Published paper presents the set-up of virus-induced gene silencing (VIGS), based on Tobacco rattle virus (TRV) in wild potato relatives for functional studies in potato–virus interactions. Screening of a large set of wild potato relatives (different Solanum species and their clones) for their susceptibility to VIGS was performed by silencing PDS gene. We identified several responsive species and further tested susceptibility of these genotypes to potato virus Y (PVY) strain NTN and N. In some species we observed that the presence of empty TRV vector restricted the movement of PVY. Fluorescently tagged PVYN-GFP spread systemically in only five of tested wild potato relatives. Based on the results, Solanum venturii (VNT366-2) was selected as the most suitable system for functional analysis of genes involved in potato–PVY interaction. The system was tested by silencing two different plant immune signalling-related kinases, StWIPK and StMKK6. Silencing of StMKK6 enabled faster spreading of the virus throughout the plant, while silencing of WIPK had no effect on spreading of the virus. The system employing S. venturii (VNT366-2) and PVYN-GFP was shown to be a suitable method for fast and simple functional analysis of genes involved in potato–PVY interactions.
COBISS.SI-ID: 3877967
We studied the involvement of cell death in hypersensitive response (HR)-conferred resistance to viral infection. We showed that potato virus Y can be detected outside the cell death zone in Ny-1-mediated HR in potato plants (cv. Rywal), observed as individual infected cells or clusters of infected cells outside the cell death zone. We confirmed that the cells at the border of the cell death zone harbour a viable virus that is able to reinitiate the infection. We further studied the dynamics of cell death zone expansion and occurrence of infected cells outside it. We compared the response of Rywal plants to their transgenic counterparts, impaired in salicylic acid accumulation, where the lesions develop but the spread of the virus is not restricted. We showed that the virus is detected outside the cell death zone in all developmental stages of HR lesions. We observed rapid lesion expansion and even faster virus spread in salicylic acid-depleted plants. On the other hand, the majority of analysed lesions slowly expand also in HR-conferred resistance opening the possibility that the infected cells are eventually engulfed by cell death zone. Thus we suggest that the HR-associated cell death is separated from the resistance mechanisms which lead to potato virus Y restriction in Ny-1 genetic background and propose that HR should be regarded as a process where the dynamics of events is crucial for the effectiveness of viral arrest.
COBISS.SI-ID: 4609615
We have shown the power of network modelling for the task of unraveling properties of complex biological systems. First, we built a highly reliable manual model of signalling in Arabidopsis, which we then extended into an Arabidopsis comprehensive knowledge network, presenting a most complete compendium of known knowledge at the time. Knowledge within the network was translated to crop species, potato. By application of graph theory approaches on the networks (shortest paths; modules) we identified a novel connection between two important pathways immune signaling pathways (ethylene and salicylic acid). Functional confirmation of the connection affirmed our belief in the strength of network modelling for analyses of complex systems. The findings were published in one of the most renowned journals in the field, Plant Physiology. In addition, the comprehensive knowledge network on both species served as prior network examples for the DINAR tool, enabling temporal visualisations of experimental data [COBISS.SI-ID 4791631; Zagorščak et al., 2018, Plant Methods; IF 4.3].
COBISS.SI-ID: 4778575
Genome sequences from over 200 plant species have already been published, with this number expected to increase rapidly due to advances in sequencing technologies. Once a new genome has been assembled and the genes identified, the functional annotation of their proteins using ontologies is of key importance as it places the sequencing data in a biological context. In this achievement, we present a redesigned and significantly enhanced MapMan4 framework. This ontology has been incorporated into Mercator4, which has been upgraded to reflect current knowledge across the land plant group. The annotation process has been optimized to allow a plant genome to be annotated in a matter of minutes. The output results continue to be compatible with the established MapMan desktop application.
COBISS.SI-ID: 4958799
We showcase the transfer of knowledge between genes of the better annotated and manually curated species (Arabidopsis) towards crop species (cacao). We depict that even computationally derived ontological descriptions represent a very important tool in systems analysis and understanding of complex consecutive coordination events between primary and secondary metabolism pathways of cacao seed development.
COBISS.SI-ID: 3869775