David J Barton
- Department of Immunology and Microbiology, University of Colorado School of Medicine, Aurora, Colorado, USA
| |
Collapse
|
11
|
Garcia-Ruiz H, Diaz A, Ahlquist P. Intermolecular RNA Recombination Occurs at Different Frequencies in Alternate Forms of Brome Mosaic Virus RNA Replication Compartments. Viruses 2018; 10:v10030131. [PMID: 29543718 PMCID: PMC5869524 DOI: 10.3390/v10030131] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/26/2018] [Revised: 03/13/2018] [Accepted: 03/14/2018] [Indexed: 01/27/2023] Open
Abstract
Positive-strand RNA viruses replicate their genomes in membrane-bound replication compartments. Brome mosaic virus (BMV) replicates in vesicular invaginations of the endoplasmic reticulum membrane. BMV has served as a productive model system to study processes like virus-host interactions, RNA replication and recombination. Here we present multiple lines of evidence showing that the structure of the viral RNA replication compartments plays a fundamental role and that recruitment of parental RNAs to a common replication compartment is a limiting step in intermolecular RNA recombination. We show that a previously defined requirement for an RNA recruitment element on both parental RNAs is not to function as a preferred crossover site, but in order for individual RNAs to be recruited into the replication compartments. Moreover, modulating the form of the replication compartments from spherular vesicles (spherules) to more expansive membrane layers increased intermolecular RNA recombination frequency by 200- to 1000-fold. We propose that intermolecular RNA recombination requires parental RNAs to be recruited into replication compartments as monomers, and that recruitment of multiple RNAs into a contiguous space is much more common for layers than for spherules. These results could explain differences in recombination frequencies between viruses that replicate in association with smaller spherules versus larger double-membrane vesicles and convoluted membranes.
Collapse
Affiliation(s)
- Hernan Garcia-Ruiz
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Nebraska Center for Virology, Department of Plant Pathology, University of Nebraska-Lincoln, Lincoln, NE 68503, USA.
| | - Arturo Diaz
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Department of Biology, La Sierra University, Riverside, CA 92515, USA.
| | - Paul Ahlquist
- Institute for Molecular Virology, University of Wisconsin-Madison, Madison, WI 53706, USA.
- Howard Hughes Medical Institute and Morgridge Institute for Research, University of Wisconsin-Madison, MadisonWI 53706, USA.
| |
Collapse
|
12
|
Ramírez M, Velázquez R, López-Piñeiro A, Naranjo B, Roig F, Llorens C. New Insights into the Genome Organization of Yeast Killer Viruses Based on "Atypical" Killer Strains Characterized by High-Throughput Sequencing. Toxins (Basel) 2017; 9:E292. [PMID: 28925975 PMCID: PMC5618225 DOI: 10.3390/toxins9090292] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/31/2017] [Revised: 09/15/2017] [Accepted: 09/16/2017] [Indexed: 01/04/2023] Open
Abstract
Viral M-dsRNAs encoding yeast killer toxins share similar genomic organization, but no overall sequence identity. The dsRNA full-length sequences of several known M-viruses either have yet to be completed, or they were shorter than estimated by agarose gel electrophoresis. High-throughput sequencing was used to analyze some M-dsRNAs previously sequenced by traditional techniques, and new dsRNAs from atypical killer strains of Saccharomyces cerevisiae and Torulaspora delbrueckii. All dsRNAs expected to be present in a given yeast strain were reliably detected and sequenced, and the previously-known sequences were confirmed. The few discrepancies between viral variants were mostly located around the central poly(A) region. A continuous sequence of the ScV-M2 genome was obtained for the first time. M1 virus was found for the first time in wine yeasts, coexisting with Mbarr-1 virus in T. delbrueckii. Extra 5'- and 3'-sequences were found in all M-genomes. The presence of repeated short sequences in the non-coding 3'-region of most M-genomes indicates that they have a common phylogenetic origin. High identity between amino acid sequences of killer toxins and some unclassified proteins of yeast, bacteria, and wine grapes suggests that killer viruses recruited some sequences from the genome of these organisms, or vice versa, during evolution.
Collapse
Affiliation(s)
- Manuel Ramírez
- Departamento de Ciencias Biomédicas (Área de Microbiología, Antiguo Rectorado), Facultad de Ciencias, Universidad de Extremadura, Badajoz 06071, Spain.
| | - Rocío Velázquez
- Departamento de Ciencias Biomédicas (Área de Microbiología, Antiguo Rectorado), Facultad de Ciencias, Universidad de Extremadura, Badajoz 06071, Spain.
| | - Antonio López-Piñeiro
- Departamento de Biología Vegetal, Ecología y Ciencias de la Tierra, Facultad de Ciencias, Universidad de Extremadura, Badajoz 06071, Spain.
| | - Belén Naranjo
- Departamento de Ciencias Biomédicas (Área de Microbiología, Antiguo Rectorado), Facultad de Ciencias, Universidad de Extremadura, Badajoz 06071, Spain.
| | - Francisco Roig
- Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, Paterna 46980 (València), Spain.
| | - Carlos Llorens
- Biotechvana, Parc Científic, Universitat de València, Calle Catedrático José Beltrán 2, Paterna 46980 (València), Spain.
| |
Collapse
|
13
|
Chao M, Wang TC, Lin CC, Yung-Liang Wang R, Lin WB, Lee SE, Cheng YY, Yeh CT, Iang SB. Analyses of a whole-genome inter-clade recombination map of hepatitis delta virus suggest a host polymerase-driven and viral RNA structure-promoted template-switching mechanism for viral RNA recombination. Oncotarget 2017; 8:60841-60859. [PMID: 28977829 PMCID: PMC5617389 DOI: 10.18632/oncotarget.18339] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2016] [Accepted: 05/22/2017] [Indexed: 01/05/2023] Open
Abstract
The genome of hepatitis delta virus (HDV) is a 1.7-kb single-stranded circular RNA that folds into an unbranched rod-like structure and has ribozyme activity. HDV redirects host RNA polymerase(s) (RNAP) to perform viral RNA-directed RNA transcription. RNA recombination is known to contribute to the genetic heterogeneity of HDV, but its molecular mechanism is poorly understood. Here, we established a whole-genome HDV-1/HDV-4 recombination map using two cloned sequences coexisting in cultured cells. Our functional analyses of the resulting chimeric delta antigens (the only viral-encoded protein) and recombinant genomes provide insights into how recombination promotes the genotypic and phenotypic diversity of HDV. Our examination of crossover distribution and subsequent mutagenesis analyses demonstrated that ribozyme activity on HDV genome, which is required for viral replication, also contributes to the generation of an inter-clade junction. These data provide circumstantial evidence supporting our contention that HDV RNA recombination occurs via a replication-dependent mechanism. Furthermore, we identify an intrinsic asymmetric bulge on the HDV genome, which appears to promote recombination events in the vicinity. We therefore propose a mammalian RNAP-driven and viral-RNA-structure-promoted template-switching mechanism for HDV genetic recombination. The present findings improve our understanding of the capacities of the host RNAP beyond typical DNA-directed transcription.
Collapse
Affiliation(s)
- Mei Chao
- Department of Microbiology and Immunology, Chang Gung University, Guishan, Taoyang, Taiwan.,Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan.,Department of Hepato-Gastroenterology, Liver Research Center, Chang Gung Memorial Hospital, Guishan, Taoyang, Taiwan
| | - Tzu-Chi Wang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Chia-Chi Lin
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Robert Yung-Liang Wang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan.,Department of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Wen-Bin Lin
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Shang-En Lee
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Ying-Yu Cheng
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| | - Chau-Ting Yeh
- Department of Hepato-Gastroenterology, Liver Research Center, Chang Gung Memorial Hospital, Guishan, Taoyang, Taiwan
| | - Shan-Bei Iang
- Division of Microbiology, Graduate Institute of Biomedical Sciences, Chang Gung University, Guishan, Taoyang, Taiwan
| |
Collapse
|
14
|
Darweesh MF, Rajput MKS, Braun LJ, Ridpath JF, Neill JD, Chase CCL. Characterization of the cytopathic BVDV strains isolated from 13 mucosal disease cases arising in a cattle herd. Virus Res 2014; 195:141-7. [PMID: 25300803 DOI: 10.1016/j.virusres.2014.09.015] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/29/2014] [Revised: 09/25/2014] [Accepted: 09/29/2014] [Indexed: 11/25/2022]
Abstract
Bovine viral diarrhea virus (BVDV) is a positive single stranded RNA virus belonging to the Pestivirus genus of the Flaviviridae family. BVDV has a wide host range that includes most ruminants. Noncytopathic (ncp) BVDV may establish lifelong persistent infections in calves following infection of the fetus between 40 and 120 days of gestation. Cytopathic (cp) BVDV strains arise from ncp strains via mutations. The most common cp mutations are insertions of RNA derived from either host or a duplication of viral sequences into the region of the genome coding for the NS2/3 protein. Superinfection of a persistently infected animal with a cp virus can give rise to mucosal disease, a condition that is invariably fatal. A herd of 136 bred 3-year old cows was studied. These cows gave birth to 41 PI animals of which 23 succumbed to mucosal disease. In this study, we characterized the ncp and cp viruses isolated from 13 of these animals. All viruses belonged to the BVDV type 2a genotype and were highly similar. All the cp viruses contained an insertion in the NS2/3 coding region consisting of the sequences derived from the transcript encoding a DnaJ protein named Jiv90. Comparison of the inserted DnaJ regions along with the flanking viral sequences in the insertion 3' end of the 13 cp isolates revealed sequence identities ranging from 96% to 99% with common borders. This suggested that one animal likely developed a cp virus that then progressively spread to the other 12 animals. Interestingly, when the inserted mammalian gene replicated within viral genome, it showed conservation of the same conserved motifs between the different species, which may indicate a role for these motifs in the insertion function within the virus genome. This is the first characterization of multiple cp bovine viral diarrhea virus isolates that spread in a herd under natural conditions.
Collapse
Affiliation(s)
- Mahmoud F Darweesh
- Department of Veterinary and Biomedical Sciences, SDSU, Brookings, SD 570076, USA.
| | - Mrigendra K S Rajput
- Department of Veterinary and Biomedical Sciences, SDSU, Brookings, SD 570076, USA.
| | - Lyle J Braun
- Department of Veterinary and Biomedical Sciences, SDSU, Brookings, SD 570076, USA.
| | - Julia F Ridpath
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
| | - John D Neill
- Ruminant Diseases and Immunology Research Unit, National Animal Disease Center, Agricultural Research Service, United States Department of Agriculture, Ames, IA 50010, USA.
| | | |
Collapse
|
15
|
Lin CC, Yang ZW, Iang SB, Chao M. Reduced genetic distance and high replication levels increase the RNA recombination rate of hepatitis delta virus. Virus Res 2014; 195:79-85. [PMID: 25172581 DOI: 10.1016/j.virusres.2014.08.011] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/27/2014] [Revised: 08/13/2014] [Accepted: 08/19/2014] [Indexed: 12/25/2022]
Abstract
Hepatitis delta virus (HDV) replication is carried out by host RNA polymerases. Since homologous inter-genotypic RNA recombination is known to occur in HDV, possibly via a replication-dependent process, we hypothesized that the degree of sequence homology and the replication level should be related to the recombination frequency in cells co-expressing two HDV sequences. To confirm this, we separately co-transfected cells with three different pairs of HDV genomic RNAs and analyzed the obtained recombinants by RT-PCR followed by restriction fragment length polymorphism and sequencing analyses. The sequence divergence between the clones ranged from 24% to less than 0.1%, and the difference in replication levels was as high as 100-fold. As expected, significant differences were observed in the recombination frequencies, which ranged from 0.5% to 47.5%. Furthermore, varying the relative amounts of parental RNA altered the dominant recombinant species produced, suggesting that template switching occurs frequently during the synthesis of genomic HDV RNA. Taken together, these data suggest that during the host RNA polymerase-driven RNA recombination of HDV, both inter- and intra-genotypic recombination events are important in shaping the genetic diversity of HDV.
Collapse
Affiliation(s)
- Chia-Chi Lin
- Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan.
| | - Zhi-Wei Yang
- Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan.
| | - Shan-Bei Iang
- Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan.
| | - Mei Chao
- Division of Mcrobiology, Graduate Institue of Biomedical Sciences, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan; Department of Microbiology and Immunology, College of Medicine, Chang Gung University, Tao-yang 333, Taiwan.
| |
Collapse
|
16
|
Lee PKK, White KA. Construction and characterization of an aureusvirus defective RNA. Virology 2014; 452-453:67-74. [PMID: 24606684 DOI: 10.1016/j.virol.2013.12.033] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2013] [Revised: 12/08/2013] [Accepted: 12/23/2013] [Indexed: 01/30/2023]
Abstract
Defective RNAs (D RNAs) are small RNA replicons derived from viral RNA genomes. No D RNAs have been found associated with members of the plus-strand RNA virus genus Aureusvirus (family Tombusviridae). Accordingly, we sought to construct a D RNA for the aureusvirus Cucumber leaf spot virus (CLSV) using the known structure of tombusvirus defective interfering RNAs as a guide. An efficiently accumulating CLSV D RNA was generated that contained four non-contiguous regions of the viral genome and this replicon was used as a tool to studying viral cis-acting RNA elements. The results of structural and functional analyses indicated that CLSV contains counterparts for several of the major RNA elements found in tombusviruses. However, although similar, the CLSV D RNA and its components are distinct and provide insights into RNA-based specificity and mechanisms of function.
Collapse
Affiliation(s)
- Pui Kei K Lee
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3
| | - K Andrew White
- Department of Biology, York University, 4700 Keele Street, Toronto, Ontario, Canada M3J 1P3.
| |
Collapse
|
17
|
Abstract
The family Closteroviridae consists of two genera, Closterovirus and Ampelovirus with monopartite genomes transmitted respectively by aphids and mealybugs and the Crinivirus with bipartite genomes transmitted by whiteflies. The Closteroviridae consists of more than 30 virus species, which differ considerably in their phytopathological significance. Some, like beet yellows virus and citrus tristeza virus (CTV) were associated for many decades with their respective hosts, sugar beets and citrus. Others, like the grapevine leafroll-associated ampeloviruses 1, and 3 were also associated with their grapevine hosts for long periods; however, difficulties in virus isolation hampered their molecular characterization. The majority of the recently identified Closteroviridae were probably associated with their vegetative propagated host plants for long periods and only detected through the considerable advances in dsRNA isolation and sequencing of PCR amplified replicons. Molecular characterization of CTV and several other Closteroviridae revealed that, in addition to genomic and subgenomic RNAs, infected plants contain several different subviral defective RNAs (dRNAs). The roles and biological functions of dRNAs associated with Closteroviridae remain terra incognita.
Collapse
Affiliation(s)
- Moshe Bar-Joseph
- The S. Tolkowsky Laboratory, Virology Department, Plant Protection Institute, Agricultural Research Organization Beit Dagan, Israel
| | | |
Collapse
|
18
|
Bujarski JJ. Genetic recombination in plant-infecting messenger-sense RNA viruses: overview and research perspectives. Front Plant Sci 2013; 4:68. [PMID: 23533000 PMCID: PMC3607795 DOI: 10.3389/fpls.2013.00068] [Citation(s) in RCA: 31] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2012] [Accepted: 03/11/2013] [Indexed: 05/09/2023]
Abstract
RNA recombination is one of the driving forces of genetic variability in (+)-strand RNA viruses. Various types of RNA-RNA crossovers were described including crosses between the same or different viral RNAs or between viral and cellular RNAs. Likewise, a variety of molecular mechanisms are known to support RNA recombination, such as replicative events (based on internal or end-to-end replicase switchings) along with non-replicative joining among RNA fragments of viral and/or cellular origin. Such mechanisms as RNA decay or RNA interference are responsible for RNA fragmentation and trans-esterification reactions which are likely accountable for ligation of RNA fragments. Numerous host factors were found to affect the profiles of viral RNA recombinants and significant differences in recombination frequency were observed among various RNA viruses. Comparative analyses of viral sequences allowed for the development of evolutionary models in order to explain adaptive phenotypic changes and co-evolving sites. Many questions remain to be answered by forthcoming RNA recombination research. (1) How various factors modulate the ability of viral replicase to switch templates, (2) What is the intracellular location of RNA-RNA template switchings, (3) Mechanisms and factors responsible for non-replicative RNA recombination, (4) Mechanisms of integration of RNA viral sequences with cellular genomic DNA, and (5) What is the role of RNA splicing and ribozyme activity. From an evolutionary stand point, it is not known how RNA viruses parasitize new host species via recombination, nor is it obvious what the contribution of RNA recombination is among other RNA modification pathways. We do not understand why the frequency of RNA recombination varies so much among RNA viruses and the status of RNA recombination as a form of sex is not well documented.
Collapse
Affiliation(s)
- Jozef J. Bujarski
- Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois UniversityDeKalb, IL, USA
- Laboratory of Molecular and Systems Biology, Institute of Bioorganic Chemistry, Polish Academy of SciencesPoznan, Poland
- *Correspondence: Jozef J. Bujarski, Plant Molecular Biology Center and the Department of Biological Sciences, Northern Illinois University, Montgomery Hall, DeKalb, IL 60115, USA. e-mail:
| |
Collapse
|
19
|
de Vries AAF, Horzinek MC, Rottier PJM, de Groot RJ. The Genome Organization of the Nidovirales: Similarities and Differences between Arteri-, Toro-, and Coronaviruses. ACTA ACUST UNITED AC 2002; 8:33-47. [PMID: 32288441 PMCID: PMC7128191 DOI: 10.1006/smvy.1997.0104] [Citation(s) in RCA: 205] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Viruses in the families Arteriviridae and Coronaviridae have enveloped virions which contain nonsegmented, positive-stranded RNA, but the constituent genera differ markedly in genetic complexity and virion structure. Nevertheless, there are striking resemblances among the viruses in the organization and expression of their genomes, and sequence conservation among the polymerase polyproteins strongly suggests that they have a common ancestry. On this basis, the International Committee on Taxonomy of Viruses recently established a new order, Nidovirales, to contain the two families. Here, the common traits and distinguishing features of the Nidovirales are reviewed.
Collapse
Affiliation(s)
- Antoine A F de Vries
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Marian C Horzinek
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Peter J M Rottier
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| | - Raoul J de Groot
- Virology Unit, Department of Infectious Diseases and Immunology, Veterinary Faculty, Utrecht University, Yalelaan 1, 3584 CL, Utrecht, The Netherlands
| |
Collapse
|
20
|
Abstract
Naturally occurring defective interfering RNAs have been found in 4 of 14 coronavirus species. They range in size from 2.2 kb to approximately 25 kb, or 80% of the 30-kb parent virus genome. The large DI RNAs do not in all cases appear to require helper virus for intracellular replication and it has been postulated that they may on their own function as agents of disease. Coronavirus DI RNAs appear to arise by internal deletions (through nonhomologous recombination events) on the virus genome or on DI RNAs of larger size by a polymerase strand-switching (copy-choice) mechanism. In addition to their use in the study of virus RNA replication and virus assembly, coronavirus DI RNAs are being used in a major way to study the mechanism of a high-frequency, site-specific RNA recombination event that leads to leader acquisition during virus replication (i.e., the leader fusion event that occurs during synthesis of subgenomic mRNAs, and the leader-switching event that can occur during DI RNA replication), a distinguishing feature of coronaviruses (and arteriviruses). Coronavirus DI RNAs are also being engineered as vehicles for the generation of targeted recombinants of the parent virus genome.
Collapse
Affiliation(s)
- David A Brian
- Department of Microbiology, College of Veterinary Medicine, M409 Walters Life Sciences Building, University of Tennessee, Knoxville, Tennessee, 37996-0845
| | - Willy J M Spaan
- Department of Virology, Institute of Medical Microbiology, Leiden University, 2300, RC Leiden, The Netherlands
| |
Collapse
|
21
|
Abstract
Coronaviruses contain a very large RNA genome, which undergoes recombination at a very high frequency of nearly 25% for the entire genome. Recombination has been demonstrated to occur between viral genomes and between defective-interfering (DI) RNAs and viral RNA. It provides an evolutionary tool for both viral RNAs and DI RNA and may account for the diversity in the genomic structure of coronaviruses. The capacity of coronaviruses to undergo recombination may be related to its mRNA transcription mechanism, which involves discontinuous RNA synthesis, suggesting the nonprocessive nature of the viral polymerase. Recombination is used as a tool for the mutagenesis of viral genomic RNA.
Collapse
Affiliation(s)
- Michael M C Lai
- From the Howard Hughes Medical Institute, Department of Molecular Microbiology and Immunology, University of Southern California School of Medicine, Los Angeles, CA, 90033-1054, USA
| |
Collapse
|