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Investigation of Virus-Induced Defence Modulations During Plant-Virus Interactions

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Investigation of Virus-Induced Defence Modulations During Plant-Virus Interactions Investigation of virus-induced defence modulations during plant-virus interactions Subtitle The Plant-Virus Relationship Status: It’s Complicated Lara-Simone Pretorius Flower‐breaking symptoms in a Tulip A thesis submitted for the degree of Doctor of Philosophy at The University of Queensland in 2018 School of Agriculture & Food Sciences 1 Abstract Turnip mosaic virus (TuMV) is a single stranded RNA (sRNAs) virus belonging to the genus Potyvirus .Turnip mosaic virus has a wide host range including several important crop plants, making it economically significant. This study investigates the relation between a strain of TuMV and two model plant systems; Arabidopsis thaliana and Nicotiana benthamiana, focusing on the viral sequence, host gene expression and defence mechanisms, and viral derived small RNAs (viRNAs). Turnip mosaic virus has been well studied and characterised with 183 complete genome nucleotide sequences available in GenBank (5 June 2018). The TuMV isolate used in this study was sequenced and submitted to GenBank, as well as the original isolate collected in 1994, under the names TuMV- QLD1b and TuMV-QLD1a, respectively (accession numbers KX641465 and KX641466). The original TuMV isolate was PCR sequenced while the 2015 isolate was sequenced by deep RNA sequencing. A comparison between the two sequences showed minor variations with 18 single- nucleotide-polymorphisms (SNPs). Another aspect of the study involved the sequencing of a Cucumber mosaic virus (CMV) isolate (strain K) as well as an Australian Cauliflower mosaic virus (CaMV) isolate belonging to the genus Cucumovirus and Caulimovirus respectively. This strain of CaMV represents the first Australian isolate to be fully sequenced. Both the CMV and the CaMV isolates were used to study plant defence pathways in Chapter 4 of this thesis. The sequence of both isolates were published and make up Chapter 2. Chapter 3 investigates the early defence response of A. thaliana 6, 24 and 48 hours after TuMV inoculation. Marker gene expression results suggest that the virus upregulated the jasmonic acid (JA) pathway 24 hours after infection. This is significant, as viruses are classified as biotrophic pathogens which usually upregulate the salicylic acid (SA) pathway leading to hyper-sensitive response and programmed cell death, preventing the virus from spreading. It is hypothesised that the upregulation of the JA pathway may favour the virus allowing it to establish more easily and systemically infect its host. The JA and other defence pathways are further researched through studying the interactions between a mediator mutant and four different viruses; TuMV, CMV, CaMV and Alternanthera mosaic virus (AltMV). The mediator complex consists of several subunits and is highly conserved among eukaryotes as it regulates transcription. Previous studies have shown that med18 plants are more resistant to Fusarium oxysporum which was also found to upregulate the JA pathway in WT plants. Results show a similar trend with viral infected med18 plants having less viral RNA than WT plants 14 days after infection, though most were not significant due to large variations of viral load between individual plants. However, med18 plants infected with CMV had significantly less viral load than WT plants. 2 Some of phenotypic symptoms caused by viral infection may be a secondary effect of RNA silencing. It is hypothesised that viRNAs can interfere with the plant’s regulations and development causing phenotypic symptoms. Similar to previous studies, small RNA sequencing of virus infected A. thaliana and N. benthamiana suggested that there was a significant increase in the number of small RNAs (sRNAs), specifically those of 21 nucleotides (nt) in length. This length would also suggest that these are produced through a specific biogenesis pathway. Studies have reported that certain areas of a virus genome, called “hotspots”, are more prone to being acted upon by the plant’s sRNAs biogenesis machinery. Chapter 5 results suggest this to be true, with certain regions producing more sRNAs and causing certain viRNAs to be more abundant. When comparing the most abundant viRNAs to host genes we identified possible targets based on complementarity. As a high degree of complementarity is believed to be required for endogenous small interfering RNAs (siRNAs) directed silencing it was hypothesized that highly abundant and complementary viRNAs had the potential to target and inhibit certain genes. The dual-luciferase report system was used to attempt to quickly validate possible viRNA targeting of host transcript sequences. The quantitative nature of this assay allowed us to determine whether viRNAs interacted with the target transcript based on the expression ratio. A mutated target sequence was included as a control to confirm viRNA interaction. Many targets from both A. thaliana and N. benthamiana were tested, though only one target sequence interaction was repeatedly confirmed using this assay system. The N. benthamiana gene 3160g02007 was confirmed to be targeted by TuMV as there was a clear decrease in the dual LUC expression ratio in the presence of the virus. The expression was restored when the target was mutated. Furthermore, no decrease was apparent when plants were not infected. 3 Declaration by Author This thesis is composed of my original work, and contains no material previously published or written by another person except where due reference has been made in the text. I have clearly stated the contribution by others to jointly-authored works that I have included in my thesis. I have clearly stated the contribution of others to my thesis as a whole, including statistical assistance, survey design, data analysis, significant technical procedures, professional editorial advice, financial support and any other original research work used or reported in my thesis. The content of my thesis is the result of work I have carried out since the commencement of my higher degree by research candidature and does not include a substantial part of work that has been submitted to qualify for the award of any other degree or diploma in any university or other tertiary institution. I have clearly stated which parts of my thesis, if any, have been submitted to qualify for another award. I acknowledge that an electronic copy of my thesis must be lodged with the University Library and, subject to the policy and procedures of The University of Queensland, the thesis be made available for research and study in accordance with the Copyright Act 1968 unless a period of embargo has been approved by the Dean of the Graduate School. I acknowledge that copyright of all material contained in my thesis resides with the copyright holder(s) of that material. Where appropriate I have obtained copyright permission from the copyright holder to reproduce material in this thesis and have sought permission from co-authors for any jointly authored works included in the thesis. 4 Publications during Candidature Peer-Reviewed-Papers Pretorius, L., Hussein, N., Al-Amery, A., Moyle, R., Schenk, P. (2017). Natural and Engineered Defences Against Plant Viruses. Current Biotechnology 6, 339-348. Pretorius, L., Moyle, R.L., Dalton-Morgan, J., Schwinghamer, M.W., Crew, K., Schenk, P.M., Geering, A.D.W. (2017). First fully sequenced genome of an Australian isolate of Cauliflower mosaic virus. Australasian Plant Pathology 46, 597-599. Moyle, R.L., Carvalhais, L.C., Pretorius, L.-S., Nowak, E., Subramaniam, G., Dalton-Morgan, J., Schenk, P.M. (2017). An Optimized Transient Dual Luciferase Assay for Quantifying MicroRNA Directed Repression of Targeted Sequences. Frontiers in Plant Science 8. Moyle, R.L., Pretorius, L., Carvalhais, L.C., Schenk, P.M. (2017). Complete Nucleotide Sequence of Australian Tomato spotted wilt virus Isolate TSWV-QLD2. Genome Announcements 5. Moyle, R., Pretorius, L. S., Shuey, L. S., Nowak, E., & Schenk, P. M. (2018). Analysis of the Complete Genome Sequence of Cucumber mosaic virus Strain K. Genome announcements, 6(7), e00053-18. Moyle, R., Pretorius, L. S., Dalton-Morgan, J., Persley, D., & Schenk, P. (2016). Analysis of the first complete genome sequence of an Australian Tomato spotted wilt virus isolate. Australasian Plant Pathology, 45(5), 509-512. Pretorius L, Moyle RL, Dalton-Morgan J, Hussein N, Schenk PM. (2016). Complete Nucleotide Sequence of an Australian Isolate of Turnip mosaic virus before and after Seven Years of Serial Passaging. Genome Announcements, 4(6):e01269-16. Conference Abstracts and Presentations Pretorius, L.S., Kidd, B.N. and Schenk, P.M (2013). Chlorosis causing compounds in the Arabidopsis – Fusarium interaction. 24th International Conference on Arabidopsis Research. Australia. 24-28 June. (Poster). Pretorius, L.S., Geering, A. and Schenk, P.M (2014). Turnip mosaic virus targets host gene HVA22D: a new opportunity to develop resistant crops. 11th Australasian Plant Virology Workshop. Australia. 13-15 August. (Oral). 5 Pretorius, L.S., Moyle, R.L., Geering, A. and Schenk, P.M (2015). MicroRNA-like fragments from Turnip mosaic virus targets host gene HVA22D – a new opportunity to develop resistant crops. XVIII International Plant Protection Congress. Germany. 24-27 August. (Oral). Pretorius L.S, Moyle R.L., Nowak K, Carvalhais L, Dalton-Morgan J, Geering A and Schenk PM (2017) Viral small RNAs that target plant genes and artificial miRNA that target plant viruses. Science Protecting Plant Health. Brisbane. 26-28 September. (Oral). Publications Included in this Thesis Pretorius, L.,
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