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Bera S, Arena GD, Ray S, Flannigan S, Casteel CL. The Potyviral Protein 6K1 Reduces Plant Proteases Activity during Turnip mosaic virus Infection. Viruses 2022; 14:1341. [PMID: 35746814 PMCID: PMC9229136 DOI: 10.3390/v14061341] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/29/2022] [Revised: 05/30/2022] [Accepted: 06/12/2022] [Indexed: 12/25/2022] Open
Abstract
Potyviral genomes encode just 11 major proteins and multifunctionality is associated with most of these proteins at different stages of the virus infection cycle. Some potyviral proteins modulate phytohormones and protein degradation pathways and have either pro- or anti-viral/insect vector functions. Our previous work demonstrated that the potyviral protein 6K1 has an antagonistic effect on vectors when expressed transiently in host plants, suggesting plant defenses are regulated. However, to our knowledge the mechanisms of how 6K1 alters plant defenses and how 6K1 functions are regulated are still limited. Here we show that the 6K1 from Turnip mosaic virus (TuMV) reduces the abundance of transcripts related to jasmonic acid biosynthesis and cysteine protease inhibitors when expressed in Nicotiana benthamiana relative to controls. 6K1 stability increased when cysteine protease activity was inhibited chemically, showing a mechanism to the rapid turnover of 6K1 when expressed in trans. Using RNAseq, qRT-PCR, and enzymatic assays, we demonstrate TuMV reprograms plant protein degradation pathways on the transcriptional level and increases 6K1 stability at later stages in the infection process. Moreover, we show 6K1 decreases plant protease activity in infected plants and increases TuMV accumulation in systemic leaves compared to controls. These results suggest 6K1 has a pro-viral function in addition to the anti-insect vector function we observed previously. Although the host targets of 6K1 and the impacts of 6K1-induced changes in protease activity on insect vectors are still unknown, this study enhances our understanding of the complex interactions occurring between plants, potyviruses, and vectors.
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Affiliation(s)
- Sayanta Bera
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Gabriella D. Arena
- Laboratório de Biologia Molecular Aplicada, Instituto Biológico de São Paulo, São Paulo 04014-002, Brazil;
| | - Swayamjit Ray
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Sydney Flannigan
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
| | - Clare L. Casteel
- School of Plant Science, Plant Pathology and Plant-Microbe Biology Section, Cornell University, Ithaca, NY 14850, USA; (S.B.); (S.R.); (S.F.)
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2
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Wang A. Cell-to-cell movement of plant viruses via plasmodesmata: a current perspective on potyviruses. Curr Opin Virol 2021; 48:10-16. [PMID: 33784579 DOI: 10.1016/j.coviro.2021.03.002] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2021] [Revised: 02/24/2021] [Accepted: 03/03/2021] [Indexed: 01/18/2023]
Abstract
Plant viruses have evolved efficient mechanisms to move cell-to-cell through plasmodesmata (PD) for systemic infection. Potyviruses including many economically important viruses constitute the largest group of known plant-infecting RNA viruses. Potyviral intercellular movement is accomplished by the coordinated action of at least three viral proteins and diverse host components. It requires the viral coat protein and is interlinked with active virus replication that generates, through RNA-polymerase slippage, a small percentage of frameshift viral RNA for the production of another essential movement protein named P3N-PIPO. This PD-located protein targets the virus-encoded cylindrical inclusion protein to PD to form special conical structures for potyviral passage, possibly in the form of virion. Here, I highlight and discuss major advances of potyviral intercellular trafficking.
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Affiliation(s)
- Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, 1391 Sandford Street, London, Ontario, N5V 4T3, Canada.
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3
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Bragard C, Dehnen-Schmutz K, Gonthier P, Jacques MA, Jaques Miret JA, Justesen AF, MacLeod A, Magnusson CS, Milonas P, Navas-Cortes JA, Parnell S, Potting R, Reignault PL, Thulke HH, van der Werf W, Civera AV, Yuen J, Zappalà L, Candresse T, Lacomme C, Bottex B, Oplaat C, Roenhorst A, Schenk M, Di Serio F. Pest categorisation of potato virus A (non-EU isolates). EFSA J 2020; 18:e05935. [PMID: 32626489 PMCID: PMC7008853 DOI: 10.2903/j.efsa.2020.5935] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022] Open
Abstract
Following a request from the EU Commission, the Panel on Plant Health has addressed the pest categorisation of non‐EU isolates of potato virus A (PVA). The information currently available on geographical distribution, biology, epidemiology, potential entry pathways, potential additional impact over the current situation and availability of control measures of non‐EU isolates of PVA has been evaluated with regard to the criteria to qualify as potential Union quarantine pest. Because non‐EU isolates of PVA are absent from the EU, they do not meet one of the requirements to be regulated as a regulated non‐quarantine pest (RNQP) (presence in the EU); as a consequence, the Panel decided not to evaluate the other RNQP criteria for these isolates. This categorisation was performed considering two groups of isolates: those reported in Solanum betaceum (PVA‐TamMV, not reported from the EU) and all other isolates (hereafter referred to as PVA, worldwide distribution). Non‐EU isolates of PVA and of PVA‐TamMV do not meet one of the criteria evaluated by EFSA to be regarded as a potential Union quarantine pest, since they are not expected to have an additional impact in the EU.
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Rasila TS, Pulkkinen E, Kiljunen S, Haapa-Paananen S, Pajunen MI, Salminen A, Paulin L, Vihinen M, Rice PA, Savilahti H. Mu transpososome activity-profiling yields hyperactive MuA variants for highly efficient genetic and genome engineering. Nucleic Acids Res 2019; 46:4649-4661. [PMID: 29294068 PMCID: PMC5961161 DOI: 10.1093/nar/gkx1281] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/05/2017] [Accepted: 12/21/2017] [Indexed: 11/22/2022] Open
Abstract
The phage Mu DNA transposition system provides a versatile species non-specific tool for molecular biology, genetic engineering and genome modification applications. Mu transposition is catalyzed by MuA transposase, with DNA cleavage and integration reactions ultimately attaching the transposon DNA to target DNA. To improve the activity of the Mu DNA transposition machinery, we mutagenized MuA protein and screened for hyperactivity-causing substitutions using an in vivo assay. The individual activity-enhancing substitutions were mapped onto the MuA–DNA complex structure, containing a tetramer of MuA transposase, two Mu end segments and a target DNA. This analysis, combined with the varying effect of the mutations in different assays, implied that the mutations exert their effects in several ways, including optimizing protein–protein and protein–DNA contacts. Based on these insights, we engineered highly hyperactive versions of MuA, by combining several synergistically acting substitutions located in different subdomains of the protein. Purified hyperactive MuA variants are now ready for use as second-generation tools in a variety of Mu-based DNA transposition applications. These variants will also widen the scope of Mu-based gene transfer technologies toward medical applications such as human gene therapy. Moreover, the work provides a platform for further design of custom transposases.
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Affiliation(s)
- Tiina S Rasila
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Elsi Pulkkinen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Kiljunen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland
| | - Maria I Pajunen
- Division of Biochemistry and Biotechnology, Department of Biosciences, FI-00014 University of Helsinki, Helsinki, Finland
| | - Anu Salminen
- Department of Biochemistry, FI-20014 University of Turku, Turku, Finland
| | - Lars Paulin
- Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
| | - Mauno Vihinen
- Department of Experimental Medical Science, Lund University, SE-221 84, Lund, Sweden
| | - Phoebe A Rice
- Department of Biochemistry and Molecular Biology, University of Chicago, Chicago, IL 60637, USA
| | - Harri Savilahti
- Division of Genetics and Physiology, Department of Biology, FI-20014 University of Turku, Turku, Finland.,Institute of Biotechnology, Viikki Biocenter, P. O. Box 56, FI-00014 University of Helsinki, Helsinki, Finland
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5
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Kushawaha AK, Dasgupta I. Infectivity of cloned begomoviral DNAs: an appraisal. Virusdisease 2018; 30:13-21. [PMID: 31143828 DOI: 10.1007/s13337-018-0453-5] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2017] [Accepted: 04/18/2018] [Indexed: 11/28/2022] Open
Abstract
Infectivity of cloned begomoviral DNAs is an important criterion to establish the etiology of the disease it causes, to study viral gene functions and host-virus interactions. Three main methods have been employed to study infectivity; mechanical inoculation with cloned viral DNA using abrasives, Agrobacterium-mediated inoculation (agroinoculation) of cloned viral DNA and bombardment using microprojectiles coated with cloned viral DNA (biolistics). Each method has its own advantages and disadvantages and the adoption of one over the other for demonstrating infectivity depends on various factors. This review compares the various features associated with the above three methods.
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Affiliation(s)
- Akhilesh Kumar Kushawaha
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
| | - Indranil Dasgupta
- Department of Plant Molecular Biology, University of Delhi South Campus, Benito Juarez Road, New Delhi, 110021 India
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Applications of the Bacteriophage Mu In Vitro Transposition Reaction and Genome Manipulation via Electroporation of DNA Transposition Complexes. Methods Mol Biol 2018; 1681:279-286. [PMID: 29134602 DOI: 10.1007/978-1-4939-7343-9_20] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023]
Abstract
The capacity of transposable elements to insert into the genomes has been harnessed during the past decades to various in vitro and in vivo applications. This chapter describes in detail the general protocols and principles applicable for the Mu in vitro transposition reaction as well as the assembly of DNA transposition complexes that can be electroporated into bacterial cells to accomplish efficient gene delivery. These techniques with their modifications potentiate various gene and genome modification applications, which are discussed briefly here, and the reader is referred to the original publications for further details.
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7
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Geng C, Yan ZY, Cheng DJ, Liu J, Tian YP, Zhu CX, Wang HY, Li XD. Tobacco vein banding mosaic virus 6K2 Protein Hijacks NbPsbO1 for Virus Replication. Sci Rep 2017; 7:43455. [PMID: 28230184 PMCID: PMC5322494 DOI: 10.1038/srep43455] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2016] [Accepted: 01/23/2017] [Indexed: 01/18/2023] Open
Abstract
Chloroplast-bound vesicles are key components in viral replication complexes (VRCs) of potyviruses. The potyviral VRCs are induced by the second 6 kDa protein (6K2) and contain at least viral RNA and nuclear inclusion protein b. To date, no chloroplast protein has been identified to interact with 6K2 and involve in potyvirus replication. In this paper, we showed that the Photosystem II oxygen evolution complex protein of Nicotiana benthamiana (NbPsbO1) was a chloroplast protein interacting with 6K2 of Tobacco vein banding mosaic virus (TVBMV; genus Potyvirus) and present in the VRCs. The first 6 kDa protein (6K1) was recruited to VRCs by 6K2 but had no interaction with NbPSbO1. Knockdown of NbPsbO1 gene expression in N. benthamiana plants through virus-induced gene silencing significantly decreased the accumulation levels of TVBMV and another potyvirus Potato virus Y, but not Potato virus X of genus Potexvirus. Amino acid substitutions in 6K2 that disrupted its interaction with NbPsbO1 also affected the replication of TVBMV. NbPsbP1 and NbPsbQ1, two other components of the Photosystem II oxygen evolution complex had no interaction with 6K2 and no effect on TVBMV replication. To conclude, 6K2 recruits 6K1 to VRCs and hijacks chloroplast protein NbPsbO1 to regulate potyvirus replication.
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Affiliation(s)
- Chao Geng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Zhi-Yong Yan
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - De-Jie Cheng
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Jin Liu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Yan-Ping Tian
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Chang-Xiang Zhu
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
| | - Hong-Yan Wang
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
| | - Xiang-Dong Li
- Laboratory of Plant Virology, Department of Plant Pathology, College of Plant Protection, Shandong Agricultural University, Tai’an, Shandong 271018, China
- Shandong Provincial Key laboratory for Agricultural Microbiology, Tai’an, Shandong, 271018, China
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8
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Lõhmus A, Varjosalo M, Mäkinen K. Protein composition of 6K2-induced membrane structures formed during Potato virus A infection. MOLECULAR PLANT PATHOLOGY 2016; 17:943-58. [PMID: 26574906 PMCID: PMC6638329 DOI: 10.1111/mpp.12341] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/18/2015] [Revised: 10/19/2015] [Accepted: 10/23/2015] [Indexed: 05/13/2023]
Abstract
The definition of the precise molecular composition of membranous replication compartments is a key to understanding the mechanisms of virus multiplication. Here, we set out to investigate the protein composition of the potyviral replication complexes. We purified the potyviral 6K2 protein-induced membranous structures from Potato virus A (PVA)-infected Nicotiana benthamiana plants. For this purpose, the 6K2 protein, which is the main inducer of potyviral membrane rearrangements, was expressed in fusion with an N-terminal Twin-Strep-tag and Cerulean fluorescent protein (SC6K) from the infectious PVA cDNA. A non-tagged Cerulean-6K2 (C6K) virus and the SC6K protein alone in the absence of infection were used as controls. A purification scheme exploiting discontinuous sucrose gradient centrifugation followed by Strep-tag-based affinity chromatography was developed. Both (+)- and (-)-strand PVA RNA and viral protein VPg were co-purified specifically with the affinity tagged PVA-SC6K. The purified samples, which contained individual vesicles and membrane clusters, were subjected to mass spectrometry analysis. Data analysis revealed that many of the detected viral and host proteins were either significantly enriched or fully specifically present in PVA-SC6K samples when compared with the controls. Eight of eleven potyviral proteins were identified with high confidence from the purified membrane structures formed during PVA infection. Ribosomal proteins were identified from the 6K2-induced membranes only in the presence of a replicating virus, reinforcing the tight coupling between replication and translation. A substantial number of proteins associating with chloroplasts and several host proteins previously linked with potyvirus replication complexes were co-purified with PVA-derived SC6K, supporting the conclusion that the host proteins identified in this study may have relevance in PVA replication.
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Affiliation(s)
- Andres Lõhmus
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, 00014 University of Helsinki, Finland
| | - Markku Varjosalo
- Institute of Biotechnology, 00014 University of Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Food and Environmental Sciences, Viikki Plant Science Centre, 00014 University of Helsinki, Finland
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Cui H, Wang A. Plum Pox Virus 6K1 Protein Is Required for Viral Replication and Targets the Viral Replication Complex at the Early Stage of Infection. J Virol 2016; 90:5119-5131. [PMID: 26962227 PMCID: PMC4859702 DOI: 10.1128/jvi.00024-16] [Citation(s) in RCA: 46] [Impact Index Per Article: 5.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2016] [Accepted: 03/07/2016] [Indexed: 01/08/2023] Open
Abstract
UNLABELLED The potyviral RNA genome encodes two polyproteins that are proteolytically processed by three viral protease domains into 11 mature proteins. Extensive molecular studies have identified functions for the majority of the viral proteins. For example, 6K2, one of the two smallest potyviral proteins, is an integral membrane protein and induces the endoplasmic reticulum (ER)-originated replication vesicles that target the chloroplast for robust viral replication. However, the functional role of 6K1, the other smallest protein, remains uncharacterized. In this study, we developed a series of recombinant full-length viral cDNA clones derived from a Canadian Plum pox virus (PPV) isolate. We found that deletion of any of the short motifs of 6K1 (each of which ranged from 5 to 13 amino acids), most of the 6K1 sequence (but with the conserved sequence of the cleavage sites being retained), or all of the 6K1 sequence in the PPV infectious clone abolished viral replication. The trans expression of 6K1 or the cis expression of a dislocated 6K1 failed to rescue the loss-of-replication phenotype, suggesting the temporal and spatial requirement of 6K1 for viral replication. Disruption of the N- or C-terminal cleavage site of 6K1, which prevented the release of 6K1 from the polyprotein, either partially or completely inhibited viral replication, suggesting the functional importance of the mature 6K1. We further found that green fluorescent protein-tagged 6K1 formed punctate inclusions at the viral early infection stage and colocalized with chloroplast-bound viral replicase elements 6K2 and NIb. Taken together, our results suggest that 6K1 is required for viral replication and is an important viral element of the viral replication complex at the early infection stage. IMPORTANCE Potyviruses account for more than 30% of known plant viruses and consist of many agriculturally important viruses. The genomes of potyviruses encode two polyproteins that are proteolytically processed into 11 mature proteins, with the majority of them having been at least partially functionally characterized. However, the functional role of a small protein named 6K1 remains obscure. In this study, we showed that deletion of 6K1 or a short motif/region of 6K1 in the full-length cDNA clones of plum pox virus abolishes viral replication and that mutation of the N- or C-terminal cleavage sites of 6K1 to prevent its release from the polyprotein greatly attenuates or completely inhibits viral replication, suggesting its important role in potyviral infection. We report that 6K1 forms punctate structures and targets the replication vesicles in PPV-infected plant leaf cells at the early infection stage. Our data reveal that 6K1 is an important viral protein of the potyviral replication complex.
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Affiliation(s)
- Hongguang Cui
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - Aiming Wang
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
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10
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High-resolution genetic profile of viral genomes: why it matters. Curr Opin Virol 2015; 14:62-70. [DOI: 10.1016/j.coviro.2015.08.005] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/19/2015] [Revised: 08/07/2015] [Accepted: 08/07/2015] [Indexed: 12/12/2022]
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Tian YP, Valkonen JPT. Recombination of strain O segments to HCpro-encoding sequence of strain N of Potato virus Y modulates necrosis induced in tobacco and in potatoes carrying resistance genes Ny or Nc. MOLECULAR PLANT PATHOLOGY 2015; 16:735-47. [PMID: 25557768 PMCID: PMC6638495 DOI: 10.1111/mpp.12231] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Hypersensitive resistance (HR) to strains O and C of Potato virus Y (PVY, genus Potyvirus) is conferred by potato genes Ny(tbr) and Nc(tbr), respectively; however, PVY N strains overcome these resistance genes. The viral helper component proteinases (HCpro, 456 amino acids) from PVY(N) and PVY(O) are distinguished by an eight-amino-acid signature sequence, causing HCpro to fold into alternative conformations. Substitution of only two residues (K269R and R270K) of the eight-amino-acid signature in PVY(N) HCpro was needed to convert the three-dimensional (3D) model of PVY(N) HCpro to a PVY(O) -like conformation and render PVY(N) avirulent in the presence of Ny(tbr), whereas four amino acid substitutions were necessary to change PVY(O) HCpro to a PVY(N) -like conformation. Hence, the HCpro conformation rather than other features ascribed to the sequence were essential for recognition by Ny(tbr). The 3D model of PVY(C) HCpro closely resembled PVY(O), but differed from PVY(N) HCpro. HCpro of all strains was structurally similar to β-catenin. Sixteen PVY(N) 605-based chimeras were inoculated to potato cv. Pentland Crown (Ny(tbr)), King Edward (Nc(tbr)) and Pentland Ivory (Ny(tbr)/Nc(tbr)). Eleven chimeras induced necrotic local lesions and caused no systemic infection, and thus differed from both parental viruses that infected King Edward systemically, and from PVY(N) 605 that infected Pentland Crown and Pentland Ivory systemically. These 11 chimeras triggered both Ny(tbr) and Nc(tbr) and, in addition, six induced veinal necrosis in tobacco. Further, specific amino acid residues were found to have an additive impact on necrosis. These results shed new light on the causes of PVY-related necrotic symptoms in potato.
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Affiliation(s)
- Yan-Ping Tian
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
| | - Jari P T Valkonen
- Department of Agricultural Sciences, University of Helsinki, PO Box 27, FI-00014, Helsinki, Finland
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12
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Abstract
Potyvirus is the largest genus of plant viruses causing significant losses in a wide range of crops. Potyviruses are aphid transmitted in a nonpersistent manner and some of them are also seed transmitted. As important pathogens, potyviruses are much more studied than other plant viruses belonging to other genera and their study covers many aspects of plant virology, such as functional characterization of viral proteins, molecular interaction with hosts and vectors, structure, taxonomy, evolution, epidemiology, and diagnosis. Biotechnological applications of potyviruses are also being explored. During this last decade, substantial advances have been made in the understanding of the molecular biology of these viruses and the functions of their various proteins. After a general presentation on the family Potyviridae and the potyviral proteins, we present an update of the knowledge on potyvirus multiplication, movement, and transmission and on potyvirus/plant compatible interactions including pathogenicity and symptom determinants. We end the review providing information on biotechnological applications of potyviruses.
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13
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Pulkkinen E, Haapa-Paananen S, Savilahti H. An assay to monitor the activity of DNA transposition complexes yields a general quality control measure for transpositional recombination reactions. Mob Genet Elements 2014; 4:1-8. [PMID: 26442171 PMCID: PMC4590003 DOI: 10.4161/21592543.2014.969576] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2014] [Revised: 08/22/2014] [Accepted: 09/01/2014] [Indexed: 12/20/2022] Open
Abstract
Transposon-based technologies have many applications in molecular biology and can be used for gene delivery into prokaryotic and eukaryotic cells. Common transpositional activity measurement assays suitable for many types of transposons would be beneficial, as diverse transposon systems could be compared for their performance attributes. Therefore, we developed a general-purpose assay to enable and standardize the activity measurement for DNA transposition complexes (transpososomes), using phage Mu transposition as a test platform. This assay quantifies transpositional recombination efficiency and is based on an in vitro transposition reaction with a target plasmid carrying a lethal ccdB gene. If transposition targets ccdB, this gene becomes inactivated, enabling plasmid-receiving Escherichia coli cells to survive and to be scored as colonies on selection plates. The assay was validated with 3 mini-Mu transposons varying in size and differing in their marker gene constitution. Tests with different amounts of transposon DNA provided a linear response and yielded a 10-fold operational range for the assay. The colony formation capacity was linearly correlated with the competence status of the E.coli cells, enabling normalization of experimental data obtained with different batches of recipient cells. The developed assay can now be used to directly compare transpososome activities with all types of mini-Mu transposons, regardless of their aimed use. Furthermore, the assay should be directly applicable to other transposition-based systems with a functional in vitro reaction, and it provides a dependable quality control measure that previously has been lacking but is highly important for the evaluation of current and emerging transposon-based applications.
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Affiliation(s)
- Elsi Pulkkinen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Saija Haapa-Paananen
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
| | - Harri Savilahti
- Division of Genetics and Physiology; Department of Biology; University of Turku; Turku, Finland
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14
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A comprehensive functional map of the hepatitis C virus genome provides a resource for probing viral proteins. mBio 2014; 5:e01469-14. [PMID: 25271282 PMCID: PMC4196222 DOI: 10.1128/mbio.01469-14] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022] Open
Abstract
Pairing high-throughput sequencing technologies with high-throughput mutagenesis enables genome-wide investigations of pathogenic organisms. Knowledge of the specific functions of protein domains encoded by the genome of the hepatitis C virus (HCV), a major human pathogen that contributes to liver disease worldwide, remains limited to insight from small-scale studies. To enhance the capabilities of HCV researchers, we have obtained a high-resolution functional map of the entire viral genome by combining transposon-based insertional mutagenesis with next-generation sequencing. We generated a library of 8,398 mutagenized HCV clones, each containing one 15-nucleotide sequence inserted at a unique genomic position. We passaged this library in hepatic cells, recovered virus pools, and simultaneously assayed the abundance of mutant viruses in each pool by next-generation sequencing. To illustrate the validity of the functional profile, we compared the genetic footprints of viral proteins with previously solved protein structures. Moreover, we show the utility of these genetic footprints in the identification of candidate regions for epitope tag insertion. In a second application, we screened the genetic footprints for phenotypes that reflected defects in later steps of the viral life cycle. We confirmed that viruses with insertions in a region of the nonstructural protein NS4B had a defect in infectivity while maintaining genome replication. Overall, our genome-wide HCV mutant library and the genetic footprints obtained by high-resolution profiling represent valuable new resources for the research community that can direct the attention of investigators toward unidentified roles of individual protein domains. Our insertional mutagenesis library provides a resource that illustrates the effects of relatively small insertions on local protein structure and HCV viability. We have also generated complementary resources, including a website (http://hangfei.bol.ucla.edu) and a panel of epitope-tagged mutant viruses that should enhance the research capabilities of investigators studying HCV. Researchers can now detect epitope-tagged viral proteins by established antibodies, which will allow biochemical studies of HCV proteins for which antibodies are not readily available. Furthermore, researchers can now quickly look up genotype-phenotype relationships and base further mechanistic studies on the residue-by-residue information from the functional profile. More broadly, this approach offers a general strategy for the systematic functional characterization of viruses on the genome scale.
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15
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He C, Zhang W, Hu X, Singh M, Xiong X, Nie X. Molecular characterization of a Chinese isolate of potato virus A (PVA) and evidence of a genome recombination event between PVA variants at the 3'-proximal end of the genome. Arch Virol 2014; 159:2457-62. [PMID: 24722969 DOI: 10.1007/s00705-014-2053-z] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2013] [Accepted: 03/07/2014] [Indexed: 10/25/2022]
Abstract
Potato plants that exhibited mosaic symptoms were collected in Xiangxi, Hunan province, China. Multiplex RT-PCR screening for common viruses revealed the presence of potato virus A (PVA) in these samples. ELISA with virus-specific antibodies confirmed infection by PVA in the plants. Rod-shaped virions of ~750 nm in length and ~13 nm in width were observed by transmission electron microscopy. One virus isolate (designated PVA-Hunan) was subjected to molecular characterization. The viral genome consisted of 9,567 nucleotides, excluding the poly(A) tail, and encoded a polyprotein of 3,059 amino acids. A second characteristic potyvirus open reading frame (ORF), pretty interesting Potyviridae ORF (pipo), was located at nucleotides 2,834-3,139. The isolate shared 84% to 98% and 93% to 99% sequence identity with other PVA isolates at the nucleotide and amino acid level, respectively. Phylogenetic analysis demonstrated that, within the PVA group, PVA-Hunan clustered most closely with the Finnish isolate Her, then with isolates 143, U, Ali, M and B11. The isolate TamMV stood alone at a separate branch. However, scanning of complete genome sequences using SimPlot revealed 99%-sequence identity between PVA-Hunan and TamMV in the 3'-proximal end of the genome (~nt 9,160 to the 3'end) and a 50%-94% (average~83%) identity upstream of nt 9,160. In contrast, 98% identity between PVA-Hunan and isolates M and B11 was detected for nucleotides 1 to ~9,160, but only ~94% for the 3'-proximal region, suggesting a genome recombination event (RE) at nt 9,133. The recombination breakpoint also was identified by the Recombination Detection Program (RDP). The RE was further confirmed by analysis of the CP gene, where the apparent RE was located.
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Affiliation(s)
- Changzheng He
- Hunan Provincial Key Laboratory of Crop Germplasm Innovation and Utilization, Hunan Provincial Engineering Research Center for Potatoes, College of Horticulture and Landscape, Hunan Agricultural University, Changsha, 410128, Hunan, China
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16
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Mäkinen K, Hafrén A. Intracellular coordination of potyviral RNA functions in infection. FRONTIERS IN PLANT SCIENCE 2014; 5:110. [PMID: 24723931 PMCID: PMC3972461 DOI: 10.3389/fpls.2014.00110] [Citation(s) in RCA: 29] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/29/2013] [Accepted: 03/07/2014] [Indexed: 05/26/2023]
Abstract
Establishment of an infection cycle requires mechanisms to allocate the genomes of (+)-stranded RNA viruses in a balanced ratio to translation, replication, encapsidation, and movement, as well as mechanisms to prevent translocation of viral RNA (vRNA) to cellular RNA degradation pathways. The ratio of vRNA allocated to various functions is likely balanced by the availability of regulatory proteins or competition of the interaction sites within regulatory ribonucleoprotein complexes. Due to the transient nature of viral processes and the interdependency between vRNA pathways, it is technically demanding to work out the exact molecular mechanisms underlying vRNA regulation. A substantial number of viral and host proteins have been identified that facilitate the steps that lead to the assembly of a functional potyviral RNA replication complex and their fusion with chloroplasts. Simultaneously with on-going viral replication, part of the replicated potyviral RNA enters movement pathways. Although not much is known about the processes of potyviral RNA release from viral replication complexes, the molecular interactions involved in these processes determine the fate of the replicated vRNA. Some viral and host cell proteins have been described that direct replicated potyviral RNA to translation to enable potyviral gene expression and productive infection. The antiviral defense of the cell causes vRNA degradation by RNA silencing. We hypothesize that also plant pathways involved in mRNA decay may have a role in the coordination of potyviral RNA expression. In this review, we discuss the roles of different potyviral and host proteins in the coordination of various potyviral RNA functions.
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Affiliation(s)
- Kristiina Mäkinen
- Department of Food and Environmental Sciences, University of HelsinkiHelsinki, Finland
| | - Anders Hafrén
- Department of Food and Environmental Sciences, University of HelsinkiHelsinki, Finland
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural SciencesUppsala, Sweden
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17
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Sorel M, Garcia JA, German-Retana S. The Potyviridae cylindrical inclusion helicase: a key multipartner and multifunctional protein. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:215-226. [PMID: 24405034 DOI: 10.1094/mpmi-11-13-0333-cr] [Citation(s) in RCA: 51] [Impact Index Per Article: 5.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/03/2023]
Abstract
A unique feature shared by all plant viruses of the Potyviridae family is the induction of characteristic pinwheel-shaped inclusion bodies in the cytoplasm of infected cells. These cylindrical inclusions are composed of the viral-encoded cylindrical inclusion helicase (CI protein). Its helicase activity was characterized and its involvement in replication demonstrated through different reverse genetics approaches. In addition to replication, the CI protein is also involved in cell-to-cell and long-distance movements, possibly through interactions with the recently discovered viral P3N-PIPO protein. Studies over the past two decades demonstrate that the CI protein is present in several cellular compartments interacting with viral and plant protein partners likely involved in its various roles in different steps of viral infection. Furthermore, the CI protein acts as an avirulence factor in gene-for-gene interactions with dominant-resistance host genes and as a recessive-resistance overcoming factor. Although a significant amount of data concerning the potential functions and subcellular localization of this protein has been published, no synthetic review is available on this important multifunctional protein. In this review, we compile and integrate all information relevant to the current understanding of this viral protein structure and function and present a mode of action for CI, combining replication and movement.
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18
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Calvo M, Malinowski T, García JA. Single amino acid changes in the 6K1-CI region can promote the alternative adaptation of Prunus- and Nicotiana-propagated Plum pox virus C isolates to either host. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2014; 27:136-49. [PMID: 24200075 DOI: 10.1094/mpmi-08-13-0242-r] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/20/2023]
Abstract
Plum pox virus (PPV) C is one of the less common PPV strains and specifically infects cherry trees in nature. Making use of two PPV-C isolates that display different pathogenicity features, i.e., SwCMp, which had been adapted to Nicotiana species, and BY101, which had been isolated from cherry rootstock L2 (Prunus lannesiana) and propagated only in cherry species, we have generated two infective full-length cDNA clones in order to determine which viral factors are involved in the adaptation to each host. According to our results, the C-P3(PIPO)/6K1/N-CI (cylindrical inclusion) region contains overlapping but not coincident viral determinants involved in symptoms development, local viral amplification, and systemic movement capacity. Amino acid changes in this region promoting the adaptation to N. benthamiana or P. avium have trade-off effects in the alternative host. In both cases, adaptation can be achieved through single amino acid changes in the NIapro protease recognition motif between 6K1 and CI or in nearby sequences. Thus, we hypothesize that the potyvirus polyprotein processing could depend on specific host factors and the adaptation of PPV-C isolates to particular hosts relies on a fine regulation of the proteolytic cleavage of the 6K1-CI junction.
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19
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Haikonen T, Rajamäki ML, Valkonen JPT. Improved silencing suppression and enhanced heterologous protein expression are achieved using an engineered viral helper component proteinase. J Virol Methods 2013; 193:687-92. [PMID: 23933077 DOI: 10.1016/j.jviromet.2013.07.054] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2013] [Revised: 07/20/2013] [Accepted: 07/22/2013] [Indexed: 12/14/2022]
Abstract
RNA silencing limits transient expression of heterologous proteins in plants. Co-expression of viral silencing suppressor proteins can increase and prolong protein expression, but highly efficient silencing suppressors may stress plant tissue and be detrimental to protein yields. Little is known whether silencing suppression could be improved without harm to plant tissues. This study reports development of enhanced silencing suppressors by engineering the helper component proteinase (HCpro) of Potato virus A (PVA). Mutations were introduced to a short region of HCpro (positions 330-335 in PVA HCpro), which is hypervariable among potyviruses. Three out of the four HCpro mutants suppressed RNA silencing more efficiently and sustained expression of co-expressed jellyfish green fluorescent protein for a longer time than wild-type HCpro in agroinfiltrated leaves of Nicotiana benthamiana. Leaf tissues remained healthy-looking without any visible signs of stress.
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Affiliation(s)
- T Haikonen
- Department of Agricultural Sciences, P.O. Box 27, University of Helsinki, FIN-00014 Helsinki, Finland
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20
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Wang A, Krishnaswamy S. Eukaryotic translation initiation factor 4E-mediated recessive resistance to plant viruses and its utility in crop improvement. MOLECULAR PLANT PATHOLOGY 2012; 13:795-803. [PMID: 22379950 PMCID: PMC6638641 DOI: 10.1111/j.1364-3703.2012.00791.x] [Citation(s) in RCA: 165] [Impact Index Per Article: 13.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/17/2023]
Abstract
The use of genetic resistance is considered to be the most effective and sustainable approach to the control of plant pathogens. Although most of the known natural resistance genes are monogenic dominant R genes that are predominant against fungi and bacteria, more and more recessive resistance genes against viruses have been cloned in the last decade. Interestingly, of the 14 natural recessive resistance genes against plant viruses that have been cloned from diverse plant species thus far, 12 encode the eukaryotic translation initiation factor 4E (eIF4E) or its isoform eIF(iso)4E. This review is intended to summarize the current state of knowledge about eIF4E and the possible mechanisms underlying its essential role in virus infection, and to discuss recent progress and the potential of eIF4E as a target gene in the development of genetic resistance to viruses for crop improvement.
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Affiliation(s)
- Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, ON, Canada, N5V 4T3.
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21
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Abstract
Human noroviruses (HuNoV) are a major cause of nonbacterial gastroenteritis worldwide, yet details of the life cycle and replication of HuNoV are relatively unknown due to the lack of an efficient cell culture system. Studies with murine norovirus (MNV), which can be propagated in permissive cells, have begun to probe different aspects of the norovirus life cycle; however, our understanding of the specific functions of the viral proteins lags far behind that of other RNA viruses. Genome-wide functional profiling by insertional mutagenesis can reveal protein domains essential for replication and can lead to generation of tagged viruses, which has not yet been achieved for noroviruses. Here, transposon-mediated insertional mutagenesis was used to create 5 libraries of mutagenized MNV infectious clones, each containing a 15-nucleotide sequence randomly inserted within a defined region of the genome. Infectious virus was recovered from each library and was subsequently passaged in cell culture to determine the effect of each insertion by insertion-specific fluorescent PCR profiling. Genome-wide profiling of over 2,000 insertions revealed essential protein domains and confirmed known functional motifs. As validation, several insertion sites were introduced into a wild-type clone, successfully allowing the recovery of infectious virus. Screening of a number of reporter proteins and epitope tags led to the generation of the first infectious epitope-tagged noroviruses carrying the FLAG epitope tag in either NS4 or VP2. Subsequent work confirmed that epitope-tagged fully infectious noroviruses may be of use in the dissection of the molecular interactions that occur within the viral replication complex.
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22
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Chowda-Reddy RV, Sun H, Hill JH, Poysa V, Wang A. Simultaneous mutations in multi-viral proteins are required for soybean mosaic virus to gain virulence on soybean genotypes carrying different R genes. PLoS One 2011; 6:e28342. [PMID: 22140577 PMCID: PMC3227670 DOI: 10.1371/journal.pone.0028342] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/28/2011] [Accepted: 11/06/2011] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Genetic resistance is the most effective and sustainable approach to the control of plant pathogens that are a major constraint to agriculture worldwide. In soybean, three dominant R genes, i.e., Rsv1, Rsv3 and Rsv4, have been identified and deployed against Soybean mosaic virus (SMV) with strain-specificities. Molecular identification of virulent determinants of SMV on these resistance genes will provide essential information for the proper utilization of these resistance genes to protect soybean against SMV, and advance knowledge of virus-host interactions in general. METHODOLOGY/PRINCIPAL FINDINGS To study the gain and loss of SMV virulence on all the three resistance loci, SMV strains G7 and two G2 isolates L and LRB were used as parental viruses. SMV chimeras and mutants were created by partial genome swapping and point mutagenesis and then assessed for virulence on soybean cultivars PI96983 (Rsv1), L-29 (Rsv3), V94-5152 (Rsv4) and Williams 82 (rsv). It was found that P3 played an essential role in virulence determination on all three resistance loci and CI was required for virulence on Rsv1- and Rsv3-genotype soybeans. In addition, essential mutations in HC-Pro were also required for the gain of virulence on Rsv1-genotype soybean. To our best knowledge, this is the first report that CI and P3 are involved in virulence on Rsv1- and Rsv3-mediated resistance, respectively. CONCLUSIONS/SIGNIFICANCE Multiple viral proteins, i.e., HC-Pro, P3 and CI, are involved in virulence on the three resistance loci and simultaneous mutations at essential positions of different viral proteins are required for an avirulent SMV strain to gain virulence on all three resistance loci. The likelihood of such mutations occurring naturally and concurrently on multiple viral proteins is low. Thus, incorporation of all three resistance genes in a soybean cultivar through gene pyramiding may provide durable resistance to SMV.
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Affiliation(s)
- R. V. Chowda-Reddy
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
- Department of Biology, University of Western Ontario, London, Ontario, Canada
| | - Haiyue Sun
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
| | - John H. Hill
- Department of Plant Pathology, Iowa State University, Ames, Iowa, United States of America
| | - Vaino Poysa
- Greenhouse and Processing Crops Research Centre, Agriculture and Agri-Food Canada, Harrow, Ontario, Canada
| | - Aiming Wang
- Southern Crop Protection and Food Research Centre, Agriculture and Agri-Food Canada, London, Ontario, Canada
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23
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Rohozková J, Navrátil M. P1 peptidase--a mysterious protein of family Potyviridae. J Biosci 2011; 36:189-200. [PMID: 21451259 DOI: 10.1007/s12038-011-9020-6] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2010] [Accepted: 02/10/2011] [Indexed: 10/18/2022]
Abstract
The Potyviridae family, named after its type member, Potato virus Y (PVY), is the largest of the 65 plant virus groups and families currently recognized. The coding region for P1 peptidase is located at the very beginning of the viral genome of the family Potyviridae. Until recently P1 was thought of as serine peptidase with RNA-binding activity and with possible influence in cell-to-cell viral spreading. This N-terminal protein, among all of the potyviruses, is the most divergent protein: varying in length and in its amino acid sequence. Nevertheless, P1 peptidase in many ways is still a mysterious viral protein. In this review, we would like to offer a comprehensive overview, discussing the proteomic, biochemical and phylogenetic views of the P1 protein.
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Affiliation(s)
- Jana Rohozková
- Faculty of Science, Palacký University in Olomouc, Slechtitelů 11, 783 71, Olomouc-Holice, Czech Republic.
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24
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Pajunen MI, Rasila TS, Happonen LJ, Lamberg A, Haapa-Paananen S, Kiljunen S, Savilahti H. Universal platform for quantitative analysis of DNA transposition. Mob DNA 2010; 1:24. [PMID: 21110848 PMCID: PMC3003695 DOI: 10.1186/1759-8753-1-24] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2010] [Accepted: 11/26/2010] [Indexed: 01/16/2023] Open
Abstract
Background Completed genome projects have revealed an astonishing diversity of transposable genetic elements, implying the existence of novel element families yet to be discovered from diverse life forms. Concurrently, several better understood transposon systems have been exploited as efficient tools in molecular biology and genomics applications. Characterization of new mobile elements and improvement of the existing transposition technology platforms warrant easy-to-use assays for the quantitative analysis of DNA transposition. Results Here we developed a universal in vivo platform for the analysis of transposition frequency with class II mobile elements, i.e., DNA transposons. For each particular transposon system, cloning of the transposon ends and the cognate transposase gene, in three consecutive steps, generates a multifunctional plasmid, which drives inducible expression of the transposase gene and includes a mobilisable lacZ-containing reporter transposon. The assay scores transposition events as blue microcolonies, papillae, growing within otherwise whitish Escherichia coli colonies on indicator plates. We developed the assay using phage Mu transposition as a test model and validated the platform using various MuA transposase mutants. For further validation and to illustrate universality, we introduced IS903 transposition system components into the assay. The developed assay is adjustable to a desired level of initial transposition via the control of a plasmid-borne E. coli arabinose promoter. In practice, the transposition frequency is modulated by varying the concentration of arabinose or glucose in the growth medium. We show that variable levels of transpositional activity can be analysed, thus enabling straightforward screens for hyper- or hypoactive transposase mutants, regardless of the original wild-type activity level. Conclusions The established universal papillation assay platform should be widely applicable to a variety of mobile elements. It can be used for mechanistic studies to dissect transposition and provides a means to screen or scrutinise transposase mutants and genes encoding host factors. In succession, improved versions of transposition systems should yield better tools for molecular biology and offer versatile genome modification vehicles for many types of studies, including gene therapy and stem cell research.
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Affiliation(s)
- Maria I Pajunen
- Division of Genetics and Physiology, Department of Biology, Vesilinnantie 5, FIN-20014 University of Turku, Finland.
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25
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Abstract
About half of the approximately 200 known virus resistance genes in plants are recessively inherited, suggesting that this form of resistance is more common for viruses than for other plant pathogens. The use of such genes is therefore a very important tool in breeding programs to control plant diseases caused by pathogenic viruses. Over the last few years, the detailed analysis of many host/virus combinations has substantially advanced basic research on recessive resistance mechanisms in crop species. This type of resistance is preferentially expressed in protoplasts and inoculated leaves, influencing virus multiplication at the single-cell level as well as cell-to-cell movement. Importantly, a growing number of recessive resistance genes have been cloned from crop species, and further analysis has shown them all to encode translation initiation factors of the 4E (eIF4E) and 4G (eIF4G) families. However, not all of the loss-of-susceptibility mutants identified in collections of mutagenized hosts correspond to mutations in eIF4E and eIF4G. This, together with other supporting data, suggests that more extensive characterization of the natural variability of resistance genes may identify new host factors conferring recessive resistance. In this chapter, we discuss the recent work carried out to characterize loss-of-susceptibility and recessive resistance genes in crop and model species. We review actual and probable recessive resistance mechanisms, and bring the chapter to a close by summarizing the current state-of-the-art and offering perspectives on potential future developments.
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Affiliation(s)
- V Truniger
- Centro de Edafología y Biología Aplicada del Segura (CEBAS), Consejo Superior de Investigaciones Científicas (CSIC), Apdo Correos 164, 30100 Espinardo (Murcia), Spain
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26
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Taliansky ME, Brown JWS, Rajamäki ML, Valkonen JPT, Kalinina NO. Involvement of the plant nucleolus in virus and viroid infections: parallels with animal pathosystems. Adv Virus Res 2010; 77:119-58. [PMID: 20951872 PMCID: PMC7149663 DOI: 10.1016/b978-0-12-385034-8.00005-3] [Citation(s) in RCA: 46] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
The nucleolus is a dynamic subnuclear body with roles in ribosome subunit biogenesis, mediation of cell-stress responses, and regulation of cell growth. An increasing number of reports reveal that similar to the proteins of animal viruses, many plant virus proteins localize in the nucleolus to divert host nucleolar proteins from their natural functions in order to exert novel role(s) in the virus infection cycle. This chapter will highlight studies showing how plant viruses recruit nucleolar functions to facilitate virus translation and replication, virus movement and assembly of virus-specific ribonucleoprotein (RNP) particles, and to counteract plant host defense responses. Plant viruses also provide a valuable tool to gain new insights into novel nucleolar functions and processes. Investigating the interactions between plant viruses and the nucleolus will facilitate the design of novel strategies to control plant virus infections.
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Affiliation(s)
- M E Taliansky
- Scottish Crop Research Institute, Invergowrie, Dundee, United Kingdom
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27
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Draghici HK, Pilot R, Thiel H, Varrelmann M. Functional mapping of PVX RNA-dependent RNA-replicase using pentapeptide scanning mutagenesis-Identification of regions essential for replication and subgenomic RNA amplification. Virus Res 2009; 143:114-24. [PMID: 19463728 DOI: 10.1016/j.virusres.2009.03.013] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2008] [Revised: 03/23/2009] [Accepted: 03/25/2009] [Indexed: 12/31/2022]
Abstract
The replicase protein of Potato virus X (PVX), type species of the genus Potexvirus, was selected to identify regions essential for replication and subgenomic RNA synthesis. Replicase amino acid (aa) sequence alignment of 16 Potexvirus species resulted in the detection of overall sequence homology of 34.4-65.4%. Two regions of consensus with a high proportion of conserved aa (1-411 and 617-1437 according to PVX) were separated by a hyper-variable linker region. Pentapeptide scanning (PS) mutagenesis in a PVX full-length clone expressing green fluorescent protein (GFP) was carried out. For 69 selected PS-mutants where insertions were spread randomly over the replicase ORF the position of the insertion was determined. The replication activity was evaluated by GFP expression from subgenomic viral RNA of PVX replicase mutants. Only one functional PS-mutant was detected in the N-terminal 430 aa, containing the conserved methyltransferase domain of the protein. In the linker region from aa 430-595, nine mutations were discovered which did not induce significant effects on the replicase replication ability. The part of the protein including helicase and polymerase domains was highly intolerant for the PS insertion as demonstrated by 24 independent more or less uniformly spread mutants.
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Affiliation(s)
- Heidrun-Katharina Draghici
- Department of Crop Sciences, Section Plant Virology, University of Göttingen, Grisebachstrasse 6, D-37077 Göttingen, Germany
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28
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Turakainen H, Saarimäki-Vire J, Sinjushina N, Partanen J, Savilahti H. Transposition-based method for the rapid generation of gene-targeting vectors to produce Cre/Flp-modifiable conditional knock-out mice. PLoS One 2009; 4:e4341. [PMID: 19194496 PMCID: PMC2632748 DOI: 10.1371/journal.pone.0004341] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2008] [Accepted: 12/24/2008] [Indexed: 11/18/2022] Open
Abstract
Conditional gene targeting strategies are progressively used to study gene function tissue-specifically and/or at a defined time period. Instrumental to all of these strategies is the generation of targeting vectors, and any methodology that would streamline the procedure would be highly beneficial. We describe a comprehensive transposition-based strategy to produce gene-targeting vectors for the generation of mouse conditional alleles. The system employs a universal cloning vector and two custom-designed mini-Mu transposons. It produces targeting constructions directly from BAC clones, and the alleles generated are modifiable by Cre and Flp recombinases. We demonstrate the applicability of the methodology by modifying two mouse genes, Chd22 and Drapc1. This straightforward strategy should be readily suitable for high-throughput targeting vector production.
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Affiliation(s)
- Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Jonna Saarimäki-Vire
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Natalia Sinjushina
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Juha Partanen
- Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Helsinki, Finland
- Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Finland
- * E-mail:
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29
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Wu Z, Xuanyuan Z, Li R, Jiang D, Li C, Xu H, Bai Y, Zhang X, Turakainen H, Saris P, Savilahti H, Qiao M. Mu transposition complex mutagenesis inLactococcus lactis- identification of genes affecting nisin production. J Appl Microbiol 2009; 106:41-8. [DOI: 10.1111/j.1365-2672.2008.03962.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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30
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Abdul-Razzak A, Guiraud T, Peypelut M, Walter J, Houvenaghel MC, Candresse T, LE Gall O, German-Retana S. Involvement of the cylindrical inclusion (CI) protein in the overcoming of an eIF4E-mediated resistance against Lettuce mosaic potyvirus. MOLECULAR PLANT PATHOLOGY 2009; 10:109-13. [PMID: 19161357 PMCID: PMC6640472 DOI: 10.1111/j.1364-3703.2008.00513.x] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/07/2023]
Abstract
The capacity of Lettuce mosaic virus to overcome the lettuce resistance conferred by the mo1(1) and mo1(2) alleles of the gene for eukaryotic translation initiation factor 4E (eIF4E) was analysed using reverse genetics. Mutations in the virus genome-linked protein (VPg) allowed mo1(1) only to be overcome, but mutations in the C-terminal portion of the cylindrical inclusion (CI) protein allowed both alleles to be overcome. Site-directed mutagenesis pinpointed a key role of the amino acid at position 621 in the virulence. This is the first example of the involvement of a potyviral CI protein in the breaking of an eIF4E-mediated resistance.
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Affiliation(s)
- Anas Abdul-Razzak
- Interactions Plante-Virus, UMR GDPP 1090, INRA Université de Bordeaux 2, BP 81, F-33883 Villenave d'Ornon, France
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31
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High-resolution functional profiling of a gammaherpesvirus RTA locus in the context of the viral genome. J Virol 2008; 83:1811-22. [PMID: 19073723 DOI: 10.1128/jvi.02302-08] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/20/2022] Open
Abstract
Gammaherpesviruses Kaposi's sarcoma-associated herpesvirus and Epstein-Barr virus are associated with multiple human cancers. Our goal was to develop a quantitative, high-throughput functional profiling system to identify viral cis-elements and protein subdomains critical for virus replication in the context of the herpesvirus genome. In gamma-2 herpesviruses, the transactivating factor RTA is essential for initiation of lytic gene expression and viral reactivation. We used the RTA locus as a model to develop the functional profiling approach. The mutant murine gammaherpesvirus 68 viral library, containing 15-bp random insertions in the RTA locus, was passaged in murine fibroblast cells for multiple rounds of selection. The effect of each 15-bp insertion was characterized using fluorescent-PCR profiling. We identified 1,229 insertions in the 3,845-bp RTA locus, of which 393, 282, and 554 were critically impaired, attenuated, and tolerated, respectively, for viral growth. The functional profiling phenotypes were verified by examining several individual RTA mutant clones for transactivating function of the RTA promoter and transcomplementing function of the RTA-null virus. Thus, the profiling approach enabled us to identify several novel functional domains in the RTA locus in the context of the herpesvirus genome. Importantly, our study has demonstrated a novel system to conduct high-density functional genetic mapping. The genome-scale expansion of the genetic profiling approach will expedite the functional genomics research on herpesvirus.
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Paatero AO, Turakainen H, Happonen LJ, Olsson C, Palomäki T, Pajunen MI, Meng X, Otonkoski T, Tuuri T, Berry C, Malani N, Frilander MJ, Bushman FD, Savilahti H. Bacteriophage Mu integration in yeast and mammalian genomes. Nucleic Acids Res 2008; 36:e148. [PMID: 18953026 PMCID: PMC2602771 DOI: 10.1093/nar/gkn801] [Citation(s) in RCA: 27] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/26/2008] [Revised: 10/09/2008] [Accepted: 10/10/2008] [Indexed: 11/14/2022] Open
Abstract
Genomic parasites have evolved distinctive lifestyles to optimize replication in the context of the genomes they inhabit. Here, we introduced new DNA into eukaryotic cells using bacteriophage Mu DNA transposition complexes, termed 'transpososomes'. Following electroporation of transpososomes and selection for marker gene expression, efficient integration was verified in yeast, mouse and human genomes. Although Mu has evolved in prokaryotes, strong biases were seen in the target site distributions in eukaryotic genomes, and these biases differed between yeast and mammals. In Saccharomyces cerevisiae transposons accumulated outside of genes, consistent with selection against gene disruption. In mouse and human cells, transposons accumulated within genes, which previous work suggests is a favorable location for efficient expression of selectable markers. Naturally occurring transposons and viruses in yeast and mammals show related, but more extreme, targeting biases, suggesting that they are responding to the same pressures. These data help clarify the constraints exerted by genome structure on genomic parasites, and illustrate the wide utility of the Mu transpososome technology for gene transfer in eukaryotic cells.
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Affiliation(s)
- Anja O. Paatero
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Lotta J. Happonen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Cia Olsson
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Tiina Palomäki
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Maria I. Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Xiaojuan Meng
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Otonkoski
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Timo Tuuri
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Charles Berry
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Nirav Malani
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Mikko J. Frilander
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Frederic D. Bushman
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, Biomedicum Stem Cell Center, Biomedicum Helsinki, University of Helsinki, Helsinki, Division of Genetics and Physiology, Department of Biology, University of Turku, Turku, Program in Developmental Biology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Hospital for Children and Adolescents, University of Helsinki, Family Federation of Finland, Helsinki, Finland and Department of Microbiology, University of Pennsylvania School of Medicine, Philadelphia, PA, USA
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Arumugaswami V, Remenyi R, Kanagavel V, Sue EY, Ngoc Ho T, Liu C, Fontanes V, Dasgupta A, Sun R. High-resolution functional profiling of hepatitis C virus genome. PLoS Pathog 2008; 4:e1000182. [PMID: 18927624 PMCID: PMC2564836 DOI: 10.1371/journal.ppat.1000182] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2008] [Accepted: 09/22/2008] [Indexed: 12/17/2022] Open
Abstract
Hepatitis C virus is a leading cause of human liver disease worldwide. Recent discovery of the JFH-1 isolate, capable of infecting cell culture, opens new avenues for studying HCV replication. We describe the development of a high-throughput, quantitative, genome-scale, mutational analysis system to study the HCV cis-elements and protein domains that are essential for virus replication. An HCV library with 15-nucleotide random insertions was passaged in cell culture to examine the effect of insertions at each genome location by insertion-specific fluorescent-PCR profiling. Of 2399 insertions identified in 9517 nucleotides of the genome, 374, 111, and 1914 were tolerated, attenuating, and lethal, respectively, for virus replication. Besides identifying novel functional domains, this approach confirmed other functional domains consistent with previous studies. The results were validated by testing several individual mutant viruses. Furthermore, analysis of the 3′ non-translated variable region revealed a spacer role in virus replication, demonstrating the utility of this approach for functional discovery. The high-resolution functional profiling of HCV domains lays the foundation for further mechanistic studies and presents new therapeutic targets as well as topological information for designing vaccine candidates. Hepatitis C virus (HCV) is a major human health concern that causes fatal liver diseases. Currently no vaccine is available to prevent HCV infection. Though the HCV was identified two decades ago, the virus has only recently been successfully grown in cell culture conditions. The role of HCV protein and regulatory element sub-domains during virus growth is poorly understood. We have developed a mutational analysis method to identify the function of HCV sub-domains at a high resolution. A collection of HCV mutants containing 15-nucleotide random insertions was tested for growth in cell culture. The precise location of the insertions and their effects on virus growth were analyzed by capillary genotyping technology and bioinformatics. Out of the total 2399 HCV mutants identified, 374 mutants grew normally, 111 mutants demonstrated reduced growth, and 1914 mutants failed to grow in cell culture. This mutational analysis method was validated by testing many individual mutant viruses. The present study identified several HCV functional sub-domains required for virus growth, presenting novel therapeutic targets. The HCV mutant viruses identified with the property of reduced growth can be used for designing vaccine candidates.
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Affiliation(s)
- Vaithilingaraja Arumugaswami
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Roland Remenyi
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Vidhya Kanagavel
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Eric Yiang Sue
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Tuyet Ngoc Ho
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Chang Liu
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Vanessa Fontanes
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
| | - Asim Dasgupta
- Department of Microbiology, Immunology, and Molecular Genetics, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- AIDS Institute, University of California, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, United States of America
- Molecular Biology Institute, University of California, Los Angeles, California, United States of America
| | - Ren Sun
- Department of Molecular and Medical Pharmacology, David Geffen School of Medicine, University of California, Los Angeles, California, United States of America
- AIDS Institute, University of California, Los Angeles, California, United States of America
- Jonsson Comprehensive Cancer Center, University of California, Los Angeles, California, United States of America
- * E-mail:
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34
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Kelloniemi J, Mäkinen K, Valkonen JPT. Three heterologous proteins simultaneously expressed from a chimeric potyvirus: infectivity, stability and the correlation of genome and virion lengths. Virus Res 2008; 135:282-91. [PMID: 18511144 DOI: 10.1016/j.virusres.2008.04.006] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2007] [Revised: 03/25/2008] [Accepted: 04/07/2008] [Indexed: 01/24/2023]
Abstract
Three heterologous proteins were simultaneously expressed from a chimeric potyvirus Potato virus A (PVA) in Nicotiana benthamiana. The genes for green fluorescent protein of Aequoria victoriae ("G"; 714 nucleotides, nt), luciferase of Renilla reniformis ("L", 933 nt) and beta-glucuronidase of Escherichia coli ("U", 1806 nt) were inserted into the engineered cloning sites at the N-terminus of the P1 domain, the junction of P1 and helper component protein (HC-Pro), and the junction of the viral replicase (NIb) and coat protein (CP), respectively, in an infectious PVA cDNA. The proteins were expressed as part of the viral polyprotein and subsequently released by cleavage at the flanking proteolytic cleavage sites by P1 (one site) or the NIa-Pro proteinase (other sites). The engineered viral genome (pGLU, 13311 nt) was 39.2% larger than wild-type PVA (9565 nt) and infected plants of N. benthamiana systemically. pGLU was stable and expressed all three heterologous proteins, also following the second infection cycle initiated by sap-inoculation of new plants with the progeny viruses. The gene for GUS showed some inherent instabilities, as also reported in other studies. Accumulation of pGLU in infected leaves was lower by a magnitude as compared to the vector viruses pG0U and p0LU used to express two heterologous proteins. Hence, pGLU may have reached the maximum genome size that can still function and complete the PVA infection cycle. Examination of virions by electron microscopy indicated that the virion lengths of PVA chimera with various numbers of inserts were directly proportional to their genome lengths.
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Affiliation(s)
- Jani Kelloniemi
- Department of Applied Biology, P.O. Box 27, FIN-00014 University of Helsinki, Finland
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35
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Hafrén A, Mäkinen K. Purification of viral genome-linked protein VPg from potato virus A-infected plants reveals several post-translationally modified forms of the protein. J Gen Virol 2008; 89:1509-1518. [PMID: 18474568 DOI: 10.1099/vir.0.83649-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
In order to be able to analyse post-translational modifications and protein interactions of viral genome-linked protein VPg taking place during potato virus A (PVA) infection, an affinity tag-based purification system was developed by inserting a sequence encoding a six-histidine and haemagglutinin (HisHA) tag to the 3' end of the VPg coding sequence within the infectious cDNA clone of PVA. The engineered virus was fully functional and the HisHA tag-encoding sequence remained stable in the PVA genome throughout the infection process. Purification under denaturing conditions resulted in a protein sample that contained multiple VPg and NIa forms carrying post-translational modifications that altered their isoelectric points. Non-modified tagged VPg (pI 8) was a minor product in the protein sample derived from total leaf proteins, but when the replication-associated membranes were used as starting material, its relative amount increased. Further characterization demonstrated that some of the PVA VPg isoforms were modified by multiple phosphorylation events. Purity of the proteins derived from the native purifications with either of the tags was evaluated. A clearly purer VPg sample was obtained by performing tandem affinity purification utilizing both tags sequentially. NIb, CI and HC-Pro co-purified in an affinity-tagged VPg-dependent manner, indicating that the system was able to isolate protein complexes operating during PVA infection.
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Affiliation(s)
- Anders Hafrén
- Department of Applied Chemistry and Microbiology, Latokartanonkaari 11, PO Box 27, University of Helsinki, FIN-00014 Helsinki, Finland
| | - Kristiina Mäkinen
- Department of Applied Chemistry and Microbiology, Latokartanonkaari 11, PO Box 27, University of Helsinki, FIN-00014 Helsinki, Finland
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36
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Ratra R, Lal SK. Functional genomics as a tool in virus research. Indian J Microbiol 2008; 48:195-201. [PMID: 23100713 PMCID: PMC3450177 DOI: 10.1007/s12088-008-0032-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/10/2008] [Accepted: 05/10/2008] [Indexed: 01/28/2023] Open
Abstract
Genomics is the study of an organism’s entire genome. It started out as a great scientific endeavor in the 1990s which aimed to sequence the complete genomes of certain biological species. However viruses are not new to this field as complete viral genomes have routinely been sequenced since the past thirty years. The ‘genomic era’ has been said to have revolutionized biology. This knowledge of full genomes has created the field of functional genomics in today’s post-genomic era, which, is in most part concerned with the studies on the expression of the organism’s genome under different conditions. This article is an attempt to introduce its readers to the application of functional genomics to address and answer several complex biological issues in virus research.
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Affiliation(s)
- Ruchi Ratra
- Virology Group, International Centre for Genetic Engineering & Biotechnology, New Delhi, India
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37
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Chen CC, Chen TC, Raja JAJ, Chang CA, Chen LW, Lin SS, Yeh SD. Effectiveness and stability of heterologous proteins expressed in plants by Turnip mosaic virus vector at five different insertion sites. Virus Res 2007; 130:210-27. [PMID: 17689817 DOI: 10.1016/j.virusres.2007.06.014] [Citation(s) in RCA: 28] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2006] [Revised: 03/09/2007] [Accepted: 06/19/2007] [Indexed: 11/29/2022]
Abstract
The N-terminal (NT) regions of particular protein-coding sequences are generally used for in-frame insertion of heterologous open reading frames (ORFs) in potyviral vectors for protein expression in plants. An infectious cDNA clone of Turnip mosaic virus (TuMV) isolate YC5 was engineered at the generally used NT regions of HC-Pro and CP, and other possibly permissive sites to investigate their effectiveness to express the GFP (jellyfish green fluorescent protein) and Der p 5 (allergen from the dust mite, Dermatophagoides pteronyssinus) ORFs. The results demonstrated the permissiveness of the NT regions of P3, CIP and NIb to carry the ORFs and express the translates as part of the viral polyprotein, the processing of which released free-form proteins in the host cell milieu. However, these sites varied in their permissiveness to retain the ORFs intact and hence affect the heterologous protein expression. Moreover, strong influence of the inserted ORF and host plants in determining the permissiveness of a viral genomic context to stably carry the alien ORFs and hence to support their prolonged expression was also noticed. In general, the engineered sites were relatively more permissive to the GFP ORF than to the Der p 5 ORF. Among the hosts, the local lesion host, Chenopodium quinoa Willd. showed the highest extent of support to TuMV to stably carry the heterologous ORFs at the engineered sites and the protein expression therefrom. Among the systemic hosts, Nicotiana benthamiana Domin proved more supportive to TuMV to carry and express the heterologous ORFs than the Brassica hosts, whereas the protein expression levels were significantly higher and more stable in the plants of Brassica campestris L. var. chinensis and B. campestris L. var. ching-geeng than those in the plants of B. juncea L. and B. campestris L. var. pekinensis.
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Affiliation(s)
- Chin-Chih Chen
- Department of Plant Pathology, National Chung-Hsing University, Taichung 40227, Taiwan, ROC
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Pajunen M, Turakainen H, Poussu E, Peränen J, Vihinen M, Savilahti H. High-precision mapping of protein protein interfaces: an integrated genetic strategy combining en masse mutagenesis and DNA-level parallel analysis on a yeast two-hybrid platform. Nucleic Acids Res 2007; 35:e103. [PMID: 17702760 PMCID: PMC2018616 DOI: 10.1093/nar/gkm563] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Understanding networks of protein–protein interactions constitutes an essential component on a path towards comprehensive description of cell function. Whereas efficient techniques are readily available for the initial identification of interacting protein partners, practical strategies are lacking for the subsequent high-resolution mapping of regions involved in protein–protein interfaces. We present here a genetic strategy to accurately map interacting protein regions at amino acid precision. The system is based on parallel construction, sampling and analysis of a comprehensive insertion mutant library. The methodology integrates Mu in vitro transposition-based random pentapeptide mutagenesis of proteins, yeast two-hybrid screening and high-resolution genetic footprinting. The strategy is general and applicable to any interacting protein pair. We demonstrate the feasibility of the methodology by mapping the region in human JFC1 that interacts with Rab8A, and we show that the association is mediated by the Slp homology domain 1.
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Affiliation(s)
- Maria Pajunen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Hilkka Turakainen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Eini Poussu
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Johan Peränen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Mauno Vihinen
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
| | - Harri Savilahti
- Program in Cellular Biotechnology, Institute of Biotechnology, Viikki Biocenter, University of Helsinki, Institute of Medical Technology, University of Tampere, Research Unit, Tampere University Hospital, Tampere and Division of Genetics and Physiology, Department of Biology, University of Turku, Finland
- *To whom correspondence should be addressed. +358 9 191 59516+358 9 191 59366
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39
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Gammelgård E, Mohan M, Valkonen JPT. Potyvirus-induced gene silencing: the dynamic process of systemic silencing and silencing suppression. J Gen Virol 2007; 88:2337-2346. [PMID: 17622640 DOI: 10.1099/vir.0.82928-0] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Potato virus A (PVA; genus Potyvirus) was used for virus-induced gene silencing in a model system that included transgenic Nicotiana benthamiana (line 16c) expressing the gfp transgene for green fluorescent protein (GFP) and chimeric PVA (PVA-GFP) carrying gfp in the P1-encoding region. Infection of the 16c plants with PVA-GFP in five experiments resulted in a reproducible pattern of systemic gfp transgene silencing, despite the presence of the strong silencing-suppressor protein, HC-Pro, produced by the virus. PVA-GFP was also targeted by silencing, and virus-specific short interfering RNA accumulated from the length of the viral genome. Viral deletion mutants lacking the gfp insert appeared in systemically infected leaves and reversed silencing of the gfp transgene in limited areas. However, systemic gfp silencing continued in newly emerging leaves in the absence of the gfp-carrying virus, which implicated a systemic silencing signal that moved from lower leaves without interference by HC-Pro. Use of GFP as a visual marker revealed a novel, mosaic-like recovery phenotype in the top leaves. The leaf areas appearing red or purple under UV light (no GFP expression) contained little PVA and gfp mRNA, and corresponded to the dark-green islands observed under visible light. The surrounding green fluorescent tissues contained actively replicating viral deletion mutants that suppressed GFP silencing. Taken together, systemic progression of gene silencing and antiviral defence (RNA silencing) and circumvention of the silencing by the virus could be visualized and analysed in a novel manner.
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Affiliation(s)
- Elin Gammelgård
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), PO Box 7080, SE-750 07 Uppsala, Sweden
| | - Maradumane Mohan
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), PO Box 7080, SE-750 07 Uppsala, Sweden
| | - Jari P T Valkonen
- Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Finland
- Department of Plant Biology and Forest Genetics, Swedish University of Agricultural Sciences (SLU), PO Box 7080, SE-750 07 Uppsala, Sweden
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40
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Orsini L, Pajunen M, Hanski I, Savilahti H. SNP discovery by mismatch-targeting of Mu transposition. Nucleic Acids Res 2007; 35:e44. [PMID: 17311815 PMCID: PMC1874615 DOI: 10.1093/nar/gkm070] [Citation(s) in RCA: 15] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022] Open
Abstract
Single nucleotide polymorphisms (SNPs) represent a valuable resource for the mapping of human disease genes and induced mutations in model organisms. SNPs may become the markers of choice also for population ecology and evolutionary studies, but their isolation for non-model organisms with unsequenced genomes is often difficult. Here, we describe a rapid and cost-effective strategy to isolate SNPs that exploits the property of the bacteriophage Mu transposition machinery to target mismatched DNA sites and thereby to effectively detect polymorphic loci. To demonstrate the methodology, we isolated 164 SNPs from the unsequenced genome of the Glanville fritillary butterfly (Melitaea cinxia), a much-studied species in population biology, and we validated 24 of them. The strategy involves standard molecular biology techniques as well as undemanding MuA transposase-catalyzed in vitro transposition reactions, and it is applicable to any organism.
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Affiliation(s)
- Luisa Orsini
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Maria Pajunen
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Ilkka Hanski
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
| | - Harri Savilahti
- Metapopulation Research Group, Department of Biological and Environmental Sciences, PO Box 65, and Research Program in Cellular Biotechnology, Institute of Biotechnology, PO Box 56, FIN-00014, University of Helsinki, Finland and Division of Genetics and Physiology, Department of Biology, FIN-20014, University of Turku, Finland
- *To whom correspondence should be addressed. +358 9 191 59516+358 9 191 59366
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41
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Nováková S, Klaudiny J, Kollerová E, Subr ZW. Expression of a part of the Potato virus A non-structural protein P3 in Escherichia coli for the purpose of antibody preparation and P3 immunodetection in plant material. J Virol Methods 2006; 137:229-35. [PMID: 16876262 DOI: 10.1016/j.jviromet.2006.06.020] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2006] [Revised: 06/12/2006] [Accepted: 06/15/2006] [Indexed: 10/24/2022]
Abstract
The N-terminal part of the Potato virus A (PVA) P3 protein was cloned into two E. coli fusion expression systems. An overexpression of the P3 fragment fused with thioredoxin was observed between 2 and 21 h after induction. The protein formed insoluble inclusions. Decreasing the cultivation temperature did not enhance its solubility. To obtain antigen for antibody preparation, inclusions were concentrated and purified by sucrose gradient centrifugation, and subjected to SDS-polyacrylamide gel electrophoresis. The band specific for the protein was excised from the gel and used for rabbit immunization. Obtained antibody tested positive with high specificity in immunoblots of expressed PVA P3 fused with either thioredoxin or GST. The antibody was also applied for the detection of P3 protein in plant material by immunoblot. Previous plant sap concentration was essential for most samples. Three concentration methods were tested: simple centrifugal size-exclusion filtration, the same preceded with high-speed centrifugation at 250,000 x g, and differential ammonium sulfate precipitation. The last approach was the most convenient. Plants tested included PVA P3-transgenic tobacco lines as well as PVA-infected wild-type tobacco. In all cases, mature P3 with a molecular mass of 40 kDa was detected.
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Affiliation(s)
- S Nováková
- Institute of Virology, Slovak Academy of Sciences, Dúbravská cesta 9, 845 45 Bratislava, Slovakia.
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42
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Krupovic M, Vilen H, Bamford JKH, Kivelä HM, Aalto JM, Savilahti H, Bamford DH. Genome characterization of lipid-containing marine bacteriophage PM2 by transposon insertion mutagenesis. J Virol 2006; 80:9270-8. [PMID: 16940538 PMCID: PMC1563929 DOI: 10.1128/jvi.00536-06] [Citation(s) in RCA: 22] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2006] [Accepted: 06/27/2006] [Indexed: 11/20/2022] Open
Abstract
Bacteriophage PM2 presently is the only member of the Corticoviridae family. The virion consists of a protein-rich lipid vesicle, which is surrounded by an icosahedral protein capsid. The lipid vesicle encloses a supercoiled circular double-stranded DNA genome of 10,079 bp. PM2 belongs to the marine phage community and is known to infect two gram-negative Pseudoalteromonas species. In this study, we present a characterization of the PM2 genome made using the in vitro transposon insertion mutagenesis approach. Analysis of 101 insertion mutants yielded information on the essential and dispensable regions of the PM2 genome and led to the identification of several new genes. A number of lysis-deficient mutants as well as mutants displaying delayed- and/or incomplete-lysis phenotypes were identified. This enabled us to identify novel lysis-associated genes with no resemblance to those previously described from other bacteriophage systems. Nonessential genome regions are discussed in the context of PM2 genome evolution.
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Affiliation(s)
- Mart Krupovic
- Department of Biological and Environmental Sciences, Institute of Biotechnology, Viikki Biocenter 2, P.O. Box 56 (Viikinkaari 5), FIN-00014 University of Helsinki, Finland
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43
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Waltermann A, Maiss E. Detection of 6K1 as a mature protein of 6 kDa in plum pox virus-infected Nicotiana benthamiana. J Gen Virol 2006; 87:2381-2386. [PMID: 16847134 DOI: 10.1099/vir.0.81873-0] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
The RNA genome of Plum pox virus (PPV) encodes one large polyprotein that is subsequently cleaved into mature viral proteins. One of the products of proteolytic processing, the 6K1 protein, has not yet been identified in vivo for any member of the genus Potyvirus. In this study, 6K1-specific polyclonal antiserum was raised against PPV 6K1 expressed in Escherichia coli as a translational fusion with the N terminus of avian troponin C and an unusual metal-binding cluster of troponin T-1. For detection of 6K1 in vivo, a pPPV-H6K1-NAT infectious clone was constructed, enabling concentration of histidine-tagged 6K1 by affinity chromatography. Affinity-purified 6K1 was detected in locally infected Nicotiana benthamiana leaves at 4, 7 and 14 days post-inoculation (d.p.i.) and, in addition, in systemically infected leaves at 14 d.p.i., 6K1 was detected exclusively as a protein of 6 kDa and no polyprotein precursors were identified with the raised anti-6K1 antiserum.
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Affiliation(s)
- Angelika Waltermann
- Institute of Plant Diseases and Plant Protection, University of Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
| | - Edgar Maiss
- Institute of Plant Diseases and Plant Protection, University of Hannover, Herrenhäuser Straße 2, 30419 Hannover, Germany
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Rajamäki ML, Kelloniemi J, Alminaite A, Kekarainen T, Rabenstein F, Valkonen JPT. A novel insertion site inside the potyvirus P1 cistron allows expression of heterologous proteins and suggests some P1 functions. Virology 2005; 342:88-101. [PMID: 16112702 DOI: 10.1016/j.virol.2005.07.019] [Citation(s) in RCA: 46] [Impact Index Per Article: 2.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2005] [Revised: 06/20/2005] [Accepted: 07/13/2005] [Indexed: 10/25/2022]
Abstract
The P1 cistron encodes the first and most variable part of the polyprotein of potyviruses. A site tolerant to a pentapeptide insertion at the N-terminus of Potato virus A P1 (Genome Res. 12, 584-594) was used to express heterologous proteins (insertions up to 783 nucleotides) with or without flanking new proteolytic sites. Aequorea victoria green fluorescent protein (GFP) accumulated to high levels when proteolytically released from P1 and showed strong fluorescence in leaves systemically infected with vector virus. Deletions in GFP and adjacent viral sequences emerged 2-4 weeks after infection, revealing putative recombination hot spots. The inserts in P1 diminished infectivity host-specifically, reduced virus accumulation in protoplasts and systemically infected leaves, alleviated symptoms and reduced accumulation of mRNA and HCpro in cis in a virus-free system. This heterologous protein expression site is the first within a protein-encoding cistron and the third in the genome of potyviruses.
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Affiliation(s)
- Minna-Liisa Rajamäki
- Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Finland
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45
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Poussu E, Jäntti J, Savilahti H. A gene truncation strategy generating N- and C-terminal deletion variants of proteins for functional studies: mapping of the Sec1p binding domain in yeast Mso1p by a Mu in vitro transposition-based approach. Nucleic Acids Res 2005; 33:e104. [PMID: 16006618 PMCID: PMC1174911 DOI: 10.1093/nar/gni102] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Bacteriophage Mu in vitro transposition constitutes a versatile tool in molecular biology, with applications ranging from engineering of single genes or proteins to modification of genome segments or entire genomes. A new strategy was devised on the basis of Mu transposition that via a few manipulation steps simultaneously generates a nested set of gene constructions encoding deletion variants of proteins. C-terminal deletions are produced using a mini-Mu transposon that carries translation stop signals close to each transposon end. Similarly, N-terminal deletions are generated using a transposon with appropriate restriction sites, which allows deletion of the 5'-distal part of the gene. As a proof of principle, we produced a set of plasmid constructions encoding both C- and N-terminally truncated variants of yeast Mso1p and mapped its Sec1p-interacting region. The most important amino acids for the interaction in Mso1p are located between residues T46 and N78, with some weaker interactions possibly within the region E79-N105. This general-purpose gene truncation strategy is highly efficient and produces, in a single reaction series, a comprehensive repertoire of gene constructions encoding protein deletion variants, valuable in many types of functional studies. Importantly, the methodology is applicable to any protein-encoding gene cloned in an appropriate vector.
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Affiliation(s)
| | - Jussi Jäntti
- VTT BiotechnologyPO Box 1500, FI-02044, VTT, Finland
| | - Harri Savilahti
- To whom correspondence should be addressed. Tel: +358 9 19159516; Fax: +358 9 19159366.
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46
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Matousek J, Orctová L, Steger G, Riesner D. Biolistic inoculation of plants with viroid nucleic acids. J Virol Methods 2005; 122:153-64. [PMID: 15542139 DOI: 10.1016/j.jviromet.2004.08.011] [Citation(s) in RCA: 24] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2004] [Revised: 08/13/2004] [Accepted: 08/16/2004] [Indexed: 11/23/2022]
Abstract
Parameters for biolistic transfer of viroid nucleic acids using a Helios Gene Gun device were assayed. The main achievement of this method is high efficiency of inoculation with linear monomeric viroid cDNAs and RNAs. This greatly facilitates the study of mutated sequence variants, viroid libraries and mixed populations. The lower limits for efficient inoculation of monomeric cDNA fragments with the sequence of potato spindle tuber viroid (PSTVd) and native PSTVd RNA as detected 21 days p.i. are in the range of 50 ng and 200 pg per tomato plant, respectively. At a higher dose, i.e. 2 ng of native RNA per plant, biolistic transfer causes drastic stunting compared to conventional mechanical inoculation, which points to higher PSTVd titers after the biolistic transfer. Infection is readily achieved with exact length monomeric RNA transcripts having 5'-triphosphate and 3'-OH termini in amounts ranging from 2 to 20 ng per plant, suggesting no need for any supplementary modifications of ends or RNA circularization. The biolistic transfer is efficient for viroid "thermomutants", which exhibit low or no infectivity with conventional mechanical inoculation with Carborundum. The biolistic inoculation is also efficient for two other members of the Pospiviroidae family, hop stunt and hop latent viroid.
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Affiliation(s)
- J Matousek
- Department of Molecular Genetics, Institute of Plant Molecular Biology, Czech Academy of Sciences, Branisovsk 31, 37005 Cesk Budĕjovice, Czech Republic.
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47
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Bubeck A, Wagner M, Ruzsics Z, Lötzerich M, Iglesias M, Singh IR, Koszinowski UH. Comprehensive mutational analysis of a herpesvirus gene in the viral genome context reveals a region essential for virus replication. J Virol 2004; 78:8026-35. [PMID: 15254174 PMCID: PMC446129 DOI: 10.1128/jvi.78.15.8026-8035.2004] [Citation(s) in RCA: 64] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022] Open
Abstract
Essential viral proteins perform vital functions during morphogenesis via a complex interaction with other viral and cellular gene products. Here, we present a novel approach to comprehensive mutagenesis of essential cytomegalovirus genes and biological analysis in the 230-kbp-genome context. A random Tn7-based mutagenesis procedure at the single-gene level was combined with site-specific recombination via the FLP/FLP recognition target site system for viral genome reconstitution. We show the function of more than 100 mutants from a larger library of M50/p35, a protein involved in capsid egress from the nucleus. This protein recruits other viral proteins and cellular enzymes to the inner nuclear membrane. Our approach enabled us to rapidly discriminate between essential and nonessential regions within the coding sequence. Based on the prediction of the screen, we were able to map a site essential for viral protein-protein interaction at the amino acid level.
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Affiliation(s)
- Anja Bubeck
- Max von Pettenkofer Institut für Virologie, Ludwig-Maximilians-Universität, 80336 Munich, Germany
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Puustinen P, Mäkinen K. Uridylylation of the potyvirus VPg by viral replicase NIb correlates with the nucleotide binding capacity of VPg. J Biol Chem 2004; 279:38103-10. [PMID: 15218030 DOI: 10.1074/jbc.m402910200] [Citation(s) in RCA: 65] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/06/2022] Open
Abstract
Poty- and picornaviruses share similar genome organizations and polyprotein processing strategies. By analogy to picornaviruses it has been proposed that the genome-linked protein VPg may serve as a primer for genome replication of potyviruses. The multifunctional VPg of potato virus A (PVA; genus Potyvirus) was found to be uridylylated by NIb, the RNA polymerase of PVA. The nucleotidylation activity of NIb is more efficient in the presence of Mn(2+) than Mg(2+) and does not require an RNA template. Our results suggest that the nucleotidylation reaction exhibits weak preference for UTP over the other NTPs. An NTP-binding experiment with oxidized [alpha-(32)P]UTP revealed that PVA VPg contains an NTP-binding site. Deletion of a 7-amino acid-long putative NTP-binding site from VPg reduced nucleotide-binding capacity and debilitated uridylylation reaction. These results provide evidence that VPg may play a similar role in RNA synthesis of potyviruses as it does in the case of picornaviruses.
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Affiliation(s)
- Pietri Puustinen
- Department of Applied Biology, P. O. Box 27, University of Helsinki, Helsinki 00014, Finland
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49
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Spetz C, Valkonen JPT. Potyviral 6K2 protein long-distance movement and symptom-induction functions are independent and host-specific. MOLECULAR PLANT-MICROBE INTERACTIONS : MPMI 2004; 17:502-10. [PMID: 15141954 DOI: 10.1094/mpmi.2004.17.5.502] [Citation(s) in RCA: 31] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Deletion of various portions, or insertion of six histidine residues (6xHis) into various positions of the membrane-bound 6K2 protein (53 amino acids) of Potato virus A (PVA, genus Potyvirus), inhibited systemic infection in Nicotiana tabacum and N. benthamiana plants. However, a spontaneous mutation (Gly2Cys) that occurred in 6K2 adjacent to the 6xHis insert placed between Ser1 and Gly2 enabled systemic infection in a single N. benthamiana plant. No symptoms were observed, but virus titers were similar to the symptom-inducing wild-type (wt) PVA. N. tabacum plants were not systemically infected, albeit virus propagation was observed in inoculated protoplasts. The 6xHis/Gly2Cys mutant was reconstructed in vitro and serially propagated by mechanical inoculation in N. benthamiana. Following the third passage, a novel viral mutant appeared, lacking the last four His residues of the insert, as well as the Gly2 and Thr3 of 6K2. It infected N. tabacum plants systemically, and in the systemically infected N. benthamiana leaves, vein chlorosis and mild yellowing symptoms were observed, typical of wt PVA infection. The mutant virus accumulated to titers similar to wt PVA in both hosts. These results show that the PVA 6K2 protein affects viral long-distance movement and symptom induction independently and in a host-specific manner.
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Affiliation(s)
- Carl Spetz
- Department of Plant Biology and Forest Genetics, Genetics Centre, SLU, PO Box 7080, SE-750 07 Uppsala, Sweden
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50
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Paalme V, Gammelgård E, Järvekülg L, Valkonen JPT. In vitro recombinants of two nearly identical potyviral isolates express novel virulence and symptom phenotypes in plants. J Gen Virol 2004; 85:739-747. [PMID: 14993660 DOI: 10.1099/vir.0.19729-0] [Citation(s) in RCA: 25] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022] Open
Abstract
Six novel chimeric viruses were constructed by sequentially exchanging segments of the viral genomes between the infectious cDNA clone (pPVA-B11) of Potato virus A (isolate PVA-B11) and pUFL, an almost identical infectious cDNA of PVA (isolate U) made in this study. The infectious in vitro transcripts of pUFL and pPVA-B11 caused similar severe mosaic and leaf malformation phenotypes in systemically infected leaves of Nicotiana benthamiana. In contrast, one chimera induced a unique phenotype of yellow vein chlorosis without leaf malformation with viral titres that were equivalent to those of the parental viruses. Furthermore, as opposed to the viral cDNAs from which it was assembled, one chimera showed no detectable infectivity of N. benthamiana plants. Thus, recombination of nearly identical, phenotypically similar virus genomes can give rise to new viral strains with novel virulence and symptom phenotypes, which has not previously been demonstrated with potyviruses. One chimera failed to cause systemic infection in potato plants, but, nevertheless, avirulence could not be attributed to a single genomic region. These data suggest that different parts of the potyviral genome function coordinately. The results provide novel insights into the evolution of the genus Potyvirus.
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Affiliation(s)
- Viiu Paalme
- Department of Plant Biology and Forest Genetics, Genetics Centre, SLU, Box 7080, SE-750 07 Uppsala, Sweden
- National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, EE-12618 Tallinn, Estonia
| | - Elin Gammelgård
- Department of Plant Biology and Forest Genetics, Genetics Centre, SLU, Box 7080, SE-750 07 Uppsala, Sweden
| | - Lilian Järvekülg
- Department of Gene Technology, Tallinn Technical University, Akadeemia tee 23, EE-12618 Tallinn, Estonia
- National Institute of Chemical Physics and Biophysics, Akadeemia tee 23, EE-12618 Tallinn, Estonia
| | - Jari P T Valkonen
- Department of Applied Biology, PO Box 27, FIN-00014 University of Helsinki, Finland
- Department of Plant Biology and Forest Genetics, Genetics Centre, SLU, Box 7080, SE-750 07 Uppsala, Sweden
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