1. Functionality of potato virus Y coat protein in cell-to-cell movement dynamics is defined by its N-terminal regionAnže Vozelj, Tjaša Mahkovec Povalej, Katja Stare, Magda Tušek-Žnidarič, Katarina Bačnik, Valentina Levak, Ion Gutiérrez-Aguirre, Marjetka Podobnik, Kristina Gruden, Anna Coll Rius, Tjaša Lukan, 2025, izvirni znanstveni članek Povzetek: Potato virus Y (PVY) is one of the top 10 economically most important plant viruses and responsible for major yield losses. We previously suggested the involvement of the N-terminal region of PVY coat protein (CP) in PVY spread. By constructing different N-terminal deletion mutants of the PVY N605 strain, we here show that deletions of 40 or more amino acid residues from the N-terminal region of the CP resulted in the PVY multiplication limited to primary infected cells in Nicotiana clevelandii plants. Deletion of 26 residues profoundly impaired PVY cell-to-cell movement and prevented systemic PVY spread, while deletions of 19-23 residues allowed delayed systemic PVY spread. Introduced point mutations in the identified region prevent (S21G) or delay (G20P) PVY movement. In summary, this work shows the significance of the CP N-terminus for movement of the PVY.
Ključne besede: potato virus Y, potato, coat proteins, viral movement, point mutations
Objavljeno v DiRROS: 18.12.2025; Ogledov: 76; Prenosov: 72
 Celotno besedilo (1,50 MB)
Gradivo ima več datotek! Več... |
2. Signalling network construction for modelling plant defence responseDragana Miljković, Tjaša Stare, Igor Mozetič, Vid Podpečan, Marko Petek, Kamil Witek, Marina Dermastia, Nada Lavrač, Kristina Gruden, 2012, izvirni znanstveni članek Objavljeno v DiRROS: 26.11.2025; Ogledov: 191; Prenosov: 109
Celotno besedilo (2,51 MB)
Gradivo ima več datotek! Več... |
3. Chloroplast redox state changes indicate cell-to-cell signalling during the hypersensitive response : version v3Tjaša Lukan, Kristina Gruden, Anže Županič, Tjaša Mahkovec Povalej, 2021, zaključena znanstvena zbirka raziskovalnih podatkov Povzetek: We performed detailed spatiotemporal analysis of chloroplast redox response to potato virus Y (PVY) infection in resistant Ny‐1-gene-bearing potato and its transgenic counterpart with impaired SA accumulation and compromised resistance. We found that the chloroplasts are highly oxidized in the cells adjacent to the cell death zone at different stages after virus inoculation in both genotypes. This hypothesis is further supported by highly induced formation of stroma filled tubules that extend from chloroplasts (stromules) in the cells adjacent to signalling cells. This dataset s a deposit of all the raw microscopy images of the study, plus the relevant metadata in ISA-tab compliant folder structure. After receiving reviews, we have made an additional experiment using a ROS inhibitor. The raw and processed data for this is in a separate file: _S_chlROS_inhibitor.zip
Ključne besede: cell signalling, chloroplasts, microscopy, ISA-tab, potato virus Y, redox responses, cell death, spatiotemporal analysis
Objavljeno v DiRROS: 24.10.2025; Ogledov: 276; Prenosov: 97
 Povezava na datoteko
Gradivo ima več datotek! Več... |
4. Evaluating plant growth–defense trade-offs by modelingthe interaction between primary and secondary metabolismJan Zrimec, Sandra Correo, Maja Zagorščak, Marko Petek, Carissa Bleker, Katja Stare, Christian Schuy, Sophia Sonnewald, Kristina Gruden, Zoran Nikoloski, 2025, izvirni znanstveni članek Povzetek: Understanding the molecular mechanisms behind plant response to stress can enhancebreeding strategies and help us design crop varieties with improved stress tolerance,yield, and quality. To investigate resource redistribution from growth- to defense-relatedprocesses in an essential tuber crop, potato, here we generate a large-scale compartmen-talized genome-scale metabolic model (GEM), potato-GEM. Apart from a large-scalereconstruction of primary metabolism, the model includes the full known potato sec-ondary metabolism, spanning over 566 reactions that facilitate the biosynthesis of 182distinct potato secondary metabolites. Constraint-based modeling identifies that theactivation of the largest amount of secondary (defense) pathways occurs at a decreaseof the relative growth rate of potato leaf, due to the costs incurred by defense. We thenobtain transcriptomics data from experiments exposing potato leaves to two bioticstress scenarios, a herbivore and a viral pathogen, and apply them as constraints toproduce condition-specific models. We show that these models recapitulate experimen-tally observed decreases in relative growth rates under treatment as well as changes inmetabolite levels between treatments, enabling us to pinpoint the metabolic rewiringunderlying growth–defense trade-offs. Potato- GEM thus presents a useful resource tostudy and broaden our understanding of potato and general plant defense responsesunder stress conditions.
Ključne besede: systems biology, constraint-based metabolic modeling, growth-defence trade-offs, secondary metabolism
Objavljeno v DiRROS: 24.09.2025; Ogledov: 363; Prenosov: 144
Celotno besedilo (1,82 MB)
Gradivo ima več datotek! Več... |
5. |
6. Methodologies for discovery and quantitative profiling of sRNAs in potatoMaja Križnik, Maja Zagorščak, Kristina Gruden, 2021, samostojni znanstveni sestavek ali poglavje v monografski publikaciji Povzetek: Small RNAs (sRNAs) are short noncoding RNAs involved in the regulation of a wide range of biological processes in plants. Advances in high-throughput sequencing and development of new computational tools had facilitated the discovery of different classes of sRNAs, their quantification, and elucidation of their functional role in gene expression regulation by target transcript predictions. The workflow presented here allows identification of different sRNA species: known and novel potato miRNAs, and their sequence variants (isomiRs), as well as identification of phased small interfering RNAs (phasiRNAs). Moreover, it includes steps for differential expression analysis to search for regulated sRNAs across different tested biological conditions. In addition, it describes two different methods for predicting sRNA targets, in silico prediction, and degradome sequencing data analysis. All steps of the workflow are written in a clear and user-friendly way; thus they can be followed also by the users with minimal bioinformatics knowledge. We also included several in-house scripts together with valuable notes to facilitate data (pre)processing steps and to reduce the analysis time.
Objavljeno v DiRROS: 06.08.2025; Ogledov: 425; Prenosov: 207
Celotno besedilo (1,17 MB)
Gradivo ima več datotek! Več... |
7. |
8. Protein complexes from edible mushrooms as a sustainable potato protection against coleopteran pestsKarmen Pogačar, Maja Grundner, Primož Žigon, Anna Coll Rius, Anastasija Panevska, Tjaša Lukan, Marko Petek, Jaka Razinger, Kristina Gruden, Kristina Sepčić, 2024, izvirni znanstveni članek Ključne besede: biopesticides, Leptinotarsa decemlineata, Solanum tuberosum, insect stress response, larval toxicity, transgenic crop
Objavljeno v DiRROS: 14.05.2025; Ogledov: 544; Prenosov: 316
Celotno besedilo (5,63 MB)
Gradivo ima več datotek! Več... |
9. Integration of multi-omics data and deep phenotyping provides insights into responses to single and combined abiotic stress in potatoMaja Zagorščak, Lamis Abdelhakim, Natalia Yaneth Rodriguez-Granados, Carissa Bleker, Andrej Blejec, Jan Zrimec, Špela Baebler, Anže Županič, Maruša Pompe Novak, Kristina Gruden, 2025, izvirni znanstveni članek Povzetek: Potato (Solanum tuberosum) is highly water and space efficient but susceptible to abiotic stresses such as heat, drought, and flooding, which are severely exacerbated by climate change. Our understanding of crop acclimation to abiotic stress, however, remains limited. Here, we present a comprehensive molecular and physiological high-throughput profiling of potato (Solanum tuberosum, cv. Désirée) under heat, drought, and waterlogging applied as single stresses or in combinations designed to mimic realistic future scenarios. Stress responses were monitored via daily phenotyping and multi-omics analyses of leaf samples comprising proteomics, targeted transcriptomics, metabolomics, and hormonomics at several timepoints during and after stress treatments. Additionally, critical metabolites of tuber samples were analyzed at the end of the stress period. We performed integrative multi-omics data analysis using a bioinformatic pipeline that we established based on machine learning and knowledge networks. Waterlogging produced the most immediate and dramatic effects on potato plants, interestingly activating ABA responses similar to drought stress. In addition, we observed distinct stress signatures at multiple molecular levels in response to heat or drought and to a combination of both. In response to all treatments, we found a downregulation of photosynthesis at different molecular levels, an accumulation of minor amino acids, and diverse stress-induced hormones. Our integrative multi-omics analysis provides global insights into plant stress responses, facilitating improved breeding strategies toward climate-adapted potato varieties.
Ključne besede: potato, Solanum tuberosum, abiotic stress responses, heat, drought, waterlogging, multi-omics, integrative omics, adaptomics, panomics
Objavljeno v DiRROS: 14.04.2025; Ogledov: 747; Prenosov: 594
Celotno besedilo (2,89 MB)
Gradivo ima več datotek! Več... |
10. Ethylene signaling is essential for mycorrhiza-induced resistance against chewing herbivores in tomatoJavier Lidoy, Javier Rivero, Živa Ramšak, Marko Petek, Maja Križnik, Victor Flors, Juan A Lopez-Raez, Ainhoa Martinez-Medina, Kristina Gruden, Maria J Pozo, 2025, izvirni znanstveni članek Povzetek: Arbuscular mycorrhizal (AM) symbiosis can prime plant defenses, leading to mycorrhiza-induced resistance (MIR) against different attackers, including insect herbivores. Still, our knowledge of the complex molecular regulation leading to MIR is very limited. Here, we showed that the AM fungus Funneliformis mosseae protects tomato plants against two different chewing herbivores, Spodoptera exigua and Manduca sexta. We explored the underlying molecular mechanism through genome-wide transcriptional profiling, bioinformatics network analyses, and functional bioassays. Herbivore-triggered jasmonate (JA)-regulated defenses were primed in leaves of mycorrhizal plants. Likewise, ethylene (ET) biosynthesis and signaling were also higher in leaves of mycorrhizal plants both before and after herbivory. We hypothesized that fine-tuned ET signaling is required for the primed defense response leading to MIR. ET is a complex regulator of plant responses to stress and is generally considered a negative regulator of plant defenses against herbivory. However, ET-deficient or insensitive lines did not show AM-primed JA biosynthesis or defense response, and were unable to develop MIR against any of the herbivores. Thus, we demonstrate that hormone crosstalk is central to the priming of plant immunity by beneficial microbes, with ET fine-tuning being essential for the primed JA biosynthesis and boosted defenses leading to MIR in tomato.
Ključne besede: chewing herbivores, defense priming, ethylene, hormonal crosstalk, jasmonate, mycorrhiza-induced resistance (MIR)
Objavljeno v DiRROS: 10.04.2025; Ogledov: 743; Prenosov: 674
Celotno besedilo (5,28 MB)
Gradivo ima več datotek! Več... |
