Athanasios Dalakouras

Athanasios Dalakouras
Hellenic Agricultural Organization - Demeter | ELGO · Institute of Industrial and Forage Crops (Larissa)

Dr. rer. nat.
HELLENIC AGRICULTURAL ORGANIZATION - DEMETER

About

39
Publications
10,944
Reads
How we measure 'reads'
A 'read' is counted each time someone views a publication summary (such as the title, abstract, and list of authors), clicks on a figure, or views or downloads the full-text. Learn more
681
Citations
Introduction
Dr. rer. nat. (Ruprecht-Karls-Universität Heidelberg)
Skills and Expertise
Additional affiliations
September 2018 - August 2020
University of Thessaly
Position
  • Postodoc (Marie Curie Fellowship)
Description
  • RNAi and plant epigenetics
October 2011 - June 2018
RLP AgroScience
Position
  • PostDoc Position
Description
  • RNAi and plant epigenetics
Education
September 2006 - June 2010
Universität Heidelberg
Field of study
  • Plant Epigenetics
September 2004 - June 2006
Univesrity of Crete, IMBB-FORTH
Field of study
  • Plant Molecular Biology and Biotechnology
September 1998 - June 2004
Agricultural University of Athens
Field of study
  • Plant Biotechnology

Publications

Publications (39)
Article
Full-text available
In this report we describe a method for the delivery of small interfering RNAs (siRNAs) into plant cells. In vitro synthesized siRNAs that were designed to target the coding region of a GREEN FLUORESCENT PROTEIN (GFP) transgene were applied by various methods onto GFP-expressing transgenic Nicotiana benthamiana plants to trigger RNA silencing. In c...
Article
Full-text available
RNA-directed DNA methylation (RdDM) in plants has been extensively studied, but the RNA molecules guiding the RdDM machinery to their targets need to be yet characterized. It is unclear whether these molecules require full complementarity with their target. In this study, we have generated Nicotiana tabacum (Nt) plants carrying an infectious Tomato...
Article
Full-text available
In plants, Potato spindle tuber viroid (PSTVd) replication triggers post-transcriptional gene silencing (PTGS) and RNA-directed DNA methylation (RdDM) of homologous RNA and DNA sequences, respectively. PTGS predominantly occurs in the cytoplasm, but nuclear PTGS has been also reported. In this study, we investigated whether the nuclear replicating...
Article
Full-text available
Landes Bioscience, RNA-directed DNA methylation (RdDM) involves sequence-specific guiding of the de novo methylation machinery to complementary genomic DNA by RNA molecules. It is still elusive whether guide RNAs bind directly to DNA or to nascent transcripts produced from it. Even the nature of the guide RNAs is not elucidated. RNA interference (R...
Article
Full-text available
So far, conventional hairpin RNA (hpRNA) constructs consisting of an inverted repeat (IR) of target promoters directly introduced into an expression cassette have been used to mediate de novo DNA methylation. Transcripts of such constructs resemble mRNA molecules, and are likely to be exported to the cytoplasm. The presence of hpRNAs in the cytopla...
Preprint
Full-text available
A growing body of evidence suggests that RNA interference (RNAi) plays a pivotal role in the communication between plants and pathogenic fungi, where a bi-directional cross-kingdom RNAi is established to the advantage of either the host or the pathogen. Similar mechanisms acting during plant association with non-pathogenic symbiotic microorganisms...
Article
Full-text available
In plants, small interfering RNAs (siRNAs) are a quintessential class of RNA interference (RNAi)‐inducing molecules produced by the endonucleolytic cleavage of double stranded RNAs (dsRNAs). In order to ensure robust RNAi, siRNAs are amplified through a positive feedback mechanism called transitivity. Transitivity relies on RNA‐DIRECTED‐RNA POLYMER...
Article
In order to tackle the cumulative adverse effects of global climate change, reduced farmland and heightened needs of an ever-increasing world population, modern agriculture is in urgent search of solutions that can ensure world food security and sustainable development. Classical crop breeding is still a powerful method to obtain crops with valued...
Article
Full-text available
Viroids are plant pathogenic, circular, non-coding, single-stranded RNAs (ssRNAs). Members of the Pospiviroidae family replicate in the nucleus of plant cells through double-stranded RNA (dsRNA) intermediates, thus triggering the host’s RNA interference (RNAi) machinery. In plants, the two RNAi pillars are Post-Transcriptional Gene Silencing (PTGS)...
Article
Full-text available
Exogenous application of RNA molecules is a potent method to trigger RNA interference (RNAi) in plants in a transgene-free manner. So far, all exogenous RNAi (exo-RNAi) applications have aimed to trigger mRNA degradation of a given target. However, the issue of concomitant epigenetic changes was never addressed. Here, we report for the first time t...
Preprint
Full-text available
In plants, small interfering RNAs (siRNAs) are a quintessential class of RNA interference (RNAi)-inducing molecules produced by the endonucleolytic cleavage of double stranded RNAs (dsRNAs). In order to ensure robust RNAi, siRNAs are amplified through a positive feedback mechanism called transitivity. Transitivity relies on RNA-DIRECTED-RNA POLYMER...
Chapter
In nature, plants are continuously challenged by biotic stressors such as pathogenic microorganisms and herbivorous pests that often cause important yield reductions in crops. To address global food security issues but also consumer demands for healthier food production, a series of environmentally friendly crop protection strategies need to be emp...
Article
Full-text available
Exogenous RNA interference (exo-RNAi) is a powerful transgene-free tool in modern crop improvement and protection platforms. In exo-RNAi approaches, double stranded RNAs (dsRNAs) or short-interfering RNAs (siRNAs) are externally applied in plants in order to selectively trigger degradation of target mRNAs. Yet, the applied dsRNAs may also trigger u...
Poster
Full-text available
So far, biotechnological RNAi approaches in plants have been based on RNAi-inducing transgenes and/or transgenic plants. Here, we describe novel methods for the exogenous delivery in plants of RNA molecules having the potential to trigger RNAi in a transgene-free manner.
Article
Full-text available
Cucurbita pepo contains two cultivated subspecies each of which encompasses four fruit-shape morphotypes (cultivar-groups). The Pumpkin, Vegetable Marrow, Cocozelle, and Zucchini Groups are of subsp. pepo and the Acorn, Crookneck, Scallop, and Straightneck Groups are of subsp. ovifera. Recently, a de novo assembly of the C. pepo subsp. pepo Zucchin...
Article
Full-text available
Main conclusion In this study, we show that aberrant pre-mRNAs from non-spliced and non-polyadenylated intron-containing transgenes are channelled to the RNA silencing pathway. In plants, improperly processed transcripts are called aberrant RNAs (ab-RNAs) and are eliminated by either RNA silencing or RNA decay mechanisms. Ab-RNAs transcribed from i...
Article
Full-text available
Since its discovery, RNA interference has been widely used in crop protection. Recently, transgene-free procedures that were based on exogenous application of RNA molecules having the capacity to trigger RNAi in planta have been reported. Yet, efficient delivery of such RNA molecules to plants and particularly to trees poses major technical challen...
Chapter
In plants, RNA silencing refers to a network of pathways where small RNAs are associated with gene regulation and the defense against foreign nucleic acids including transgenes, viruses, and viroids. Replicating viroids recruit host RNA silencing machinery and trigger the production of abundant viroid-derived small interfering RNAs. Here, the recen...
Article
Full-text available
In South Asia, Cotton leaf curl disease (CLCuD) is caused by a complex of phylogenetically-related begomovirus species and a specific betasatellite, Cotton leaf curl Multan betasatellite (CLCuMuB). The post-transcriptional gene silencing (PTGS) suppression activities of the transcriptional activator protein (TrAP), C4, V2 and βC1 proteins encoded b...
Article
Full-text available
Viroids are non-encapsidated, non-coding, circular, single-stranded RNAs (ssRNAs). They are classified into the families Pospiviroidae and Avsunviroidae, whose members replicate in the nucleus and chloroplast of plant cells, respectively. Viroids have a wide host range, including crop and ornamental plants, and can cause devastating diseases with s...
Article
Full-text available
In plants, endogenes are less prone to RNA silencing than transgenes. While both can be efficiently targeted by small RNAs for post-transcriptional gene silencing (PTGS), generally only transgene PTGS is accompanied by transitivity, RNA-directed DNA methylation (RdDM) and systemic silencing. In order to investigate whether a transgene could mimick...
Poster
Full-text available
In plants, endogenes are less prone to RNA silencing than transgenes. While both can be efficiently targeted by small RNAs for post-transcriptional gene silencing (PTGS), generally only transgene PTGS is accompanied by transitivity, RNA-directed DNA methylation (RdDM) and systemic silencing. In order to investigate whether a transgene could mimick...
Poster
Full-text available
In plants, transgenes are generally more sensitive against RNA silencing than endogenes are. In this study, we generated a transgene that structurally mimicks an endogene. It is composed of promoter, 5’-UTR, introns, 3’-UTR and terminator elements of one of the Nicotiana tabacum RIBULOSE-1,5-BIPHOSPHATE CARBOXYLASE OXYGENASE (RuBisCO) genes (Fig. 1...
Article
Full-text available
Abstract In eukaryotes, DNA methylation refers to the addition of a methyl group to the fifth atom in the six-atom ring of cytosine residues. At least in plants, DNA regions that become de novo methylated can be defined by homologous RNA molecules in a process termed RNA-directed DNA methylation (RdDM). RdDM was first discovered in viroid-infected...
Poster
Full-text available
Viroids are small, circular, single stranded RNA (ssRNA) pathogens. Members of the Pospiviroidae family replicate in the host nucleus via rolling circle mechanism and produce abundant double stranded RNA (dsRNA) intermediates and small interfering RNAs (siRNAs). During Potato spindle tuber viroid (PSTVd) infection, homologous sequences were efficie...
Article
Full-text available
In plants, transgenes are generally more sensitive against RNA silencing than endogenes are. In this study, we generated a transgene that structurally mimicks an endogene. It is composed of endogenous promoter, 5' UTR, introns, 3' UTR and terminator elements. Our data revealed that, in contrast to a conventional transgene, an endogene-resembling tr...
Poster
Full-text available
RNA-directed DNA methylation (RdDM) involves sequence-specific guiding of the de novo methylation machinery to complementary genomic DNA by RNA molecules. It is still elusive whether guide RNAs bind directly to DNA or to nascent transcripts produced from it. Even the nature of the guide RNAs is not elucidated. RNA interference (RNAi) studies provid...
Article
Full-text available
In plants, RNA-directed DNA methylation (RdDM) can target both transgene promoters and coding regions/gene bodies. RdDM leads to methylation of cytosines in all sequence contexts: CG, CHG and CHH. Upon segregation of the RdDM trigger, at least CG methylation can be maintained at promoter regions in the progeny. So far, it is not clear whether codin...
Article
Full-text available
In plants, transgenes frequently become spontaneously silenced for unknown reasons. Typically, transgene silencing involves the generation of small interfering RNAs (siRNAs) that directly or indirectly target cognate DNA and mRNA sequences for methylation and degradation, respectively. In this report, we compared spontaneous silencing of a transgen...
Article
Full-text available
Previously, we had shown that stable expression of a hairpin RNA sharing homology with the coat protein (CP) of the Cucumber mosaic virus (CMV) (hpRNA(CMV)) produced CMV resistant Nicotiana tabacum plants. However, only 17% of the hpRNA(CMV)-expressing plants generated substantial amounts of siRNAs that mediated CMV resistance (siRNAs(CMV)). Here,...
Article
Full-text available
In plants, transgenes containing Potato spindle tuber viroid (PSTVd) cDNA sequences were efficient targets of PSTVd infection-mediated RNA-directed DNA methylation. Here, we demonstrate that in PSTVd-infected tobacco plants, a 134 bp PSTVd fragment (PSTVd-134) did not become densely methylated when it was inserted into a chimeric Satellite tobacco...
Article
Full-text available
The influenza virus surface glycoprotein antigen neuraminidase (NA) is a crucial viral enzyme with many potential medical applications; therefore, the development of efficient upstream and downstream processing strategy for the expression and purification of NA is of high importance. In the present work the NA gene from the H1N1 influenza virus str...

Network

Cited By

Projects

Projects (7)
Project
Low risk pesticides (LRP) including (i) plant extracts (ii) semiochemicals like pheromones and allelochemicals, (iii) microbial pesticides, are gaining ground in the global market, as substitutes of synthetic pesticides. In addition, new microbial solutions (phages, protists, microbial consortia) and ds-RNA pesticides are emerging, low-risk solutions expect to reach the market in coming years. Despite ongoing regulatory efforts by the European Commission, we are still lacking a concrete risk assessment (RA) scheme relevant to LRPs, a point which blocks LRPs reaching the EU market. RATION timely comes to address these regulatory constraints and aims to develop a novel RA scheme, supported by the necessary guidance on methods and tools, tailored to the specific characteristics of established and emerging LRP solutions. This main goal will be achieved through a series of interrelated WPs aiming (i) to map the current status of LRPs in Europe and identify main regulatory constraints (WP1). In this quest it will be supported by a stakeholders forum composed of all relevant actors (industry, regulators, academics, famers, general public); (ii) to develop and validate, through a proof-of-concept exercise, innovative RA (and associated tools) for microbials (WP2), plant extracts, semiochemicals, pheromones (WP3) and, ds-RNA (WP4); and from there (iii) build a harmonized RA for all LRP and determine its socioeconomic impact (WP5), (iv) to effectively communicate and disseminate the new RA knowledge and its associated tools developed by RATION to relevant actors ensuring sustainability beyond project duration (WP6). RATION will benchmark EU regulatory science, uplift blockers holding back LRP uptake by the EU market and motivate research innovation in plant protection. To achieve these goals 22 partners from academia, industry and regulatory bodies, representing 10 member states and 2 non-EU member states, will join forces in a multi-sectoral and multidisciplinary effort.
Project
- Analysis of natural epigenetic diversity and identification of epimarkers associated to desired traits. - Development of methods and tools to induce artificial epigenetic diversity that will lead to novel phenotypic variability.
Project
INTOMED Research and Innovation Activities (RIA) primarily consist of activities aiming to establish new knowledge in the field of microbe-plant-arthropod interactions and explore the feasibility of new products/solutions/services for the sustainable control of pests in three major crops in the Meditterenean. INTOMED objectives and goals will produce new knowledge through scientific research that will be pursued with the collaborative research of the consortium partners from 3 Universities, 5 Research Institutes and one company. FUNDING The PRIMA programme is supported under Horizon 2020, the European Union’s Framework Programme for Research and Innovation. Budget: 823.000€ Starting date: 15th November 2019