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Koloniuk I, Fránová J, Přibylová J, Sarkisova T, Špak J, Tan JL, Zemek R, Čmejla R, Rejlová M, Valentová L, Sedlák J, Holub J, Skalík J, Blystad DR, Sapkota B, Hamborg Z. Molecular Characterization of a Novel Enamovirus Infecting Raspberry. Viruses 2023; 15:2281. [PMID: 38140523 PMCID: PMC10747458 DOI: 10.3390/v15122281] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Revised: 11/10/2023] [Accepted: 11/16/2023] [Indexed: 12/24/2023] Open
Abstract
Raspberry plants, valued for their fruits, are vulnerable to a range of viruses that adversely affect their yield and quality. Utilizing high-throughput sequencing (HTS), we identified a novel virus, tentatively named raspberry enamovirus 1 (RaEV1), in three distinct raspberry plants. This study provides a comprehensive characterization of RaEV1, focusing on its genomic structure, phylogeny, and possible transmission routes. Analysis of nearly complete genomes from 14 RaEV1 isolates highlighted regions of variance, particularly marked by indel events. The evidence from phylogenetic and sequence analyses supports the classification of RaEV1 as a distinct species within the Enamovirus genus. Among the 289 plant and 168 invertebrate samples analyzed, RaEV1 was detected in 10.4% and 0.4%, respectively. Most detections occurred in plants that were also infected with other common raspberry viruses. The virus was present in both commercial and wild raspberries, indicating the potential of wild plants to act as viral reservoirs. Experiments involving aphids as potential vectors demonstrated their ability to acquire RaEV1 but not to successfully transmit it to plants.
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Affiliation(s)
- Igor Koloniuk
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jana Fránová
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jaroslava Přibylová
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Tatiana Sarkisova
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Josef Špak
- Institute of Plant Molecular Biology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.F.); (J.P.); (T.S.); (J.Š.)
| | - Jiunn Luh Tan
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.L.T.); (R.Z.)
- Faculty of Science, University of South Bohemia, 370 05 Ceske Budejovice, Czech Republic
| | - Rostislav Zemek
- Institute of Entomology, Biology Centre, Czech Academy of Sciences, 370 05 Ceske Budejovice, Czech Republic; (J.L.T.); (R.Z.)
| | - Radek Čmejla
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Martina Rejlová
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Lucie Valentová
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Jiří Sedlák
- Research and Breeding Institute of Pomology Holovousy Ltd., 508 01 Horice, Czech Republic; (R.Č.); (M.R.); (L.V.); (J.S.)
| | - Jan Holub
- Jan Holub Ltd., 783 25 Bouzov, Czech Republic; (J.H.); (J.S.)
| | - Jan Skalík
- Jan Holub Ltd., 783 25 Bouzov, Czech Republic; (J.H.); (J.S.)
| | - Dag-Ragnar Blystad
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
| | - Bijaya Sapkota
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
| | - Zhibo Hamborg
- Norwegian Institute of Bioeconomy Research, 1433 Aas, Norway; (D.-R.B.); (B.S.); (Z.H.)
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2
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Peng Q, Li W, Zhou X, Sun C, Hou Y, Hu M, Fu S, Zhang J, Kundu JK, Lei L. Genetic Diversity Analysis of Brassica Yellows Virus Causing Aberrant Color Symptoms in Oilseed Rape. PLANTS (BASEL, SWITZERLAND) 2023; 12:1008. [PMID: 36903869 PMCID: PMC10005696 DOI: 10.3390/plants12051008] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/20/2023] [Accepted: 02/21/2023] [Indexed: 06/18/2023]
Abstract
The emergence of brassica yellow virus (BrYV) has increasingly damaged crucifer crops in China in recent years. In 2020, a large number of oilseed rape in Jiangsu showed aberrant leaf color. A combined RNA-seq and RT-PCR analysis identified BrYV as the major viral pathogen. A subsequent field survey showed that the average incidence of BrYV was 32.04%. In addition to BrYV, turnip mosaic virus (TuMV) was also frequently detected. As a result, two near full-length BrYV isolates, BrYV-814NJLH and BrYV-NJ13, were cloned. Based on the newly obtained sequences and the reported BrYV and turnip yellow virus (TuYV) isolates, a phylogenetic analysis was performed, and it was found that all BrYV isolates share a common root with TuYV. Pairwise amino acid identity analysis revealed that both P2 and P3 were conserved in BrYV. Additionally, recombination analysis revealed seven recombinant events in BrYV as TuYV. We also attempted to determine BrYV infection by quantitative leaf color index, but no significant correlation was found between the two. Systemic observations indicated that BrYV-infected plants had different symptoms, such as no symptom, purple stem base and red old leaves. Overall, our work proves that BrYV is closely related to TuYV and could be considered as an epidemic strain for oilseed rape in Jiangsu.
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Affiliation(s)
- Qi Peng
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
- Institute of Life Sciences, Jiangsu University, Zhenjiang 212013, China
| | - Wei Li
- College of Agronomy and Biotechnology, China Agricultural University, Beijing 100193, China
| | - Xiaoying Zhou
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Chengming Sun
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Yan Hou
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
| | - Maolong Hu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Sanxiong Fu
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jiefu Zhang
- Key Laboratory of Cotton and Rapeseed, Ministry of Agriculture, Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China
| | - Jiban Kumar Kundu
- Plant Virus and Vector Interactions-Centre for Plant Virus Research, Crop Research Institute, Drnovska 507/73, 161 06 Praha, Czech Republic
- Laboratory of Virology-Centre for Plant Virus Research, Institute of Experimental Botany of the Czech Academy of Sciences, Rozvojová 263, 165 02 Prague, Czech Republic
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China
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3
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Lappe RR, Elmore MG, Lozier ZR, Jander G, Miller WA, Whitham SA. Metagenomic identification of novel viruses of maize and teosinte in North America. BMC Genomics 2022; 23:767. [DOI: 10.1186/s12864-022-09001-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 11/10/2022] [Indexed: 11/25/2022] Open
Abstract
Abstract
Background
Maize-infecting viruses are known to inflict significant agronomic yield loss throughout the world annually. Identification of known or novel causal agents of disease prior to outbreak is imperative to preserve food security via future crop protection efforts. Toward this goal, a large-scale metagenomic approach utilizing high throughput sequencing (HTS) was employed to identify novel viruses with the potential to contribute to yield loss of graminaceous species, particularly maize, in North America.
Results
Here we present four novel viruses discovered by HTS and individually validated by Sanger sequencing. Three of these viruses are RNA viruses belonging to either the Betaflexiviridae or Tombusviridae families. Additionally, a novel DNA virus belonging to the Geminiviridae family was discovered, the first Mastrevirus identified in North American maize.
Conclusions
Metagenomic studies of crop and crop-related species such as this may be useful for the identification and surveillance of known and novel viral pathogens of crops. Monitoring related species may prove useful in identifying viruses capable of infecting crops due to overlapping insect vectors and viral host-range to protect food security.
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Boissinot S, Ducousso M, Brault V, Drucker M. Bioluminescence Production by Turnip Yellows Virus Infectious Clones: A New Way to Monitor Plant Virus Infection. Int J Mol Sci 2022; 23:ijms232213685. [PMID: 36430165 PMCID: PMC9692398 DOI: 10.3390/ijms232213685] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2022] [Revised: 10/25/2022] [Accepted: 10/29/2022] [Indexed: 11/10/2022] Open
Abstract
We used the NanoLuc luciferase bioluminescent reporter system to detect turnip yellows virus (TuYV) in infected plants. For this, TuYV was genetically tagged by replacing the C-terminal part of the RT protein with full-length NanoLuc (TuYV-NL) or with the N-terminal domain of split NanoLuc (TuYV-N65-NL). Wild-type and recombinant viruses were agro-infiltrated in Nicotiana benthamiana, Montia perfoliata, and Arabidopsis thaliana. ELISA confirmed systemic infection and similar accumulation of the recombinant viruses in N. benthamiana and M. perfoliata but reduced systemic infection and lower accumulation in A. thaliana. RT-PCR analysis indicated that the recombinant sequences were stable in N. benthamiana and M. perfoliata but not in A. thaliana. Bioluminescence imaging detected TuYV-NL in inoculated and systemically infected leaves. For the detection of split NanoLuc, we constructed transgenic N. benthamiana plants expressing the C-terminal domain of split NanoLuc. Bioluminescence imaging of these plants after agro-infiltration with TuYV-N65-NL allowed the detection of the virus in systemically infected leaves. Taken together, our results show that NanoLuc luciferase can be used to monitor infection with TuYV.
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Affiliation(s)
- Sylvaine Boissinot
- Santé de la Vigne et Qualiité du Vin, Unité Mixte de Recherche 1131, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre Grand Est, Université Strasbourg, 68000 Colmar, France
| | - Marie Ducousso
- Plant Health Institute Montpellier, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, CIRAD, Institut de Recherche pour le Développement, Institut Agro, Université Montpellier, 34980 Montferrier sur Lez, France
| | - Véronique Brault
- Santé de la Vigne et Qualiité du Vin, Unité Mixte de Recherche 1131, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre Grand Est, Université Strasbourg, 68000 Colmar, France
| | - Martin Drucker
- Santé de la Vigne et Qualiité du Vin, Unité Mixte de Recherche 1131, Institut National de Recherche pour l’Agriculture, l’Alimentation et l’Environnement, Centre Grand Est, Université Strasbourg, 68000 Colmar, France
- Correspondence:
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5
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Schiltz CJ, Wilson JR, Hosford CJ, Adams MC, Preising SE, DeBlasio SL, MacLeod HJ, Van Eck J, Heck ML, Chappie JS. Polerovirus N-terminal readthrough domain structures reveal molecular strategies for mitigating virus transmission by aphids. Nat Commun 2022; 13:6368. [PMID: 36289207 PMCID: PMC9606263 DOI: 10.1038/s41467-022-33979-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2022] [Accepted: 10/10/2022] [Indexed: 12/25/2022] Open
Abstract
Poleroviruses, enamoviruses, and luteoviruses are icosahedral, positive sense RNA viruses that cause economically important diseases in food and fiber crops. They are transmitted by phloem-feeding aphids in a circulative manner that involves the movement across and within insect tissues. The N-terminal portion of the viral readthrough domain (NRTD) has been implicated as a key determinant of aphid transmission in each of these genera. Here, we report crystal structures of the NRTDs from the poleroviruses turnip yellow virus (TuYV) and potato leafroll virus (PLRV) at 1.53-Å and 2.22-Å resolution, respectively. These adopt a two-domain arrangement with a unique interdigitated topology and form highly conserved dimers that are stabilized by a C-terminal peptide that is critical for proper folding. We demonstrate that the PLRV NRTD can act as an inhibitor of virus transmission and identify NRTD mutant variants that are lethal to aphids. Sequence conservation argues that enamovirus and luteovirus NRTDs will follow the same structural blueprint, which affords a biological approach to block the spread of these agricultural pathogens in a generalizable manner.
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Affiliation(s)
- Carl J Schiltz
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
- Department of Biological Sciences, Vanderbilt University, Nashville, TN, 37232, USA
| | - Jennifer R Wilson
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- USDA-Agricultural Research Service, Corn, Soybean & Wheat Quality Research Unit, Wooster, OH, 44691, USA
| | - Christopher J Hosford
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
- LifeMine Therapeutics, Cambridge, MA, 02140, USA
| | - Myfanwy C Adams
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA
| | - Stephanie E Preising
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
| | - Stacy L DeBlasio
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA
| | - Hannah J MacLeod
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA
- Accelevir Diagnostics, Baltimore, MD, 21202, USA
| | - Joyce Van Eck
- Section of Plant Breeding and Genetics, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA
| | - Michelle L Heck
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrative Plant Sciences, Cornell University, Ithaca, NY, 14853, USA.
- USDA-Agricultural Research Service, Emerging Pest and Pathogen Research Unit, Ithaca, NY, 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY, 14853, USA.
| | - Joshua S Chappie
- Department of Molecular Medicine, Cornell University, Ithaca, NY, 14853, USA.
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Farooq T, Hussain MD, Shakeel MT, Riaz H, Waheed U, Siddique M, Shahzadi I, Aslam MN, Tang Y, She X, He Z. Global genetic diversity and evolutionary patterns among Potato leafroll virus populations. Front Microbiol 2022; 13:1022016. [PMID: 36590416 PMCID: PMC9801716 DOI: 10.3389/fmicb.2022.1022016] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2022] [Accepted: 09/12/2022] [Indexed: 01/04/2023] Open
Abstract
Potato leafroll virus (PLRV) is a widespread and one of the most damaging viral pathogens causing significant quantitative and qualitative losses in potato worldwide. The current knowledge of the geographical distribution, standing genetic diversity and the evolutionary patterns existing among global PLRV populations is limited. Here, we employed several bioinformatics tools and comprehensively analyzed the diversity, genomic variability, and the dynamics of key evolutionary factors governing the global spread of this viral pathogen. To date, a total of 84 full-genomic sequences of PLRV isolates have been reported from 22 countries with most genomes documented from Kenya. Among all PLRV-encoded major proteins, RTD and P0 displayed the highest level of nucleotide variability. The highest percentage of mutations were associated with RTD (38.81%) and P1 (31.66%) in the coding sequences. We detected a total of 10 significantly supported recombination events while the most frequently detected ones were associated with PLRV genome sequences reported from Kenya. Notably, the distribution patterns of recombination breakpoints across different genomic regions of PLRV isolates remained variable. Further analysis revealed that with exception of a few positively selected codons, a major part of the PLRV genome is evolving under strong purifying selection. Protein disorder prediction analysis revealed that CP-RTD had the highest percentage (48%) of disordered amino acids and the majority (27%) of disordered residues were positioned at the C-terminus. These findings will extend our current knowledge of the PLRV geographical prevalence, genetic diversity, and evolutionary factors that are presumably shaping the global spread and successful adaptation of PLRV as a destructive potato pathogen to geographically isolated regions of the world.
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Affiliation(s)
- Tahir Farooq
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Muhammad Dilshad Hussain
- State Key Laboratory for Agro-Biotechnology, and Ministry of Agriculture and Rural Affairs, Key Laboratory for Pest Monitoring and Green Management, Department of Plant Pathology, China Agricultural University, Beijing, China
| | - Muhammad Taimoor Shakeel
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Hasan Riaz
- Institute of Plant Protection, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Ummara Waheed
- Institute of Plant Breeding and Biotechnology, Muhammad Nawaz Shareef University of Agriculture, Multan, Pakistan
| | - Maria Siddique
- Department of Environmental Sciences, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Irum Shahzadi
- Department of Biotechnology, COMSATS University Islamabad, Abbottabad, Pakistan
| | - Muhammad Naveed Aslam
- Department of Plant Pathology, Faculty of Agriculture & Environment, The Islamia University of Bahawalpur, Bahawalpur, Pakistan
| | - Yafei Tang
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China
| | - Xiaoman She
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
| | - Zifu He
- Guangdong Academy of Agricultural Sciences, Plant Protection Research Institute and Guangdong Provincial Key Laboratory of High Technology for Plant Protection, Guangzhou, China,*Correspondence: Xiaoman She, ; Zifu He,
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Miller WA, Lozier Z. Yellow Dwarf Viruses of Cereals: Taxonomy and Molecular Mechanisms. ANNUAL REVIEW OF PHYTOPATHOLOGY 2022; 60:121-141. [PMID: 35436423 DOI: 10.1146/annurev-phyto-121421-125135] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/14/2023]
Abstract
Yellow dwarf viruses are the most economically important and widespread viruses of cereal crops. Although they share common biological properties such as phloem limitation and obligate aphid transmission, the replication machinery and associated cis-acting signals of these viruses fall into two unrelated taxa represented by Barley yellow dwarf virus and Cereal yellow dwarf virus. Here, we explain the reclassification of these viruses based on their very different genomes. We also provide an overview of viral protein functions and their interactions with the host and vector, replication mechanisms of viral and satellite RNAs, and the complex gene expression strategies. Throughout, we point out key unanswered questions in virus evolution, structural biology, and genome function and replication that, when answered, may ultimately provide new tools for virus management.
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Affiliation(s)
- W Allen Miller
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
| | - Zachary Lozier
- Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, USA;
- Bioinformatics and Computational Biology Program, Iowa State University, Ames, Iowa, USA
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8
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Xu T, Lei L, Fu Y, Yang X, Luo H, Chen X, Wu X, Wang Y, Jia MA. Molecular Characterization of a Novel Polerovirus Infecting Soybean in China. Viruses 2022; 14:v14071428. [PMID: 35891408 PMCID: PMC9322011 DOI: 10.3390/v14071428] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Revised: 06/24/2022] [Accepted: 06/27/2022] [Indexed: 02/01/2023] Open
Abstract
Poleroviruses are positive-sense, single-stranded viruses. In this study, we describe the identification of a novel polerovirus isolated from soybean displaying curled leaves. The complete viral genome sequence was identified using high-throughput sequencing and confirmed using rapid amplification of cDNA ends (RACE), RT-PCR and Sanger sequencing. Its genome organization is typical of the members of genus Polerovirus, containing seven putative open reading frames (ORFs). The full genome is composed of single-stranded RNA of 5822 nucleotides in length, with the highest nucleotide sequence identity (79.07% with 63% coverage) for cowpea polerovirus 2 (CPPV2). Amino acid sequence identities of the protein products between the virus and its relatives are below the threshold determined by the International Committee of Taxonomy of Viruses (ICTV) for species demarcation, and this strongly supports this virus’ status as a novel species, for which the name soybean chlorotic leafroll virus (SbCLRV) is proposed. Recombination analysis identified a recombination event in the ORF5 of the 3’ portion in the genome. Phylogenetic analyses of the genome and encoded protein sequences revealed that the new virus is closely related to phasey bean mild yellows virus, CPPV2 and siratro latent polerovirus. Subsequently, we demonstrated the infectivity of SbCLRV in Nicotiana benthamiana via infectious cDNA clone generation and agroinoculation.
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Affiliation(s)
- Tengzhi Xu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Lei Lei
- Guizhou Rapeseed Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550008, China;
| | - Yong Fu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Xiaolan Yang
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Hao Luo
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Xiangru Chen
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Xiaomao Wu
- Institute of Crop Protection, College of Agriculture, Guizhou University, Guiyang 550025, China; (T.X.); (Y.F.); (X.Y.); (H.L.); (X.C.); (X.W.)
| | - Yaqin Wang
- State Key Laboratory of Rice Biology Institute of Biotechnology, Zhejiang University, Hangzhou 310058, China
- Correspondence: (Y.W.); (M.-a.J.)
| | - Meng-ao Jia
- Guizhou Academy of Tobacco Sciences, Guiyang 550001, China
- Correspondence: (Y.W.); (M.-a.J.)
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9
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Sahoo S, Singh D, Singh A, Pandit M, Vasu K, Som S, Pullagurla NJ, Laha D, Eswarappa SM. Identification and functional characterization of mRNAs that exhibit stop codon readthrough in Arabidopsis thaliana. J Biol Chem 2022; 298:102173. [PMID: 35752360 PMCID: PMC9293766 DOI: 10.1016/j.jbc.2022.102173] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Revised: 06/16/2022] [Accepted: 06/18/2022] [Indexed: 11/29/2022] Open
Abstract
Stop codon readthrough (SCR) is the process of continuation of translation beyond the stop codon, generating protein isoforms with C-terminal extensions. SCR has been observed in viruses, fungi, and multicellular organisms, including mammals. However, SCR is largely unexplored in plants. In this study, we have analyzed ribosome profiling datasets to identify mRNAs that exhibit SCR in Arabidopsis thaliana. Analyses of the ribosome density, ribosome coverage, and three-nucleotide periodicity of the ribosome profiling reads in the mRNA region downstream of the stop codon provided strong evidence for SCR in mRNAs of 144 genes. We show that SCR generated putative evolutionarily conserved nuclear localization signals, transmembrane helices, and intrinsically disordered regions in the C-terminal extensions of several of these proteins. Furthermore, gene ontology (GO) functional enrichment analysis revealed that these 144 genes belong to three major functional groups - translation, photosynthesis, and abiotic stress tolerance. Using a luminescence-based readthrough assay, we experimentally demonstrated SCR in representative mRNAs belonging to each of these functional classes. Finally, using microscopy, we show that the SCR product of one gene that contains a nuclear localization signal at the C-terminal extension, CURT1B, localizes to the nucleus as predicted. Based on these observations, we propose that SCR plays an important role in plant physiology by regulating protein localization and function.
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Affiliation(s)
- Sarthak Sahoo
- Undergraduate Program, Indian Institute of Science, Bengaluru, India; Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Divyoj Singh
- Undergraduate Program, Indian Institute of Science, Bengaluru, India
| | - Anumeha Singh
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Madhuparna Pandit
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Kirtana Vasu
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | - Saubhik Som
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
| | | | - Debabrata Laha
- Department of Biochemistry, Indian Institute of Science, Bengaluru, India
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10
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LaTourrette K, Holste NM, Garcia-Ruiz H. Polerovirus genomic variation. Virus Evol 2021; 7:veab102. [PMID: 35299789 PMCID: PMC8923251 DOI: 10.1093/ve/veab102] [Citation(s) in RCA: 20] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Revised: 11/21/2021] [Accepted: 12/03/2021] [Indexed: 01/01/2023] Open
Abstract
Abstract
The polerovirus (family Solemoviridae, genus Polerovirus) genome consists of single-, positive-strand RNA organized in overlapping open reading frames (ORFs) that, in addition to others, code for protein 0 (P0, a gene silencing suppressor), a coat protein (CP, ORF3), and a read-through domain (ORF5) that is fused to the CP to form a CP-read-through (RT) protein. The genus Polerovirus contains twenty-six virus species that infect a wide variety of plants from cereals to cucurbits, to peppers. Poleroviruses are transmitted by a wide range of aphid species in the genera Rhopalosiphum, Stiobion, Aphis, and Myzus. Aphid transmission is mediated both by the CP and by the CP-RT. In viruses, mutational robustness and structural flexibility are necessary for maintaining functionality in genetically diverse sets of host plants and vectors. Under this scenario, within a virus genome, mutations preferentially accumulate in areas that are determinants of host adaptation or vector transmission. In this study, we profiled genomic variation in poleroviruses. Consistent with their multifunctional nature, single-nucleotide variation and selection analyses showed that ORFs coding for P0 and the read-through domain within the CP-RT are the most variable and contain the highest frequency of sites under positive selection. An order/disorder analysis showed that protein P0 is not disordered. In contrast, proteins CP-RT and virus protein genome-linked (VPg) contain areas of disorder. Disorder is a property of multifunctional proteins with multiple interaction partners. The results described here suggest that using contrasting mechanisms, P0, VPg, and CP-RT mediate adaptation to host plants and to vectors and are contributors to the broad host and vector range of poleroviruses. Profiling genetic variation across the polerovirus genome has practical applications in diagnostics, breeding for resistance, and identification of susceptibility genes and contributes to our understanding of virus interactions with their host, vectors, and environment.
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Affiliation(s)
- Katherine LaTourrette
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
- Complex Biosystems Interdisciplinary Life Sciences Program, Institute of Agriculture and Natural Resources, University of Nebraska-Lincoln, 2200 Vine Street, Lincoln, NE 68583, USA
| | - Natalie M Holste
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
| | - Hernan Garcia-Ruiz
- Nebraska Center for Virology, University of Nebraska-Lincoln, 4240 Fair Street, Lincoln, NE 68583, USA
- Department of Plant Pathology, University of Nebraska-Lincoln, 406 Plant Science Hall, Lincoln, NE 68583, USA
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11
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Tissue-specific dynamic codon redefinition in Drosophila. Proc Natl Acad Sci U S A 2021; 118:2012793118. [PMID: 33500350 DOI: 10.1073/pnas.2012793118] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Translational stop codon readthrough occurs in organisms ranging from viruses to mammals and is especially prevalent in decoding Drosophila and viral mRNAs. Recoding of UGA, UAG, or UAA to specify an amino acid allows a proportion of the protein encoded by a single gene to be C-terminally extended. The extended product from Drosophila kelch mRNA is 160 kDa, whereas unextended Kelch protein, a subunit of a Cullin3-RING ubiquitin ligase, is 76 kDa. Previously we reported tissue-specific regulation of readthrough of the first kelch stop codon. Here, we characterize major efficiency differences in a variety of cell types. Immunoblotting revealed low levels of readthrough in malpighian tubules, ovary, and testis but abundant readthrough product in lysates of larval and adult central nervous system (CNS) tissue. Reporters of readthrough demonstrated greater than 30% readthrough in adult brains, and imaging in larval and adult brains showed that readthrough occurred in neurons but not glia. The extent of readthrough stimulatory sequences flanking the readthrough stop codon was assessed in transgenic Drosophila and in human tissue culture cells where inefficient readthrough occurs. A 99-nucleotide sequence with potential to form an mRNA stem-loop 3' of the readthrough stop codon stimulated readthrough efficiency. However, even with just six nucleotides of kelch mRNA sequence 3' of the stop codon, readthrough efficiency only dropped to 6% in adult neurons. Finally, we show that high-efficiency readthrough in the Drosophila CNS is common; for many neuronal proteins, C-terminal extended forms of individual proteins are likely relatively abundant.
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Urquidi-Camacho RA, Lokdarshi A, von Arnim AG. Translational gene regulation in plants: A green new deal. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1597. [PMID: 32367681 PMCID: PMC9258721 DOI: 10.1002/wrna.1597] [Citation(s) in RCA: 31] [Impact Index Per Article: 7.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/06/2020] [Revised: 03/31/2020] [Accepted: 04/01/2020] [Indexed: 01/09/2023]
Abstract
The molecular machinery for protein synthesis is profoundly similar between plants and other eukaryotes. Mechanisms of translational gene regulation are embedded into the broader network of RNA-level processes including RNA quality control and RNA turnover. However, over eons of their separate history, plants acquired new components, dropped others, and generally evolved an alternate way of making the parts list of protein synthesis work. Research over the past 5 years has unveiled how plants utilize translational control to defend themselves against viruses, regulate translation in response to metabolites, and reversibly adjust translation to a wide variety of environmental parameters. Moreover, during seed and pollen development plants make use of RNA granules and other translational controls to underpin developmental transitions between quiescent and metabolically active stages. The economics of resource allocation over the daily light-dark cycle also include controls over cellular protein synthesis. Important new insights into translational control on cytosolic ribosomes continue to emerge from studies of translational control mechanisms in viruses. Finally, sketches of coherent signaling pathways that connect external stimuli with a translational response are emerging, anchored in part around TOR and GCN2 kinase signaling networks. These again reveal some mechanisms that are familiar and others that are different from other eukaryotes, motivating deeper studies on translational control in plants. This article is categorized under: Translation > Translation Regulation RNA Structure and Dynamics > Influence of RNA Structure in Biological Systems RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
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Affiliation(s)
- Ricardo A. Urquidi-Camacho
- UT-ORNL Graduate School of Genome Science and Technology, The University of Tennessee, Knoxville, TN 37996
| | - Ansul Lokdarshi
- Department of Biochemistry & Cellular and Molecular Biology, University of Tennessee, Knoxville, TN 37996
| | - Albrecht G von Arnim
- Department of Biochemistry & Cellular and Molecular Biology and UT-ORNL Graduate School of Genome Science and Technology, University of Tennessee, Knoxville, TN 37996
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Introduction of a leaky stop codon as molecular tool in Chlamydomonas reinhardtii. PLoS One 2020; 15:e0237405. [PMID: 32817702 PMCID: PMC7440625 DOI: 10.1371/journal.pone.0237405] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2020] [Accepted: 07/24/2020] [Indexed: 02/07/2023] Open
Abstract
Expression of proteins in the chloroplast or mitochondria of the model green alga Chlamydomonas reinhardtii can be achieved by directly inserting transgenes into organellar genomes, or through nuclear expression and post-translational import. A number of tools have been developed in the literature for achieving high expression levels from the nuclear genome despite messy genomic integration and widespread silencing of transgenes. Here, recent advances in the field are combined and two systems of bicistronic expression, based on ribosome reinitiation or ribosomal skip induced by a viral 2A sequence, are compared side-by-side. Further, the small subunit of Rubisco (RBCS) was developed as a functional nuclear reporter for successful chloroplast import and restoration of photosynthesis: To be able to combine RBCS with a Venus fluorescent reporter without compromising photosynthetic activity, a leaky stop codon is introduced as a novel molecular tool that allows the simultaneous expression of functional and fluorescently tagged versions of the protein from a single construct.
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Gupta A, Bansal M. RNA-mediated translation regulation in viral genomes: computational advances in the recognition of sequences and structures. Brief Bioinform 2020; 21:1151-1163. [PMID: 31204430 PMCID: PMC7109810 DOI: 10.1093/bib/bbz054] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/25/2018] [Revised: 03/24/2019] [Accepted: 04/15/2019] [Indexed: 12/30/2022] Open
Abstract
RNA structures are widely distributed across all life forms. The global conformation of these structures is defined by a variety of constituent structural units such as helices, hairpin loops, kissing-loop motifs and pseudoknots, which often behave in a modular way. Their ubiquitous distribution is associated with a variety of functions in biological processes. The location of these structures in the genomes of RNA viruses is often coordinated with specific processes in the viral life cycle, where the presence of the structure acts as a checkpoint for deciding the eventual fate of the process. These structures have been found to adopt complex conformations and exert their effects by interacting with ribosomes, multiple host translation factors and small RNA molecules like miRNA. A number of such RNA structures have also been shown to regulate translation in viruses at the level of initiation, elongation or termination. The role of various computational studies in the preliminary identification of such sequences and/or structures and subsequent functional analysis has not been fully appreciated. This review aims to summarize the processes in which viral RNA structures have been found to play an active role in translational regulation, their global conformational features and the bioinformatics/computational tools available for the identification and prediction of these structures.
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Affiliation(s)
- Asmita Gupta
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
| | - Manju Bansal
- Molecular Biophysics Unit, Indian Institute of Science, Bangalore, India
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15
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Dyle MC, Kolakada D, Cortazar MA, Jagannathan S. How to get away with nonsense: Mechanisms and consequences of escape from nonsense-mediated RNA decay. WILEY INTERDISCIPLINARY REVIEWS. RNA 2020; 11:e1560. [PMID: 31359616 PMCID: PMC10685860 DOI: 10.1002/wrna.1560] [Citation(s) in RCA: 67] [Impact Index Per Article: 16.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Revised: 06/25/2019] [Accepted: 07/04/2019] [Indexed: 11/04/2023]
Abstract
Nonsense-mediated RNA decay (NMD) is an evolutionarily conserved RNA quality control process that serves both as a mechanism to eliminate aberrant transcripts carrying premature stop codons, and to regulate expression of some normal transcripts. For a quality control process, NMD exhibits surprising variability in its efficiency across transcripts, cells, tissues, and individuals in both physiological and pathological contexts. Whether an aberrant RNA is spared or degraded, and by what mechanism, could determine the phenotypic outcome of a disease-causing mutation. Hence, understanding the variability in NMD is not only important for clinical interpretation of genetic variants but also may provide clues to identify novel therapeutic approaches to counter genetic disorders caused by nonsense mutations. Here, we discuss the current knowledge of NMD variability and the mechanisms that allow certain transcripts to escape NMD despite the presence of NMD-inducing features. This article is categorized under: RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA in Disease and Development > RNA in Disease RNA Turnover and Surveillance > Regulation of RNA Stability.
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Affiliation(s)
- Michael C. Dyle
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Divya Kolakada
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- Molecular Biology Graduate Program, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Michael A. Cortazar
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
| | - Sujatha Jagannathan
- Department of Biochemistry and Molecular Genetics, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
- RNA Bioscience Initiative, University of Colorado Anschutz Medical Campus, Aurora, CO 80045, USA
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Debat HJ, Bejerman N. Novel bird’s-foot trefoil RNA viruses provide insights into a clade of legume-associated enamoviruses and rhabdoviruses. Arch Virol 2019; 164:1419-1426. [DOI: 10.1007/s00705-019-04193-1] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2018] [Accepted: 02/02/2019] [Indexed: 10/27/2022]
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17
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Kamoshita N, Tominaga SI. UGA stop codon readthrough to translate intergenic region of Plautia stali intestine virus does not require RNA structures forming internal ribosomal entry site. RNA (NEW YORK, N.Y.) 2019; 25:90-104. [PMID: 30337458 PMCID: PMC6298568 DOI: 10.1261/rna.065466.117] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 12/25/2017] [Accepted: 10/08/2018] [Indexed: 06/08/2023]
Abstract
The translation of capsid proteins of Plautia stali intestine virus (PSIV), encoded in its second open reading frame (ORF2), is directed by an internal ribosomal entry site (IRES) located in the intergenic region (IGR). Owing to the specific properties of PSIV IGR in terms of nucleotide length and frame organization, capsid proteins are also translated via stop codon readthrough in mammalian cultured cells as an extension of translation from the first ORF (ORF1) and IGR. To delineate stop codon readthrough in PSIV, we determined requirements of cis-acting elements through a molecular genetics approach applied in both cell-free translation systems and cultured cells. Mutants with deletions from the 3' end of IGR revealed that almost none of the sequence of IGR is necessary for readthrough, apart from the 5'-terminal codon CUA. Nucleotide replacement of this CUA trinucleotide or change of the termination codon from UGA severely impaired readthrough. Chemical mapping of the IGR region of the most active 3' deletion mutant indicated that this defined minimal element UGACUA, together with its downstream sequence, adopts a single-stranded conformation. Stimulatory activities of downstream RNA structures identified to date in gammaretrovirus, coltivirus, and alphavirus were not detected in the context of PSIV IGR, despite the presence of structures for IRES. To our knowledge, PSIV IGR is the first example of stop codon readthrough that is solely defined by the local hexamer sequence, even though the sequence is adjacent to an established region of RNA secondary/tertiary structures.
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Affiliation(s)
- Nobuhiko Kamoshita
- Department of Biochemistry, Jichi Medical University, Shimotsuke-shi, Tochigi-ken, 329-0498, Japan
| | - Shin-Ichi Tominaga
- Department of Biochemistry, Jichi Medical University, Shimotsuke-shi, Tochigi-ken, 329-0498, Japan
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Targeted disruption of aphid transmission: a vision for the management of crop diseases caused by Luteoviridae members. Curr Opin Virol 2018; 33:24-32. [DOI: 10.1016/j.coviro.2018.07.007] [Citation(s) in RCA: 26] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2018] [Accepted: 07/05/2018] [Indexed: 12/18/2022]
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Xu Y, Da Silva WL, Qian Y, Gray SM. An aromatic amino acid and associated helix in the C-terminus of the potato leafroll virus minor capsid protein regulate systemic infection and symptom expression. PLoS Pathog 2018; 14:e1007451. [PMID: 30440046 PMCID: PMC6264904 DOI: 10.1371/journal.ppat.1007451] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2018] [Revised: 11/29/2018] [Accepted: 11/01/2018] [Indexed: 12/26/2022] Open
Abstract
The C-terminal region of the minor structural protein of potato leafroll virus (PLRV), known as the readthrough protein (RTP), is involved in efficient virus movement, tissue tropism and symptom development. Analysis of numerous C-terminal deletions identified a five-amino acid motif that is required for RTP function. A PLRV mutant expressing RTP with these five amino acids deleted (Δ5aa-RTP) was compromised in systemic infection and symptom expression. Although the Δ5aa-RTP mutant was able to move long distance, limited infection foci were observed in systemically infected leaves suggesting that these five amino acids regulate virus phloem loading in the inoculated leaves and/or unloading into the systemically infected tissues. The 5aa deletion did not alter the efficiency of RTP translation, nor impair RTP self-interaction or its interaction with P17, the virus movement protein. However, the deletion did alter the subcellular localization of RTP. When co-expressed with a PLRV infectious clone, a GFP tagged wild-type RTP was localized to discontinuous punctate spots along the cell periphery and was associated with plasmodesmata, although localization was dependent upon the developmental stage of the plant tissue. In contrast, the Δ5aa-RTP-GFP aggregated in the cytoplasm. Structural modeling indicated that the 5aa deletion would be expected to perturb an α-helix motif. Two of 30 plants infected with Δ5aa-RTP developed a wild-type virus infection phenotype ten weeks post-inoculation. Analysis of the virus population in these plants by deep sequencing identified a duplication of sequences adjacent to the deletion that were predicted to restore the α-helix motif. The subcellular distribution of the RTP is regulated by the 5-aa motif which is under strong selection pressure and in turn contributes to the efficient long distance movement of the virus and the induction of systemic symptoms.
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Affiliation(s)
- Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Washington Luis Da Silva
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
| | - Yajuan Qian
- Institute of Biotechnology, Zhejiang University, Hangzhou, China
| | - Stewart M. Gray
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY, United States of America
- Emerging Pest and Pathogens Research Unit, USDA, ARS, Ithaca, NY, United States of America
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DeBlasio SL, Xu Y, Johnson RS, Rebelo AR, MacCoss MJ, Gray SM, Heck M. The Interaction Dynamics of Two Potato Leafroll Virus Movement Proteins Affects Their Localization to the Outer Membranes of Mitochondria and Plastids. Viruses 2018; 10:E585. [PMID: 30373157 PMCID: PMC6265731 DOI: 10.3390/v10110585] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2018] [Revised: 10/19/2018] [Accepted: 10/19/2018] [Indexed: 12/15/2022] Open
Abstract
The Luteoviridae is an agriculturally important family of viruses whose replication and transport are restricted to plant phloem. Their genomes encode for four proteins that regulate viral movement. These include two structural proteins that make up the capsid and two non-structural proteins known as P3a and P17. Little is known about how these proteins interact with each other and the host to coordinate virus movement within and between cells. We used quantitative, affinity purification-mass spectrometry to show that the P3a protein of Potato leafroll virus complexes with virus and that this interaction is partially dependent on P17. Bimolecular complementation assays (BiFC) were used to validate that P3a and P17 self-interact as well as directly interact with each other. Co-localization with fluorescent-based organelle markers demonstrates that P3a directs P17 to the mitochondrial outer membrane while P17 regulates the localization of the P3a-P17 heterodimer to plastids. Residues in the C-terminus of P3a were shown to regulate P3a association with host mitochondria by using mutational analysis and also varying BiFC tag orientation. Collectively, our work reveals that the PLRV movement proteins play a game of intracellular hopscotch along host organelles to transport the virus to the cell periphery.
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Affiliation(s)
- Stacy L DeBlasio
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
| | - Yi Xu
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Richard S Johnson
- Department of Genome Sciences, University of Washington, Seattle WA 98109, USA.
| | - Ana Rita Rebelo
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
| | - Michael J MacCoss
- Department of Genome Sciences, University of Washington, Seattle WA 98109, USA.
| | - Stewart M Gray
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
| | - Michelle Heck
- United States Department of Agriculture, Biological Integrated Pest Management Research Unit, Robert W. Holley Center for Agriculture and Health, 538 Tower Road, Ithaca, NY 14853, USA.
- Boyce Thompson Institute for Plant Research, Ithaca, NY 14853, USA.
- Section of Plant Pathology and Plant-Microbe Biology, School of Integrated Plant Science, Cornell University, Ithaca, NY 14853, USA.
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