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Characterization of Rose Rosette Virus and Development of Reverse Genetic System for Studying bioRxiv preprint doi: https://doi.org/10.1101/712000; this version posted May 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Characterization of Rose rosette virus and development of reverse genetic system for studying 2 virus accumulation and movement in whole plants. 3 Jeanmarie Verchotab1, Venura Herathab, Cesar D. Urrutiab, Mathieu Gayrala, Kelsey Lylead, 4 Madalyn K. Shiresb, Kevin Ongb, David Byrned, 5 aTexas A&M Agrilife Center in Dallas, Dallas Texas, USA 6 bDepartment of Plant Pathology & Microbiology, Texas A&M University, College Station, Texas, 7 USA 8 cDepartment of Horticultural Sciences, Texas A&M University, College Station, Texas, USA 9 dDepartment of Biological Sciences, University of Texas at Dallas, Dallas, Texas, USA 10 11 Running Head: Advancing Rose Rosette virus infectious clone 12 1 Address correspondence to Jeanmarie Verchot, [email protected] 13 Present Address: Department of Plant Pathology & Microbiology, Texas A&M University, 14 College Station, Texas, USA 15 Word count for Abstract: 247 For text: 16 Keywords: Reverse genetic system, Emaravirus, plant virus, infectious clone, 17 18 19 20 21 1 bioRxiv preprint doi: https://doi.org/10.1101/712000; this version posted May 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 ABSTRACT 2 Rose rosette virus (RRV) is an Emaravirus, a negative-sense RNA virus with a 7-segmented 3 genome that is enclosed by a double membrane. While the genome sequences of many 4 emaraviruses are reported, there is negligible information concerning virus replication and 5 movement in host plants. Computational methods determined that RNA1 encoded the RNA 6 dependent RNA polymerase (RdRp), RNA2 encoded glycoprotein precursor, and the RNA3 7 encoded the nucleocapsid (N), all share significant homologies with similar proteins of the 8 Orthobunyavirus family. The RRV terminal UTR sequences are complementary and share 9 significant identity with the UTR sequences of Bunyamwera virus. We report a minireplicon 10 system and a full length infectious clone of RRV, which are the first for any emaravirus species. 11 The photoreversible fluorescent iLOV protein was used to replace the RNA5 open reading 12 frame (R5-iLOV). We demonstrate that agro-infiltration of Nicotiana benthamiana leaves to 13 deliver RNA1, RNA3, and R5-iLOV cDNAs led to iLOV expression. A mutation was introduced 14 into the RdRp active site and iLOV expression was eliminated. Delivery of four segments or 15 seven segments of the RRV infectious clone produced systemic infection in N. benthamiana 16 and rose plants. iLOV was also fused to the glycoprotein precursor (R2-iLOV). Using confocal 17 microscopy, the R2-iLOV was seen in spherical bodies along membrane strands inside N. 18 benthamiana epidermal cells. This new technology will enable future research to functionally 19 characterize the RRV proteins, to study the virus-host interactions governing local and systemic 20 infection, and examine the subcellular functions of the Gc. 21 IMPORTANCE RRV has emerged as a severe threat to cultivated roses, causing millions of 22 dollars in losses to commercial producers. The majority of the viral gene products have not 23 been researched or characterized until now. We constructed a minireplicon system and an 24 infectious clone of the seven-segmented RRV genome that is contained in a binary vector and 25 delivered by Agrobacterium. This technology has been slow to develop for viruses with 2 bioRxiv preprint doi: https://doi.org/10.1101/712000; this version posted May 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 negative-strand RNA genomes. It has been especially tricky for plant viruses with 2 multicomponent negative-strand RNA genomes. We report the first reverse genetic system for 3 a member of the genus Emaravirus, Rose rosette virus (RRV). We introduced the iLOV 4 fluorescent protein as a fusion to the Gc protein and as a replacement for the open reading 5 frame in genome segment 5. This game-changing reverse genetic system creates new 6 opportunities for studying negative-strand RNA viruses in plants. 7 INTRODUCTION 8 Among the most significant technological advances for research into virus life cycles has 9 been the development of cDNA copies of viral genomes that can be reverse transcribed to 10 produce infectious virus (1). This technology enables the genetic manipulation of cDNA for 11 reverse genetic analysis of the virus life cycle, and investigations into the molecular basis of 12 virus-host interactions for susceptibility and immunity. The infectious cDNA technology is 13 routinely used to study positive-strand RNA viruses. Infectious virus cDNAs are inserted into 14 plasmids by fusing the exact 5' end of the virus genomic cDNA to the bacteriophage T7, SP6, 15 RNA pol I, or RNA pol II promoters (2–5). A transcriptional terminator or hepatitis delta virus 16 ribozyme (HDRz) can be located at the 3’ ends to produce transcripts with exact 3’ ends (6–8). 17 The second advance in infectious clone technology was the discovery that genetic sequences 18 encoding fluorescent proteins can be introduced into specific locations within the viral genome 19 to visualize the effects of mutations on virus replication in reverse genetic experiments (9–16). 20 Among plant RNA viruses, green fluorescent protein (GFP) and derivatives, or iLOV genes, 21 have been incorporated into viral genomes (17). Combining visual markers of infection with 22 reverse genetic technology has been a powerful combination for functional imaging to uncover 23 critical roles of viral proteins in the virus life cycle. These combined technologies have been 24 central to the discovery of molecular plant-virus interactions occurring in susceptible hosts or 25 that govern gene-for-gene resistance. 3 bioRxiv preprint doi: https://doi.org/10.1101/712000; this version posted May 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 Infectious clone technology has been tricky to develop for plant viruses with negative- 2 strand RNA genomes because the naked genomic or antigenomic RNAs are not able to initiate 3 infection by themselves. The minimum infectious unit for viruses with negative-strand RNA 4 genomes requires a ribonucleoprotein (RNP) complex composed of viral genomic RNA and 5 RNA dependent RNA polymerase (RdRp). For plant infecting viruses, a movement protein 6 (MP) is also essential for whole plant infection. Considering the many successful examples of 7 infectious clones developed for negative-strand RNA viruses such as species belonging to the 8 families Rhabdoviridae, Paramyxoviridae, and Filoviridae (18–20), infection is achievable by 9 delivering viral genomic cDNAs that produce transcripts functioning as the antigenomic RNAs 10 (agRNA). Plasmids encoding the nucleocapsid core or subunits of the viral polymerase are co- 11 delivered with the agRNA encoding cDNAs that successfully spur the replication process. The 12 first infectious clone of a plant-infecting negative-strand RNA virus was Sonchus yellow net virus 13 (SYNV) (18, 19, 21). This construction consists of a binary vector containing the SYNV full- 14 length cDNA fused to a duplicated Cauliflower mosaic virus (CaMV) 35S promoter. Additional 15 binary plasmids expressing the NC (nucleocapsid), P (phosphoprotein), and L (polymerase) 16 proteins are co-delivered to leaves for active SYNV infection. 17 The order Bunyavirales includes nine families of enveloped viruses with segmented 18 negative-strand RNA genomes. These viruses infect animals, plants, and invertebrates. Four 19 families contain viruses that cause disease in humans, including La Cross virus (LACV), Rift 20 valley fever virus (RVFV), Crimean-Congo hemorrhagic fever virus (CCHFV) and Hantaan virus 21 (HTNV) (22, 23). Three families within this order encode viruses that infect plants: Fimoviridae, 22 Phenuiviridae, and Tospoviridae. Their genomes consist of three to eight segments with the 23 largest segment (named L or RNA1) encoding the RNA dependent RNA polymerase (RdRp). 24 For viruses with three genome segments, the M segment encodes two glycoproteins (Gn and 25 Gc), and the S segment encodes the nucleocapsid (named NC or N for different genera or 4 bioRxiv preprint doi: https://doi.org/10.1101/712000; this version posted May 16, 2020. The copyright holder for this preprint (which was not certified by peer review) is the author/funder. All rights reserved. No reuse allowed without permission. 1 species) protein. The untranslated regions (UTRs) at the 3’ and 5' ends direct transcription of 2 mRNA and replication to generate agRNA as intermediates for synthesis of further genomic 3 RNAs. Full-length infectious clones and "minireplicon” systems are available for studying the 4 bunyavirus replication and transcription at the cellular level (24). These systems are successful 5 for achieving RNA synthesis when the RdRp and NC are expressed from cDNA plasmids as the 6 minimum requirements to achieve transcription and replication-competent RNP particles. Co- 7 transfecting plasmids encoding the viral glycoprotein precursor stimulates the packaging of the 8 RNPs into virus-like particles. 9 Rose rosette virus (RRV) is a negative-strand RNA virus with seven genome segments 10 and belongs to the Emaravirus genus within the family Fimoviridae. Beyond reporting the 11 genome sequence for RRV, there is very little known about the functional roles of proteins 12 encoded by each RNA segment. Roses are the economically most important ornamental plants 13 in the Rosaceae family. RRV has been devastating roses and the rose industry in the USA, 14 causing millions of dollars in losses (25).
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