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  1. Article ; Online: Understanding Nod factor signalling paves the way for targeted engineering in legumes and non-legumes.

    Krönauer, Christina / Radutoiu, Simona

    Current opinion in plant biology

    2021  Volume 62, Page(s) 102026

    Abstract: Legumes evolved LysM receptors for recognition of rhizobial Nod factors and initiation of signalling pathways for nodule organogenesis and infection. Intracellularly hosted bacteria are supplied with carbon resources in exchange for fixed nitrogen. Nod ... ...

    Abstract Legumes evolved LysM receptors for recognition of rhizobial Nod factors and initiation of signalling pathways for nodule organogenesis and infection. Intracellularly hosted bacteria are supplied with carbon resources in exchange for fixed nitrogen. Nod factor recognition is crucial for initial signalling, but is reiterated in growing roots initiating novel symbiotic events, and in developing primordia until symbiosis is well-established. Understanding how this signalling coordinates the entire process from cellular to plant level is key for de novo engineering in non-legumes and for improved efficiency in legumes. Here we discuss how recent studies bring new insights into molecular determinants of specificity and sensitivity in Nod factor signalling in legumes, and present some of the unknowns and challenges for engineering.
    Language English
    Publishing date 2021-03-05
    Publishing country England
    Document type Journal Article ; Review ; Research Support, Non-U.S. Gov't
    ZDB-ID 1418472-2
    ISSN 1879-0356 ; 1369-5266
    ISSN (online) 1879-0356
    ISSN 1369-5266
    DOI 10.1016/j.pbi.2021.102026
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  2. Article: Understanding Nod factor signalling paves the way for targeted engineering in legumes and non-legumes

    Krönauer, Christina / Radutoiu, Simona

    Current opinion in plant biology. 2021 Aug., v. 62

    2021  

    Abstract: Legumes evolved LysM receptors for recognition of rhizobial Nod factors and initiation of signalling pathways for nodule organogenesis and infection. Intracellularly hosted bacteria are supplied with carbon resources in exchange for fixed nitrogen. Nod ... ...

    Abstract Legumes evolved LysM receptors for recognition of rhizobial Nod factors and initiation of signalling pathways for nodule organogenesis and infection. Intracellularly hosted bacteria are supplied with carbon resources in exchange for fixed nitrogen. Nod factor recognition is crucial for initial signalling, but is reiterated in growing roots initiating novel symbiotic events, and in developing primordia until symbiosis is well-established. Understanding how this signalling coordinates the entire process from cellular to plant level is key for de novo engineering in non-legumes and for improved efficiency in legumes. Here we discuss how recent studies bring new insights into molecular determinants of specificity and sensitivity in Nod factor signalling in legumes, and present some of the unknowns and challenges for engineering.
    Keywords carbon ; nitrogen ; organogenesis ; symbiosis
    Language English
    Dates of publication 2021-08
    Publishing place Elsevier Ltd
    Document type Article
    Note NAL-AP-2-clean
    ZDB-ID 1418472-2
    ISSN 1879-0356 ; 1369-5266
    ISSN (online) 1879-0356
    ISSN 1369-5266
    DOI 10.1016/j.pbi.2021.102026
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    In stock of ZB MED Bonn / Germany

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  3. Article: Integrative transcript to proteome analysis of barley during

    Lemcke, René / Kamble, Manoj / Schneider, Sebastian / Lyngkjær, Michael F / Radutoiu, Simona / Wienkoop, Stefanie

    Frontiers in plant science

    2024  Volume 15, Page(s) 1367271

    Abstract: Introduction: Ramularia: Methods: Utilizing the strength of proteomics in understanding plant-pathogen interactions, we performed an integrative analysis of a published transcriptome dataset with a parallel generated proteome dataset. Therefore, we ... ...

    Abstract Introduction: Ramularia
    Methods: Utilizing the strength of proteomics in understanding plant-pathogen interactions, we performed an integrative analysis of a published transcriptome dataset with a parallel generated proteome dataset. Therefore, we included two spring barley cultivars with contrasting susceptibilities to
    Results: Interestingly, early responses in the pathogen recognition phase of the host were driven by strong responses differing between isolates. An important enzyme in this process is a xylanase inhibitor, which protected the plant from cell wall degradation by the fungal xylanase. At later time points, the differences were driven by cultivar-specific responses, affecting mostly features contributing to the pathogenesis- and senescence-related pathways or photosynthesis.
    Discussion: This supports the hypothesis of a hemibiotrophic lifestyle of
    Language English
    Publishing date 2024-03-28
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2024.1367271
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  4. Article ; Online: Unraveling the secrets of plant roots: Simplified method for large scale root exudate sampling and analysis in

    Subrahmaniam, Harihar Jaishree / Lind Salomonsen, Camilla / Radutoiu, Simona / Ehlers, Bodil K / Glasius, Marianne

    Open research Europe

    2023  Volume 3, Page(s) 12

    Abstract: Background: Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. ... ...

    Abstract Background: Plants exude a plethora of compounds to communicate with their environment. Although much is known about above-ground plant communication, we are only beginning to fathom the complexities of below-ground chemical communication channels. Studying root-exuded compounds and their role in plant communication has been difficult due to the lack of standardized methodologies. Here, we develop an interdisciplinary workflow to explore the natural variation in root exudate chemical composition of the model plant
    Methods: Our method involves cultivating individual seedlings
    Results: Based on 28 replicates of the Columbia genotype (Col-0) compared with 10 random controls, MZmine3 annotated 354 metabolites to be present only in Col-0 by negative ionization. Of these, 254 compounds could be annotated by SIRIUS 5 software.
    Conclusions: The methodology developed in this study can be used to broadly investigate the role of root exudates as chemical signals in plant belowground interactions.
    Language English
    Publishing date 2023-10-20
    Publishing country Belgium
    Document type Journal Article
    ISSN 2732-5121
    ISSN (online) 2732-5121
    DOI 10.12688/openreseurope.15377.3
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  5. Article ; Online: A simple and efficient protocol for generating transgenic hairy roots using Agrobacterium rhizogenes.

    Ferguson, Shaun / Abel, Nikolaj B / Reid, Dugald / Madsen, Lene H / Luu, Thi-Bich / Andersen, Kasper R / Stougaard, Jens / Radutoiu, Simona

    PloS one

    2023  Volume 18, Issue 11, Page(s) e0291680

    Abstract: For decades, Agrobacterium rhizogenes (now Rhizobium rhizogenes), the causative agent of hairy root disease, has been harnessed as an interkingdom DNA delivery tool for generating transgenic hairy roots on a wide variety of plants. One of the strategies ... ...

    Abstract For decades, Agrobacterium rhizogenes (now Rhizobium rhizogenes), the causative agent of hairy root disease, has been harnessed as an interkingdom DNA delivery tool for generating transgenic hairy roots on a wide variety of plants. One of the strategies involves the construction of transconjugant R. rhizogenes by transferring gene(s) of interest into previously constructed R. rhizogenes pBR322 acceptor strains; little has been done, however, to improve upon this system since its implementation. We developed a simplified method utilising bi-parental mating in conjunction with effective counterselection for generating R. rhizogenes transconjugants. Central to this was the construction of a new Modular Cloning (MoClo) compatible pBR322-derived integration vector (pIV101). Although this protocol remains limited to pBR322 acceptor strains, pIV101 facilitated an efficient construction of recombinant vectors, effective screening of transconjugants, and RP4-based mobilisation compatibility that enabled simplified conjugal transfer. Transconjugants from this system were tested on Lotus japonicus and found to be efficient for the transformation of transgenic hairy roots and supported infection of nodules by a rhizobia symbiont. The expedited protocol detailed herein substantially decreased both the time and labour for creating transconjugant R. rhizogenes for the subsequent transgenic hairy root transformation of Lotus, and it could readily be applied for the transformation of other plants.
    MeSH term(s) Transformation, Genetic ; Agrobacterium/genetics ; Plants/genetics ; Rhizobium/genetics ; Plant Roots/genetics ; Plant Roots/microbiology ; Plants, Genetically Modified/genetics
    Language English
    Publishing date 2023-11-01
    Publishing country United States
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2267670-3
    ISSN 1932-6203 ; 1932-6203
    ISSN (online) 1932-6203
    ISSN 1932-6203
    DOI 10.1371/journal.pone.0291680
    Database MEDical Literature Analysis and Retrieval System OnLINE

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  6. Article: Microbial associations enabling nitrogen acquisition in plants

    Tao, Ke / Kelly, Simon / Radutoiu, Simona

    Current opinion in microbiology. 2019 June, v. 49

    2019  

    Abstract: Large flows of nitrogen between the atmosphere, terrestrial and aquatic ecosystems contribute to the global cycle on Earth. When balanced, this cycle ensures that life at every level can flourish and diversify. However, in the past 50 years, humans have ... ...

    Abstract Large flows of nitrogen between the atmosphere, terrestrial and aquatic ecosystems contribute to the global cycle on Earth. When balanced, this cycle ensures that life at every level can flourish and diversify. However, in the past 50 years, humans have had a large, negative influence on nitrogen cycle pushing it beyond safe boundaries at the global level. Alternative, wholesome strategies are needed for the agricultural systems to achieve sustainability without compromising crop yields. Decades of research in the field of biological nitrogen fixation in symbiotic root nodules paved the way for ambitious bioengineering projects aiming to meet the nitrogen request in a sustainable manner. Parallel studies of the other microbes that associate with healthy plants in nature unveiled a tremendous, untapped resource for biostimulants. Many of these interactions are now worth investigating in detail to enable understanding at the molecular and ecological level and facile transfer into agricultural settings.
    Keywords aquatic ecosystems ; bioengineering ; crop yield ; microorganisms ; nitrogen ; nitrogen cycle ; nitrogen fixation ; root nodules
    Language English
    Dates of publication 2019-06
    Size p. 83-89.
    Publishing place Elsevier Ltd
    Document type Article
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2019.10.005
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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5514: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 51: Show issues

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  7. Article ; Online: Nitrogen and Nod factor signaling determine Lotus japonicus root exudate composition and bacterial assembly.

    Tao, Ke / Jensen, Ib T / Zhang, Sha / Villa-Rodríguez, Eber / Blahovska, Zuzana / Salomonsen, Camilla Lind / Martyn, Anna / Björgvinsdóttir, Þuríður Nótt / Kelly, Simon / Janss, Luc / Glasius, Marianne / Waagepetersen, Rasmus / Radutoiu, Simona

    Nature communications

    2024  Volume 15, Issue 1, Page(s) 3436

    Abstract: Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia ... ...

    Abstract Symbiosis with soil-dwelling bacteria that fix atmospheric nitrogen allows legume plants to grow in nitrogen-depleted soil. Symbiosis impacts the assembly of root microbiota, but it is unknown how the interaction between the legume host and rhizobia impacts the remaining microbiota and whether it depends on nitrogen nutrition. Here, we use plant and bacterial mutants to address the role of Nod factor signaling on Lotus japonicus root microbiota assembly. We find that Nod factors are produced by symbionts to activate Nod factor signaling in the host and that this modulates the root exudate profile and the assembly of a symbiotic root microbiota. Lotus plants with different symbiotic abilities, grown in unfertilized or nitrate-supplemented soils, display three nitrogen-dependent nutritional states: starved, symbiotic, or inorganic. We find that root and rhizosphere microbiomes associated with these states differ in composition and connectivity, demonstrating that symbiosis and inorganic nitrogen impact the legume root microbiota differently. Finally, we demonstrate that selected bacterial genera characterizing state-dependent microbiomes have a high level of accurate prediction.
    MeSH term(s) Lotus/microbiology ; Lotus/metabolism ; Symbiosis ; Nitrogen/metabolism ; Plant Roots/microbiology ; Plant Roots/metabolism ; Signal Transduction ; Microbiota/physiology ; Rhizosphere ; Bacterial Proteins/metabolism ; Bacterial Proteins/genetics ; Soil Microbiology ; Nitrogen Fixation ; Plant Exudates/metabolism
    Chemical Substances Nitrogen (N762921K75) ; Bacterial Proteins ; Plant Exudates
    Language English
    Publishing date 2024-04-23
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 2553671-0
    ISSN 2041-1723 ; 2041-1723
    ISSN (online) 2041-1723
    ISSN 2041-1723
    DOI 10.1038/s41467-024-47752-0
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  8. Article ; Online: Microbial associations enabling nitrogen acquisition in plants.

    Tao, Ke / Kelly, Simon / Radutoiu, Simona

    Current opinion in microbiology

    2019  Volume 49, Page(s) 83–89

    Abstract: Large flows of nitrogen between the atmosphere, terrestrial and aquatic ecosystems contribute to the global cycle on Earth. When balanced, this cycle ensures that life at every level can flourish and diversify. However, in the past 50 years, humans have ... ...

    Abstract Large flows of nitrogen between the atmosphere, terrestrial and aquatic ecosystems contribute to the global cycle on Earth. When balanced, this cycle ensures that life at every level can flourish and diversify. However, in the past 50 years, humans have had a large, negative influence on nitrogen cycle pushing it beyond safe boundaries at the global level. Alternative, wholesome strategies are needed for the agricultural systems to achieve sustainability without compromising crop yields. Decades of research in the field of biological nitrogen fixation in symbiotic root nodules paved the way for ambitious bioengineering projects aiming to meet the nitrogen request in a sustainable manner. Parallel studies of the other microbes that associate with healthy plants in nature unveiled a tremendous, untapped resource for biostimulants. Many of these interactions are now worth investigating in detail to enable understanding at the molecular and ecological level and facile transfer into agricultural settings.
    MeSH term(s) Agriculture ; Bacteria ; Ecosystem ; Fungi/physiology ; Nitrogen/metabolism ; Nitrogen Cycle ; Nitrogen Fixation ; Soil Microbiology ; Symbiosis
    Chemical Substances Nitrogen (N762921K75)
    Language English
    Publishing date 2019-11-14
    Publishing country England
    Document type Journal Article ; Research Support, Non-U.S. Gov't ; Review
    ZDB-ID 1418474-6
    ISSN 1879-0364 ; 1369-5274
    ISSN (online) 1879-0364
    ISSN 1369-5274
    DOI 10.1016/j.mib.2019.10.005
    Database MEDical Literature Analysis and Retrieval System OnLINE

    Full text online

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    In stock of ZB MED Cologne/Königswinter

    Zs.A 5514: Show issues Location:
    Je nach Verfügbarkeit (siehe Angabe bei Bestand)
    bis Jg. 1994: Bestellungen von Artikeln über das Online-Bestellformular
    Jg. 1995 - 2021: Lesesall (2.OG)
    ab Jg. 2022: Lesesaal (EG)
    Zs.MG 51: Show issues

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  9. Article: The

    Vittozzi, Ylenia / Nadzieja, Marcin / Rogato, Alessandra / Radutoiu, Simona / Valkov, Vladimir Totev / Chiurazzi, Maurizio

    Frontiers in plant science

    2021  Volume 12, Page(s) 688187

    Abstract: Nitrogen-fixing nodules are new organs formed on legume roots as a result of the beneficial interaction with the soil bacteria, rhizobia. Proteins of the nitrate transporter 1/peptide transporter family (NPF) are largely represented in the subcategory of ...

    Abstract Nitrogen-fixing nodules are new organs formed on legume roots as a result of the beneficial interaction with the soil bacteria, rhizobia. Proteins of the nitrate transporter 1/peptide transporter family (NPF) are largely represented in the subcategory of nodule-induced transporters identified in mature nodules. The role of nitrate as a signal/nutrient regulating nodule functioning has been recently highlighted in the literature, and NPFs may play a central role in both the permissive and inhibitory pathways controlling N
    Language English
    Publishing date 2021-06-18
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2613694-6
    ISSN 1664-462X
    ISSN 1664-462X
    DOI 10.3389/fpls.2021.688187
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  10. Article: Application of ecosystem-specific reference databases for increased taxonomic resolution in soil microbial profiling.

    Overgaard, Christina Karmisholt / Tao, Ke / Zhang, Sha / Christensen, Bent Tolstrup / Blahovska, Zuzana / Radutoiu, Simona / Kelly, Simon / Dueholm, Morten Kam Dahl

    Frontiers in microbiology

    2022  Volume 13, Page(s) 942396

    Abstract: Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial ... ...

    Abstract Intensive agriculture systems have paved the way for a growing human population. However, the abundant use of mineral fertilizers and pesticides may negatively impact nutrient cycles and biodiversity. One potential alternative is to harness beneficial relationships between plants and plant-associated rhizobacteria to increase nutrient-use efficiency and provide pathogen resistance. Plant-associated microbiota profiling can be achieved using high-throughput 16S rRNA gene amplicon sequencing. However, interrogation of these data is limited by confident taxonomic classifications at high taxonomic resolution (genus- or species level) with the commonly applied universal reference databases. High-throughput full-length 16S rRNA gene sequencing combined with automated taxonomy assignment (AutoTax) can be used to create amplicon sequence variant resolved ecosystems-specific reference databases that are superior to the traditional universal reference databases. This approach was used here to create a custom reference database for bacteria and archaea based on 987,353 full-length 16S rRNA genes from Askov and Cologne soils. We evaluated the performance of the database using short-read amplicon data and found that it resulted in the increased genus- and species-level classification compared to commonly use universal reference databases. The custom database was utilized to evaluate the ecosystem-specific primer bias and taxonomic resolution of amplicon primers targeting the V5-V7 region of the 16S rRNA gene commonly used within the plant microbiome field. Finally, we demonstrate the benefits of custom ecosystem-specific databases through the analysis of V5-V7 amplicon data to identify new plant-associated microbes for two legumes and two cereal species.
    Language English
    Publishing date 2022-11-03
    Publishing country Switzerland
    Document type Journal Article
    ZDB-ID 2587354-4
    ISSN 1664-302X
    ISSN 1664-302X
    DOI 10.3389/fmicb.2022.942396
    Database MEDical Literature Analysis and Retrieval System OnLINE

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