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22 results on '"Križnik, Maja"'

6. Stress Knowledge Map: A knowledge graph resource for systems biology analysis of plant stress responses

Author

Bleker, Carissa, primary, Ramšak, Živa, additional, Bittner, Andras, additional, Podpečan, Vid, additional, Zagorščak, Maja, additional, Wurzinger, Bernhard, additional, Baebler, Špela, additional, Petek, Marko, additional, Križnik, Maja, additional, van Dieren, Annelotte, additional, Gruber, Juliane, additional, Afjehi-Sadat, Leila, additional, Županič, Anže, additional, Teige, Markus, additional, Vothknecht, Ute C., additional, and Gruden, Kristina, additional

Published
2023
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11. Differential response of grapevine to infection with 'Candidatus Phytoplasma solani' in early and late growing season through complex regulation of mRNA and small RNA transcriptomes

Author

Dermastia, Marina, Škrlj, Blaž, Strah, Rebeka, Anžič, Barbara, Tomaž, Špela, Križnik, Maja, Schönhuber, Christina, Riedle-bauer, Monika, Ramšak, Živa, Petek, Marko, Kladnik, Aleš, Lavrač, Nada, Gruden, Kristina, Roitsch, Thomas, Brader, Günter, Pompe-novak, Maruša, Dermastia, Marina, Škrlj, Blaž, Strah, Rebeka, Anžič, Barbara, Tomaž, Špela, Križnik, Maja, Schönhuber, Christina, Riedle-bauer, Monika, Ramšak, Živa, Petek, Marko, Kladnik, Aleš, Lavrač, Nada, Gruden, Kristina, Roitsch, Thomas, Brader, Günter, and Pompe-novak, Maruša

Abstract

Bois noir is the most widespread phytoplasma grapevine disease in Europe. It is associated with ‘Candidatus Phytoplasma solani’, but molecular interactions between the causal pathogen and its host plant are not well understood. In this work, we combined the analysis of high-throughput RNA- Seq and sRNA-Seq data with interaction network analysis for finding new cross-talks among pathways involved in infection of grapevine cv. Zweigelt with ‘Ca. P. solani’ in early and late growing seasons. While the early growing season was very dynamic at the transcriptional level in asymptomatic grape-vines, the regulation at the level of small RNAs was more pronounced later in the season when symptoms developed in infected grapevines. Most differentially expressed small RNAs were associated with biotic stress. Our study also exposes the less-studied role of hormones in disease development and shows that hormonal balance was already perturbed before symptoms development in infected grapevines. Analysis at the level of communities of genes and mRNA-microRNA interaction networks revealed sev-eral new genes (e.g., expansins and cryptdin) that have not been associated with phytoplasma patho-genicity previously. These novel actors may present a new reference framework for research and diag-nostics of phytoplasma diseases of grapevine.

Published
2021

14. Spatial accumulation of salicylic acid is in effector-triggered immunity of potato against viruses regulated by RBOHD

Author

Lukan, Tjaša, Pompe-Novak, Maruša, Baebler, Špela, Tušek-Žnidarič, Magda, Kladnik, Aleš, Križnik, Maja, Blejec, Andrej, Zagorščak, Maja, Stare, Katja, Dušak, Barbara, Coll, Anna, Pollmann, Stephan, Morgiewicz, Karolina, Hennig, Jacek, and Gruden, Kristina

Abstract

While activation of resistance (R) proteins has been intensively studied, the mechanisms acting downstream of R protein activation remain elusive. We studied effector-triggered immunity (ETI) conditioned by the potato Ny-1 gene against potato virus Y. Transcriptomic, ultrastructural and biochemical analyses of four consecutive tissue sections in and surrounding the foci of viral infection at three different lesion developmental stages revealed processes that are spatiotemporally regulated. The transcriptional response in the cell death zone and surrounding tissue is dependent on SA. For some of the genes, spatiotemporal regulation is completely lost while for others, the regulation is different in SA-deficient line indicating multiple connections between hormonal signaling modules. The induction of RBOHD NADPH oxidase expression, together with expression of Thioredoxin H gene, occurs specifically in the border region of the lesion during ETI. In plants with silenced RBOHD, ETI is perturbed and virus spread is not arrested at the site of infection. Expression of RBOHD is under the control of SA. On the other hand, RBOHD activity is required for spatial regulation of SA accumulation. We identified an UDP-glucosyltransferase, encoding an enzyme involved in feedback activation of SA biosynthesis, that is derepressed at the border of the lesion in RBOHD silenced plants. Altogether, we revealed a novel aspect of viral ETI, the RBOHD-SA feedback loop required for its spatial regulation. SIGNIFICANCE To get towards sustainable resistance in the field, it is important to understand mechanisms of immune signaling. We here show novel aspects of spatial regulation in effector-triggered immunity (ETI) against potato virus Y. A detailed spatiotemporal analysis in and surrounding the foci of viral infection, on ultrastructural, biochemical and gene expression levels revealed that redox state maintenance is tightly spatiotemporally regulated. We also show the interconnection of salicylic acid and RBOHD through a feedback loop, regulated through UDP-glucosyltransferase, revealing the mechanism of this spatial regulation. The proper function of this loop is essential for successful ETI leading to viral arrest.

Published
2020
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15. Differential Response of Grapevine to Infection with ‘Candidatus Phytoplasma solani’ in Early and Late Growing Season through Complex Regulation of mRNA and Small RNA Transcriptomes

Author

Dermastia, Marina, primary, Škrlj, Blaž, additional, Strah, Rebeka, additional, Anžič, Barbara, additional, Tomaž, Špela, additional, Križnik, Maja, additional, Schönhuber, Christina, additional, Riedle-Bauer, Monika, additional, Ramšak, Živa, additional, Petek, Marko, additional, Kladnik, Aleš, additional, Lavrač, Nada, additional, Gruden, Kristina, additional, Roitsch, Thomas, additional, Brader, Günter, additional, and Pompe-Novak, Maruša, additional

Published
2021
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16. Precision transcriptomics of viral foci reveals the spatial regulation of immune‐signaling genes and identifies RBOHD as an important player in the incompatible interaction between potato virus Y and potato

Author

Lukan, Tjaša, primary, Pompe‐Novak, Maruša, additional, Baebler, Špela, additional, Tušek‐Žnidarič, Magda, additional, Kladnik, Aleš, additional, Križnik, Maja, additional, Blejec, Andrej, additional, Zagorščak, Maja, additional, Stare, Katja, additional, Dušak, Barbara, additional, Coll, Anna, additional, Pollmann, Stephan, additional, Morgiewicz, Karolina, additional, Hennig, Jacek, additional, and Gruden, Kristina, additional

Published
2020
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17. Spatial accumulation of salicylic acid is regulated by RBOHD in potato immunity against viruses

Author

Lukan, Tjaša, primary, Pompe-Novak, Maruša, additional, Baebler, Špela, additional, Tušek-Žnidarič, Magda, additional, Kladnik, Aleš, additional, Križnik, Maja, additional, Blejec, Andrej, additional, Zagorščak, Maja, additional, Stare, Katja, additional, Dušak, Barbara, additional, Coll, Anna, additional, Pollmann, Stephan, additional, Morgiewicz, Karolina, additional, Hennig, Jacek, additional, and Gruden, Kristina, additional

Published
2020
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20. List of Contributors

Author

Ali, Akhtar, Al-Tawaha, Abdelrazzaq, Aslam, Mariyah, Aslam, Roohi, Awasthi, L.P., Ayyaz, Mahmood, Badillo-Vargas, Ismael E., Baebler, Špela, Bagewadi, Basavaraj, Balaji, S., Baranwal, Virendra Kumar, Barba, Marina, Batool, Riffat, Bernards, Mark, Bhardwaj, Abhishek, Bhat, Goureesh, Boubourakas, Iraklis I., Briard, Pascal, Bukhari, Sayyad Ali Raza, Celia Chalam, V., Chandra, Prem, Chattopadhyay, Anirudha, Chen, Jianping, Choudhary, Nandlal, Creamer, Rebecca, Enespa, Ertunç, Filiz, Gaur, R.K., Giolitti, Fabián, Gruden, Kristina, Gupta, Taruna, Hadidi, Ahmed, Hameed, Amir, Haq, Quazi Mohd. Imranul, Hussain, Mujahid, Iftikhar, Romana, Jahan, Nusrat, Jangre, Anjeet, Jayasudha, S.M., Ji, Mengfei, Jones, Tara-Kay L., Kaponi, Maria S., Kapoor, Reetika, Kirankumar, K.C., Koch, Kyle G., Križnik, Maja, Kulshrestha, Saurabh, Kumar, Shailender, Kumar, Susheel, Kumari, Aarti, Kumari, Pooja, Kyriakopoulou, Panayota E., Lee, Richard F., Mandal, Bikash, Manjunath, N., Marwal, Avinash, Maurya, A.K., Mederos, Dariel Cabrera, Mora, Michel Leiva, Mushtaq, Sehrish, Nirmalkar, Vinod Kumar, Nusayr, Tesneem, Palaniswami, M.S., Panda, Soumya, Pant, R.P., Portal, Orelvis, Prasad, Vivek, Priya, N., Qaisi, Ali M., Qurashi, Fasiha, Raj, Rashmi, Raj, Shri Krishna, Rao, G.P., Rashmi, E.R., Ravelonandro, Michel, Raza, Amir, Reddy, Madem Gurivi, Rishi, Narayan, Roy, Reshma, Sai Gopal, D.V.R., Saleem Haider, Muhammad, Sanmukh, Swapnil Ganesh, Sarwar, Muhammad, Sarwar, Sidra, Serra, Eduard Torrents, Shad, Naveed Akhter, Shafiq, Muhammad, Shahid, Muhammad Shafiq, Sharma, Ruchi, Sharma, Vaishali Dutt, Singh, Manoj Kumar, Singh, Rachana, Singh, Shyam, Sohrab, Sayed Sartaj, Song, Junqi, Srivastava, Amrisha, Srivastava, Ashish, Srivastava, Nishant, Srivastava, Shalini, Sumida, Ciro H., Suresh, Shobith, Syller, Jerzy, Tang, Ziwei, Tawaha, Abdel Rahman, Ulubaş Serçe, Çiğdem, Varma, Anupam, Verma, H.N., Vrient, Albert, Wang, Aiming, Wedyan, Moh'd Ali, Yan, Fei, Zhang, Shulu, and Zhao, Jinping

Published
2020
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22. Methodologies for Discovery and Quantitative Profiling of sRNAs in Potato.

Author

Križnik M, Zagorščak M, and Gruden K

Subjects
Computational Biology, Gene Expression Profiling, High-Throughput Nucleotide Sequencing, MicroRNAs, RNA, Plant genetics, RNA, Small Untranslated genetics, Solanum tuberosum genetics
Abstract

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., (© 2021. Springer Science+Business Media, LLC, part of Springer Nature.)

Published
2021
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