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2. Viroids and protein translation

Author

Lisón, Purificación, primary, Vázquez-Prol, Francisco, additional, Bardani, Irene, additional, Rodrigo, Ismael, additional, Kryovrysanaki, Nikoleta, additional, and Kalantidis, Kriton, additional

Published
2024
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3. Contributors

Author

Adkar-Purushothama, Charith Raj, primary, Bardani, Irene, additional, Beltrán, M. Francisca, additional, Bolduc, François, additional, Chiumenti, Michela, additional, Cueto, C.A., additional, Daròs, José-Antonio, additional, de la Peña, Marcos, additional, Di Serio, Francesco, additional, Elleuch, Amine, additional, Fiore, Nicola, additional, Gómez, Gustavo, additional, Hamdi, Imen, additional, Hammond, Rosemarie W., additional, Hanold, D., additional, Harper, Scott, additional, Iftikhar, Y., additional, Jakše, Jernej, additional, Kalantidis, Kriton, additional, Krueger, Robert, additional, Kryovrysanaki, Nikoleta, additional, Lavagi-Craddock, Irene, additional, Li, Shifang, additional, Lisón, Purificación, additional, López-Galiano, Maria José, additional, Marquez-Molins, Joan, additional, Martinez, German, additional, Matoušek, Jaroslav, additional, Navarro, Beatriz, additional, Nie, Xianzhou, additional, Owens, Robert A., additional, Pallás, Vicente, additional, Perreault, Jean-Pierre, additional, Quijia-Lamiña, Paulina, additional, Randles, J.W., additional, Riesner, Detlev, additional, Rodrigo, Ismael, additional, Sano, Teruo, additional, Shruthi, B., additional, Škorić, Dijana, additional, Steger, Gerhard, additional, Thanarajoo, S.S., additional, Vadamalai, G., additional, Vázquez-Prol, Francisco, additional, Vidalakis, Georgios, additional, Wang, Ying, additional, Yanjarappa, Sreenivasa Marikunte, additional, and Zhang, Zhixiang, additional

Published
2024
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7. Viroids and Satellites and Their Vector Interactions.

Author

Hadidi, Ahmed, Czosnek, Henryk H., Kalantidis, Kriton, and Palukaitis, Peter

Subjects
LIFE sciences, HOPS, MOLECULAR biology, BOVINE spongiform encephalopathy, GLOBAL warming, NICOTIANA benthamiana, EGGPLANT, MOSAIC viruses
Abstract

The document discusses the discovery and characteristics of viroids, satellites, and prions, focusing on their interactions with vectors and host plants. Viroids, small RNA molecules, replicate autonomously and do not encode proteins, impacting various fields of science. Satellites, like betasatellites, enhance the virulence of begomoviruses, affecting plant health and crop yields. Prions, proteinaceous particles, cause diseases like scrapie and Creutzfeldt–Jakob disease. The text also explores the potential use of CRISPR technology for viroid detection and the role of host factors in viroid replication. [Extracted from the article]

Published
2024
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9. Isoprenoid biosynthesis in the diatom Haslea ostrearia

Author

Athanasakoglou, Anastasia, Grypioti, Emilia, Michailidou, Sofia, Ignea, Codruta, Makris, Antonios M., Kalantidis, Kriton, Massé, Guillaume, Argiriou, Anagnostis, Verret, Frederic, and Kampranis, Sotirios C.

Published
2019

12. A Bromodomain-Containing Host Protein Mediates the Nuclear Importation of a Satellite RNA of Cucumber Mosaic Virus

Author

Chaturvedi, Sonali, Kalantidis, Kriton, and Rao, ALN

Subjects
Agricultural, Veterinary and Food Sciences, Plant Biology, Biological Sciences, Horticultural Production, Infection, Active Transport, Cell Nucleus, Cell Nucleus, Cucumovirus, DNA Primers, Electrophoretic Mobility Shift Assay, Immunoblotting, Immunoprecipitation, Microscopy, Confocal, Nuclear Proteins, RNA, Satellite, Subcellular Fractions, Tobacco, Agricultural and Veterinary Sciences, Medical and Health Sciences, Virology, Agricultural, veterinary and food sciences, Biological sciences, Biomedical and clinical sciences
Abstract

Replication of the satellite RNA (satRNA) of Cucumber Mosaic Virus is dependent on replicase proteins of helper virus (HV). However, we recently demonstrated that like with Potato spindle tuber viroid (PSTVd), a satRNA associated with Cucumber Mosaic Virus strain Q (Q-satRNA) has the propensity to localize in the nucleus and generate multimers that subsequently serve as templates for HV-dependent replication. But the mechanism regulating the nuclear importation of Q-satRNA is unknown. Here we show that the nuclear importation of Q-satRNA is mediated by a bromodomain-containing host protein (BRP1), which is also apparently involved in the nuclear localization of PSTVd. A comparative analysis of nuclear and cytoplasmic fractions from Nicotiana benthamiana plants coinfected with Q-satRNA and its HV confirmed the association of Q-satRNA but not HV with the nuclear compartment. A combination of the MS2-capsid protein-based RNA tagging assay and confocal microscopy demonstrated that the nuclear localization of Q-satRNA was completely blocked in transgenic lines of Nicotiana benthamiana (ph5.2nb) that are defective in BRP1 expression. This defect, however, was restored when the ph5.2nb lines of N. benthamiana were trans-complemented by ectopically expressed BRP1. The binding specificity of BRP1 with Q-satRNA was confirmed in vivo and in vitro by coimmunoprecipitation and electrophoretic mobility shift assays, respectively. Finally, infectivity assays involving coexpression of Q-satRNA and its HV in wild-type and ph5.2nb lines of N. benthamiana accentuated a biological role for BRP1 in the Q-satRNA infection cycle. The significance of these results in relation to a possible evolutionary relationship to viroids is discussed.

Published
2014

18. Dicer‐dependent heterochromatic small RNAs in the model diatom species Phaeodactylum tricornutum.

Author

Grypioti, Emilia, Richard, Hugues, Kryovrysanaki, Nikoleta, Jaubert, Marianne, Falciatore, Angela, Verret, Frédéric, and Kalantidis, Kriton

Subjects
PHAEODACTYLUM tricornutum, NON-coding RNA, SMALL interfering RNA, RNA interference, DIATOMS
Abstract

Summary: Diatoms are eukaryotic microalgae responsible for nearly half of the marine productivity. RNA interference (RNAi) is a mechanism of regulation of gene expression mediated by small RNAs (sRNAs) processed by the endoribonuclease Dicer (DCR). To date, the mechanism and physiological role of RNAi in diatoms are unknown.We mined diatom genomes and transcriptomes for key RNAi effectors and retraced their phylogenetic history. We generated DCR knockout lines in the model diatom species Phaeodactylum tricornutum and analyzed their mRNA and sRNA populations, repression‐associated histone marks, and acclimatory response to nitrogen starvation.Diatoms presented a diversification of key RNAi effectors whose distribution across species suggests the presence of distinct RNAi pathways. P. tricornutum DCR was found to process 26–31‐nt‐long double‐stranded sRNAs originating mostly from transposons covered by repression‐associated epigenetic marks. In parallel, P. tricornutum DCR was necessary for the maintenance of the repression‐associated histone marks H3K9me2/3 and H3K27me3. Finally, PtDCR‐KO lines presented a compromised recovery post nitrogen starvation suggesting a role for P. tricornutum DCR in the acclimation to nutrient stress.Our study characterized the molecular function of the single DCR homolog of P. tricornutum suggesting an association between RNAi and heterochromatin maintenance in this model diatom species. [ABSTRACT FROM AUTHOR]

Published
2024
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25. Viroid Replication

Author

Flores, Ricardo, primary, Minoia, Sofia, additional, López-Carrasco, Amparo, additional, Delgado, Sonia, additional, Martínez de Alba, Ángel-Emilio, additional, and Kalantidis, Kriton, additional

Published
2017
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26. List of Contributors

Author

Alazem, Mazen, primary, Al-Tuwariqi, Hani Z., additional, Barba, Marina, additional, Boubourakas, Iraklis N., additional, Çağlayan, Kadriye, additional, Candresse, Thierry, additional, Conejero, Vicente, additional, Dadami, Elena, additional, Dalakouras, Athanasios, additional, Daròs, José-Antonio, additional, De la Peña, Marcos, additional, Delgado, Sonia, additional, Di Serio, Francesco, additional, Dixon, Jonathan, additional, Duran-Vila, Nuria, additional, El-Dougdoug, Khaled A., additional, Elleuch, Amine, additional, Faggioli, Francesco, additional, Flores, Ricardo, additional, Fraile, Aurora, additional, Gago-Zachert, Selma, additional, Gallitelli, Donato, additional, García-Arenal, Fernando, additional, Geering, Andrew D.W., additional, Giunchedi, Luciano, additional, Gómez, Gustavo, additional, Gyamera, Ebenezer A., additional, Habili, Nuredin, additional, Hadidi, Ahmed, additional, Hallan, Vipin, additional, Hammond, Rosemarie W., additional, Hanold, Dagmar, additional, Hataya, Tatsuji, additional, Hernández, Carmen, additional, Hong, Ni, additional, Hosakawa, Munetaka, additional, Hsu, Yau-Heiu, additional, Hu, Chung-Chi, additional, Huang, Ying-Wen, additional, James, Delano, additional, Joseph, Hendry, additional, Kalantidis, Kriton, additional, Kaponi, Maria S., additional, Kim, Mikyeong, additional, Kinard, Gary R., additional, Kong, Lih L., additional, Kovalskaya, Natalia, additional, Kuhn, David N., additional, Kyriakopoulou, Panayota E., additional, Lavagi, Irene, additional, Li, Shi-Fang, additional, Lin, Na-Sheng, additional, Ling, Kai-Shu, additional, Liou, Ming-Ru, additional, Lisón, Purificación, additional, López-Carrasco, Amparo, additional, Luigi, Marta, additional, Martínez de Alba, Ángel-Emilio, additional, Mascia, Tiziana, additional, Masuta, Chikara, additional, Matoušek, Jaroslav, additional, Maurel, Marie-Christine, additional, Meekes, Ellis T.M., additional, Minoia, Sofia, additional, Navarro, Beatriz, additional, Nie, Xianzhou, additional, Owens, Robert A., additional, Pallás, Vicente, additional, Palukaitis, Peter, additional, Parakh, Dattaraj B., additional, Perreault, Jean-Pierre, additional, Podleckis, Edward V., additional, Pyle, Jesse D., additional, Randles, John W., additional, Riesner, Detlev, additional, Rodriguez, M. Judith B., additional, Roenhorst, Johanna W., additional, Roossinck, Marilyn J., additional, Rubino, Luisa, additional, Sánchez-Navarro, Jesus A., additional, Sano, Teruo, additional, Scholthof, Karen-Beth G., additional, Serra, Pedro, additional, Shimura, Hanako, additional, Singh, Rudra P., additional, Škorić, Dijana, additional, Stancanelli, Giuseppe, additional, Steger, Gerhard, additional, Taglienti, Anna, additional, Tessitori, Matilde, additional, Thanarajoo, Sathis S., additional, Tiberini, Antonio, additional, Torchetti, Enza M., additional, Tsagris, Mina, additional, Tsushima, Taro, additional, Vadamalai, Ganesan, additional, Verhoeven, Jacobus Th.J., additional, Vidalakis, Georgios, additional, Wang, Qiao-Chun, additional, Wassenegger, Michael, additional, Winter, Stephan, additional, Xu, Wen-Xing, additional, Yang, Xiuling, additional, Zhang, Yongjiang, additional, Zhang, Zhibo, additional, Zhou, Xueping, additional, and Zhu, Shuifang, additional

Published
2017
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28. Revisiting the Non-Coding Nature of Pospiviroids

Author

Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia, European Regional Development Fund, General Secretariat for Research and Technology, Grecia, Natural Sciences and Engineering Research Council of Canada, Katsarou, Konstantina, Adkar-Purushothama, Charith Raj, Tassios, Emilios, Samiotaki, Martina, Andronis, Christos, Lisón, Purificación, Nikolaou, Christoforos, Perreault, Jean-Pierre, Kalantidis, Kriton, Universitat Politècnica de València. Departamento de Biotecnología - Departament de Biotecnologia, European Regional Development Fund, General Secretariat for Research and Technology, Grecia, Natural Sciences and Engineering Research Council of Canada, Katsarou, Konstantina, Adkar-Purushothama, Charith Raj, Tassios, Emilios, Samiotaki, Martina, Andronis, Christos, Lisón, Purificación, Nikolaou, Christoforos, Perreault, Jean-Pierre, and Kalantidis, Kriton

Abstract

[EN] Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.

Published
2022

29. RNA silencing pathways in plant development and defense

Author

Kryovrysanaki, Nikoleta, James, Anthony, Tselika, Martha, Bardani, Eirini, Kalantidis, Kriton, Kryovrysanaki, Nikoleta, James, Anthony, Tselika, Martha, Bardani, Eirini, and Kalantidis, Kriton

Abstract

RNA silencing refers to a conserved eukaryotic process and is regarded as one of the most important processes in plants, with the ability to regulate gene expression both transcriptionally and post-transcriptionally. Different classes of non-coding RNAs (ncRNAs) constitute key components of the RNA silencing pathways and play pivotal roles in modulating various biological processes as well as host-pathogen interactions. One of the most extensively studied classes of ncRNAs are the 20–24 nucleotide (nt) long microRNAs (miRNAs), which are core components of the endogenous gene silencing pathway. miRNAs act as negative regulators of endogenous gene expression through either mRNA-target cleavage, translational inhibition, or DNA methylation, and are inextricably linked to a plethora of developmental processes, such as leaf pattern formation as well as abiotic and biotic stress responses. In this review, we focus on the role of the RNA silencing pathways in the regulation of developmental processes as well as in the plant responses to biotic stress.

Published
2022

30. Revisiting the Non-Coding Nature of Pospiviroids

Author

Katsarou, Konstantina, Adkar-Purushothama, Charith Raj, Tassios, Emilios, Samiotaki, Martina, Andronis, Christos, Lisón, Purificación, Nikolaou, Christoforos, Perreault, Jean-Pierre, Kalantidis, Kriton, Katsarou, Konstantina, Adkar-Purushothama, Charith Raj, Tassios, Emilios, Samiotaki, Martina, Andronis, Christos, Lisón, Purificación, Nikolaou, Christoforos, Perreault, Jean-Pierre, and Kalantidis, Kriton

Abstract

Viroids are small, circular, highly structured pathogens that infect a broad range of plants, causing economic losses. Since their discovery in the 1970s, they have been considered as non-coding pathogens. In the last few years, the discovery of other RNA entities, similar in terms of size and structure, that were shown to be translated (e.g., cirRNAs, precursors of miRNA, RNA satellites) as well as studies showing that some viroids are located in ribosomes, have reignited the idea that viroids may be translated. In this study, we used advanced bioinformatic analysis, in vitro experiments and LC-MS/MS to search for small viroid peptides of the PSTVd. Our results suggest that in our experimental conditions, even though the circular form of PSTVd is found in ribosomes, no produced peptides were identified. This indicates that the presence of PSTVd in ribosomes is most probably not related to peptide production but rather to another unknown function that requires further study.

Published
2022

31. Revisiting the Non-Coding Nature of Pospiviroids

Author

Katsarou, Konstantina, primary, Adkar-Purushothama, Charith Raj, additional, Tassios, Emilios, additional, Samiotaki, Martina, additional, Andronis, Christos, additional, Lisón, Purificación, additional, Nikolaou, Christoforos, additional, Perreault, Jean-Pierre, additional, and Kalantidis, Kriton, additional

Published
2022
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34. Prediction of miRNA Targets

Author

Oulas, Anastasis, primary, Karathanasis, Nestoras, additional, Louloupi, Annita, additional, Pavlopoulos, Georgios A., additional, Poirazi, Panayiota, additional, Kalantidis, Kriton, additional, and Iliopoulos, Ioannis, additional

Published
2014
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35. DNA Preparation in Vitis vinifera L. For Third Generation Sequencing

Author

Bibi C. Androniki, Kollias Anastasios, Astrinaki Maria, Vassou Despoina, Kafetzopoulos Dimitris, Kalantidis Kriton, and Moschou N. Panagiotis

Abstract

BackgroundThere have been several attempts to sequence the genome of Vitis vinifera L. (grapevine), utilizing low-resolution second-generation platforms. Nevertheless, the characterization of the grapevine genetic resources and its adaptation to vulnerable conditions could be better addressed through extensive and high-resolution genome sequencing.MinION is a third-generation sequencer preferred by many laboratories due to its relatively low cost, ease of use and small size. Even though this long-read technology has been rapidly improving, to reach its full potential requires high-quality DNA.ResultsHere we establish a workflow for DNA extraction suitable for MinION sequencing long reads from grapevine. This protocol was tested with leaf samples from different positions on annual growing branches of grapevine, Purified nuclei from fresh young leaves that led to high quality, long DNA fragments, suitable for long-read sequencing were successfully generated. It is evident that longer reads in grapevine associate with both fresh tissue and adjusted conditions used for nuclei purification.ConclusionsWe propose that this workflow presents a significant advancement for long-read quality DNA isolation for grapevine and likely other plant species.

Published
2021
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38. DCL‐suppressed Nicotiana benthamiana plants: valuable tools in research and biotechnology

Author

Katsarou, Konstantina, Mitta, Eleni, Bardani, Eirini, Oulas, Anastasis, Dadami, Elena, and Kalantidis, Kriton

Subjects
DCL, Technical Advances, fungi, CMV, food and beverages, High-Throughput Nucleotide Sequencing, TuMV, TRV, GFP, Technical Advance, Gene Expression Regulation, Plant, RNAi, Mutation, Tobacco, Nicotiana benthamiana, RNA Interference, Dicer, miRNA, Biotechnology, Plant Proteins
Abstract

Summary RNA silencing is a universal mechanism involved in development, epigenetic modifications and responses to biotic and abiotic stresses. The major components of this mechanism are Dicer‐like (DCL), Argonaute (AGO) and RNA‐dependent RNA polymerase (RDR) proteins. Understanding the role of each component is of great scientific and agronomic importance. Plants, including Nicotiana benthamiana, an important plant model, usually possess four DCL proteins, each of which has a specific role, namely being responsible for the production of an exclusive small RNA population. Here, we used RNA interference (RNAi) technology to target DCL proteins and produced single and combinatorial mutants for DCL. We analysed the phenotype for each DCL knockdown plant, together with the small RNA profile, by next‐generation sequencing (NGS). We also investigated transgene expression, as well as viral infections, and were able to show that DCL suppression results in distinct developmental defects, changes in small RNA populations, increases in transgene expression and, finally, higher susceptibility in certain RNA viruses. Therefore, these plants are excellent tools for the following: (i) to study the role of DCL enzymes; (ii) to overexpress proteins of interest; and (iii) to understand the complex relationship between the plant silencing mechanism and biotic or abiotic stresses.

Published
2018

48. Chromatin dynamics during interphase and cell division: similarities and differences between model and crop plants

Author

European Commission, European Research Council, General Secretariat of Research and Technology (Greece), Consiglio Nazionale delle Ricerche, United States - Israel Binational Agricultural Research and Development Fund, Czech Science Foundation, Ministerio de Economía y Competitividad (España), Vallés Brau, María Pilar [0000-0002-8649-2362], Pecinka, Ales, Chevalier, Christian, Colas, Isabelle, Kalantidis, Kriton, Varotto, Serena, Krugman, Tamar, Michailidis, Christos, Vallés Brau, María Pilar, Muñoz, Aitor, Pradillo, Mónica, European Commission, European Research Council, General Secretariat of Research and Technology (Greece), Consiglio Nazionale delle Ricerche, United States - Israel Binational Agricultural Research and Development Fund, Czech Science Foundation, Ministerio de Economía y Competitividad (España), Vallés Brau, María Pilar [0000-0002-8649-2362], Pecinka, Ales, Chevalier, Christian, Colas, Isabelle, Kalantidis, Kriton, Varotto, Serena, Krugman, Tamar, Michailidis, Christos, Vallés Brau, María Pilar, Muñoz, Aitor, and Pradillo, Mónica

Abstract

Genetic information in the cell nucleus controls organismal development and responses to the environment, and finally ensures its own transmission to the next generations. To achieve so many different tasks, the genetic information is associated with structural and regulatory proteins, which orchestrate nuclear functions in time and space. Furthermore, plant life strategies require chromatin plasticity to allow a rapid adaptation to abiotic and biotic stresses. Here, we summarize current knowledge on the organization of plant chromatin and dynamics of chromosomes during interphase and mitotic and meiotic cell divisions for model and crop plants differing as to genome size, ploidy, and amount of genomic resources available. The existing data indicate that chromatin changes accompany most (if not all) cellular processes and that there are both shared and unique themes in the chromatin structure and global chromosome dynamics among species. Ongoing efforts to understand the molecular mechanisms involved in chromatin organization and remodeling have, together with the latest genome editing tools, potential to unlock crop genomes for innovative breeding strategies and improvements of various traits.

Published
2020

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