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Chkuaseli T, White KA. Complex and simple translational readthrough signals in pea enation mosaic virus 1 and potato leafroll virus, respectively. PLoS Pathog 2022; 18:e1010888. [PMID: 36174104 PMCID: PMC9553062 DOI: 10.1371/journal.ppat.1010888] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Revised: 10/11/2022] [Accepted: 09/20/2022] [Indexed: 11/26/2022] Open
Abstract
Different essential viral proteins are translated via programmed stop codon readthrough. Pea enation mosaic virus 1 (PEMV1) and potato leafroll virus (PLRV) are related positive-sense RNA plant viruses in the family Solemoviridae, and are type members of the Enamovirus and Polerovirus genera, respectively. Both use translational readthrough to express a C-terminally extended minor capsid protein (CP), termed CP-readthrough domain (CP-RTD), from a viral subgenomic mRNA that is transcribed during infections. Limited incorporation of CP-RTD subunits into virus particles is essential for aphid transmission, however the functional readthrough structures that mediate CP-RTD translation have not yet been defined. Through RNA solution structure probing, RNA secondary structure modeling, site-directed mutagenesis, and functional in vitro and in vivo analyses, we have investigated in detail the readthrough elements and complex structure involved in expression of CP-RTD in PEMV1, and assessed and deduced a comparatively simpler readthrough structure for PLRV. Collectively, this study has (i) generated the first higher-order RNA structural models for readthrough elements in an enamovirus and a polerovirus, (ii) revealed a stark contrast in the complexity of readthrough structures in these two related viruses, (iii) provided compelling experimental evidence for the strict requirement for long-distance RNA-RNA interactions in generating the active readthrough signals, (iv) uncovered what could be considered the most complex readthrough structure reported to date, that for PEMV1, and (v) proposed plausible assembly pathways for the formation of the elaborate PEMV1 and simple PLRV readthrough structures. These findings notably advance our understanding of this essential mode of gene expression in these agriculturally important plant viruses.
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Affiliation(s)
- Tamari Chkuaseli
- Department of Biology, York University, Toronto, Ontario, Canada
| | - K. Andrew White
- Department of Biology, York University, Toronto, Ontario, Canada
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2
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Cornejo-Franco JF, Flores F, Mollov D, Quito-Avila DF. An umbra-related virus found in babaco (Vasconcellea × heilbornii). Arch Virol 2021; 166:2321-2324. [PMID: 34046760 DOI: 10.1007/s00705-021-05117-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2021] [Accepted: 04/11/2021] [Indexed: 11/24/2022]
Abstract
The complete sequence of a new viral RNA from babaco (Vasconcellea × heilbornii) was determined. The genome consisted of 4,584 nucleotides, containing two open reading frames (ORFs 1 and 2), a 9-nt-long noncoding region (NCR) at the 5' terminus, and an unusually long (1,843 nt) NCR at the 3' terminus. The presence of a potential heptameric slippery signal located 12 nt upstream the stop codon of ORF 1 suggests a -1 ribosomal frameshift mechanism for the translation of ORF 2. Sequence comparisons of ORF 2 revealed similarity to the RNA-dependent RNA polymerase (RdRp) of several umbra- and umbra-like viruses. Phylogenetic analysis of the RdRp placed the new virus in a well-supported and cohesive clade that includes umbra-like viruses reported in papaya, citrus, opuntia, maize, and sugarcane hosts. Viruses of this clade share a most recent ancestor with the umbraviruses but have different genomic features. The creation of a new genus within the family Tombusviridae is proposed for the classification of these novel viruses.
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Affiliation(s)
- Juan F Cornejo-Franco
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador
| | - Francisco Flores
- Centro de Investigación de Alimentos, CIAL, Facultad de Ciencias de la Ingeniería e Industrias, Universidad UTE, Quito, Ecuador.,Departamento de Ciencias de la Vida y la Agricultura, Universidad de las Fuerzas Armadas-ESPE, Sangolquí, Ecuador
| | - Dimitre Mollov
- National Germplasm Resources Laboratory, USDA-ARS, Beltsville, MD, USA
| | - Diego F Quito-Avila
- Centro de Investigaciones Biotecnológicas del Ecuador, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador. .,Facultad de Ciencias de la Vida, Escuela Superior Politécnica del Litoral, ESPOL, Guayaquil, Ecuador.
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Newburn LR, Wu B, White KA. Investigation of Novel RNA Elements in the 3'UTR of Tobacco Necrosis Virus-D. Viruses 2020; 12:E856. [PMID: 32781505 PMCID: PMC7472153 DOI: 10.3390/v12080856] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/17/2020] [Revised: 08/01/2020] [Accepted: 08/04/2020] [Indexed: 11/16/2022] Open
Abstract
RNA elements in the untranslated regions of plus-strand RNA viruses can control a variety of viral processes including translation, replication, packaging, and subgenomic mRNA production. The 3' untranslated region (3'UTR) of Tobacco necrosis virus strain D (TNV-D; genus Betanecrovirus, family Tombusviridae) contains several well studied regulatory RNA elements. Here, we explore a previously unexamined region of the viral 3'UTR, the sequence located upstream of the 3'-cap independent translation enhancer (3'CITE). Our results indicate that (i) a long-range RNA-RNA interaction between an internal RNA element and the 3'UTR facilitates translational readthrough, and may also promote viral RNA synthesis; (ii) a conserved RNA hairpin, SLX, is required for efficient genome accumulation; and (iii) an adenine-rich region upstream of the 3'CITE is dispensable, but can modulate genome accumulation. These findings identified novel regulatory RNA elements in the 3'UTR of the TNV-D genome that are important for virus survival.
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Affiliation(s)
| | | | - K. Andrew White
- Department of Biology, York University, Toronto, ON M3J 1P3, Canada; (L.R.N.); (B.W.)
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4
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Newburn LR, White KA. A trans-activator-like structure in RCNMV RNA1 evokes the origin of the trans-activator in RNA2. PLoS Pathog 2020; 16:e1008271. [PMID: 31905231 PMCID: PMC6964918 DOI: 10.1371/journal.ppat.1008271] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2019] [Revised: 01/16/2020] [Accepted: 12/10/2019] [Indexed: 11/19/2022] Open
Abstract
The Red clover necrotic mosaic virus (RCNMV) genome consists of two plus-strand RNA genome segments, RNA1 and RNA2. RNA2 contains a multifunctional RNA structure known as the trans-activator (TA) that (i) promotes subgenomic mRNA transcription from RNA1, (ii) facilitates replication of RNA2, and (iii) mediates particle assembly and copackaging of genome segments. The TA has long been considered a unique RNA element in RCNMV. However, by examining results from RCNMV genome analyses in the ViRAD virus (re-)annotation database, a putative functional RNA element in the polymerase-coding region of RNA1 was identified. Structural and functional analyses revealed that the novel RNA element adopts a TA-like structure (TALS) and, similar to the requirement of the TA for RNA2 replication, the TALS is necessary for the replication of RNA1. Both the TA and TALS possess near-identical asymmetrical internal loops that are critical for efficient replication of their corresponding genome segments, and these structural motifs were found to be functionally interchangeable. Moreover, replacement of the TA in RNA2 with a stabilized form of the TALS directed both RNA2 replication and packaging of both genome segments. Based on their comparable properties and considering evolutionary factors, we propose that the TALS appeared de novo in RNA1 first and, subsequently, the TA arose de novo in RNA2 as a functional mimic of the TALS. This and other related information were used to formulate a plausible evolutionary pathway to describe the genesis of the bi-segmented RCNMV genome. The resulting scenario provides an evolutionary framework to further explore and test possible origins of this segmented RNA plant virus.
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Affiliation(s)
- Laura R. Newburn
- Department of Biology, York University, Toronto, Ontario, Canada
| | - K. Andrew White
- Department of Biology, York University, Toronto, Ontario, Canada
- * E-mail:
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Gunawardene CD, Newburn LR, White K. A 212-nt long RNA structure in the Tobacco necrosis virus-D RNA genome is resistant to Xrn degradation. Nucleic Acids Res 2019; 47:9329-9342. [PMID: 31392982 PMCID: PMC6755097 DOI: 10.1093/nar/gkz668] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2018] [Revised: 06/26/2019] [Accepted: 07/25/2019] [Indexed: 12/16/2022] Open
Abstract
Plus-strand RNA viruses can accumulate viral RNA degradation products during infections. Some of these decay intermediates are generated by the cytosolic 5'-to-3' exoribonuclease Xrn1 (mammals and yeast) or Xrn4 (plants) and are formed when the enzyme stalls on substrate RNAs upon encountering inhibitory RNA structures. Many Xrn-generated RNAs correspond to 3'-terminal segments within the 3'-UTR of viral genomes and perform important functions during infections. Here we have investigated a 3'-terminal small viral RNA (svRNA) generated by Xrn during infections with Tobacco necrosis virus-D (family Tombusviridae). Our results indicate that (i) unlike known stalling RNA structures that are compact and modular, the TNV-D structure encompasses the entire 212 nt of the svRNA and is not functionally transposable, (ii) at least two tertiary interactions within the RNA structure are required for effective Xrn blocking and (iii) most of the svRNA generated in infections is derived from viral polymerase-generated subgenomic mRNA1. In vitro and in vivo analyses allowed for inferences on roles for the svRNA. Our findings provide a new and distinct addition to the growing list of Xrn-resistant viral RNAs and stalling structures found associated with different plant and animal RNA viruses.
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Affiliation(s)
| | - Laura R Newburn
- Department of Biology, York University, Toronto, Ontario, M3J 1P3, Canada
| | - K Andrew White
- Department of Biology, York University, Toronto, Ontario, M3J 1P3, Canada
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Gunawardene CD, Donaldson LW, White KA. Tombusvirus polymerase: Structure and function. Virus Res 2017; 234:74-86. [PMID: 28111194 DOI: 10.1016/j.virusres.2017.01.012] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2016] [Revised: 12/30/2016] [Accepted: 01/13/2017] [Indexed: 12/25/2022]
Abstract
Tombusviruses are small icosahedral viruses that possess plus-sense RNA genomes ∼4.8kb in length. The type member of the genus, tomato bushy stunt virus (TBSV), encodes a 92kDa (p92) RNA-dependent RNA polymerase (RdRp) that is responsible for viral genome replication and subgenomic (sg) mRNA transcription. Several functionally relevant regions in p92 have been identified and characterized, including transmembrane domains, RNA-binding segments, membrane targeting signals, and oligomerization domains. Moreover, conserved tombusvirus-specific motifs in the C-proximal region of the RdRp have been shown to modulate viral genome replication, sg mRNA transcription, and trans-replication of subviral replicons. Interestingly, p92 is initially non-functional, and requires an accessory viral protein, p33, as well as viral RNA, host proteins, and intracellular membranes to become active. These and other host factors, through a well-orchestrated process guided by the viral replication proteins, mediate the assembly of membrane-associated virus replicase complexes (VRCs). Here, we describe what is currently known about the structure and function of the tombusvirus RdRp and how it utilizes host components to build VRCs that synthesize viral RNAs.
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Affiliation(s)
| | - Logan W Donaldson
- Department of Biology, York University, Toronto, Ontario, M3J 1P3, Canada
| | - K Andrew White
- Department of Biology, York University, Toronto, Ontario, M3J 1P3, Canada.
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A novel member of the Tombusviridae from a wild legume, Gompholobium preissii. Arch Virol 2016; 161:2893-8. [PMID: 27456427 DOI: 10.1007/s00705-016-2992-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2016] [Accepted: 07/16/2016] [Indexed: 10/21/2022]
Abstract
As part of an investigation into viruses of wild plants in Australia, a contiguous sequence of 3935 nucleotides was obtained after shotgun sequencing of RNA isolated from an asymptomatic wild legume, Gompholobium preissii. Phylogenetic analysis of the sequence revealed that it most closely resembled that of Trailing lespedeza virus 1 (TLV1), a virus isolated from a wild legume in America. The proposed virus, named Gompholobium virus A, and TLV1 are genetically closest to viruses in the genera Alphacarmovirus and Pelarspovirus, family Tombusviridae, but they share features distinguishing them from both groups.
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Scheets K, Jordan R, White KA, Hernández C. Pelarspovirus, a proposed new genus in the family Tombusviridae. Arch Virol 2015; 160:2385-93. [PMID: 26149249 DOI: 10.1007/s00705-015-2500-5] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2015] [Accepted: 06/13/2015] [Indexed: 11/29/2022]
Abstract
Currently, the family Tombusviridae encompasses thirteen viral genera that contain single-stranded, positive-sense RNA genomes and isometric virions; the exception being the genus Umbravirus, whose members do not encode a coat protein (CP). A new genus, tentatively named Pelarspovirus, is proposed to be added to this family and would include five members, with Pelargonium line pattern virus recommended as the type species. Viruses assigned to this proposed genus have monopartite genomes encoding five open reading frames (ORFs) that include two 5'-proximal replication proteins, two centrally located movement proteins (MP1 and MP2) and a 3'-proximal CP that, at least for pelargonium line pattern virus (PLPV), has been shown to act also as suppressor of RNA silencing. Distinguishing characteristics of these viruses include i) production of a single, tricistronic subgenomic RNA for expression of MP and CP genes, ii) presence of a non-AUG start codon (CUG or GUG) initiating the MP2 ORF, iii) absence of AUG codons in any frame between the AUG initiation codons of MP1 and CP genes, and iv) sequence-based phylogenetic clustering of all encoded proteins in separate clades from those of other family members.
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Affiliation(s)
- Kay Scheets
- Department of Botany, 301 Physical Sciences, Oklahoma State University, Stillwater, OK, 74078-3013, USA,
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Sõmera M, Sarmiento C, Truve E. Overview on Sobemoviruses and a Proposal for the Creation of the Family Sobemoviridae. Viruses 2015; 7:3076-115. [PMID: 26083319 PMCID: PMC4488728 DOI: 10.3390/v7062761] [Citation(s) in RCA: 48] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/18/2015] [Accepted: 06/02/2015] [Indexed: 12/26/2022] Open
Abstract
The genus Sobemovirus, unassigned to any family, consists of viruses with single-stranded plus-oriented single-component RNA genomes and small icosahedral particles. Currently, 14 species within the genus have been recognized by the International Committee on Taxonomy of Viruses (ICTV) but several new species are to be recognized in the near future. Sobemovirus genomes are compact with a conserved structure of open reading frames and with short untranslated regions. Several sobemoviruses are important pathogens. Moreover, over the last decade sobemoviruses have become important model systems to study plant virus evolution. In the current review we give an overview of the structure and expression of sobemovirus genomes, processing and functions of individual proteins, particle structure, pathology and phylogenesis of sobemoviruses as well as of satellite RNAs present together with these viruses. Based on a phylogenetic analysis we propose that a new family Sobemoviridae should be recognized including the genera Sobemovirus and Polemovirus. Finally, we outline the future perspectives and needs for the research focusing on sobemoviruses.
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Affiliation(s)
- Merike Sõmera
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Cecilia Sarmiento
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
| | - Erkki Truve
- Department of Gene Technology, Tallinn University of Technology, Akadeemia tee 15, 12618 Tallinn, Estonia.
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