Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis
- Publication type:
- Journal article
- Metadata:
-
- Autoren
- Karin Groten
- Nabin T Pahari
- Shuqing Xu
- Maja Miloradovic van Doorn
- Ian T Baldwin
- Autoren-URL
- https://www.webofscience.com/api/gateway?GWVersion=2&SrcApp=fis-test-1&SrcAuth=WosAPI&KeyUT=WOS:000359919900069&DestLinkType=FullRecord&DestApp=WOS_CPL
- DOI
- 10.1371/journal.pone.0136234
- Externe Identifier
- Clarivate Analytics Document Solution ID: CP5KH
- PubMed Identifier: 26291081
- ISSN
- 1932-6203
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- PLOS ONE
- Artikelnummer
- ARTN e0136234
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Titel
- Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between <i>Nicotiana attenuata</i> and <i>Rhizophagus irregularis</i>
- Sub types
- Article
- Ausgabe der Zeitschrift
- 10
Data source: Web of Science (Lite)
- Other metadata sources:
-
- Autoren
- Karin Groten
- Nabin T Pahari
- Shuqing Xu
- Maja Miloradovic van Doorn
- Ian T Baldwin
- DOI
- 10.1371/journal.pone.0136234
- Editoren
- Raffaella Balestrini
- eISSN
- 1932-6203
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- PLOS ONE
- Sprache
- en
- Online publication date
- 2015
- Paginierung
- e0136234 - e0136234
- Status
- Published online
- Herausgeber
- Public Library of Science (PLoS)
- Herausgeber URL
- http://dx.doi.org/10.1371/journal.pone.0136234
- Datum der Datenerfassung
- 2018
- Titel
- Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis
- Ausgabe der Zeitschrift
- 10
Data source: Crossref
- Abstract
- Most land plants live in a symbiotic association with arbuscular mycorrhizal fungi (AMF) that belong to the phylum Glomeromycota. Although a number of plant genes involved in the plant-AMF interactions have been identified by analyzing mutants, the ability to rapidly manipulate gene expression to study the potential functions of new candidate genes remains unrealized. We analyzed changes in gene expression of wild tobacco roots (Nicotiana attenuata) after infection with mycorrhizal fungi (Rhizophagus irregularis) by serial analysis of gene expression (SuperSAGE) combined with next generation sequencing, and established a virus-induced gene-silencing protocol to study the function of candidate genes in the interaction. From 92,434 SuperSAGE Tag sequences, 32,808 (35%) matched with our in-house Nicotiana attenuata transcriptome database and 3,698 (4%) matched to Rhizophagus genes. In total, 11,194 Tags showed a significant change in expression (p<0.05, >2-fold change) after infection. When comparing the functions of highly up-regulated annotated Tags in this study with those of two previous large-scale gene expression studies, 18 gene functions were found to be up-regulated in all three studies mainly playing roles related to phytohormone metabolism, catabolism and defense. To validate the function of identified candidate genes, we used the technique of virus-induced gene silencing (VIGS) to silence the expression of three putative N. attenuata genes: germin-like protein, indole-3-acetic acid-amido synthetase GH3.9 and, as a proof-of-principle, calcium and calmodulin-dependent protein kinase (CCaMK). The silencing of the three plant genes in roots was successful, but only CCaMK silencing had a significant effect on the interaction with R. irregularis. Interestingly, when a highly activated inoculum was used for plant inoculation, the effect of CCaMK silencing on fungal colonization was masked, probably due to trans-complementation. This study demonstrates that large-scale gene expression studies across different species induce of a core set of genes of similar functions. However, additional factors seem to influence the overall pattern of gene expression, resulting in high variability among independent studies with different hosts. We conclude that VIGS is a powerful tool with which to investigate the function of genes involved in plant-AMF interactions but that inoculum strength can strongly influence the outcome of the interaction.
- Addresses
- Department of Molecular Ecology, Max Planck Institute for Chemical Ecology, Hans-Knöll-Str. 8, 07745, Jena, Germany.
- Autoren
- Karin Groten
- Nabin T Pahari
- Shuqing Xu
- Maja Miloradovic van Doorn
- Ian T Baldwin
- DOI
- 10.1371/journal.pone.0136234
- eISSN
- 1932-6203
- Externe Identifier
- PubMed Identifier: 26291081
- PubMed Central ID: PMC4546398
- Funding acknowledgements
- Swiss National Science Foundation: 142886
- Open access
- true
- ISSN
- 1932-6203
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- PloS one
- Schlüsselwörter
- Plant Viruses
- Mycorrhizae
- Plant Roots
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Plant
- Gene Silencing
- Sequence Homology
- Genes, Plant
- Glomeromycota
- Real-Time Polymerase Chain Reaction
- Gene Ontology
- Nicotiana
- Sprache
- eng
- Medium
- Electronic-eCollection
- Online publication date
- 2015
- Open access status
- Open Access
- Paginierung
- e0136234
- Datum der Veröffentlichung
- 2015
- Status
- Published
- Publisher licence
- CC BY
- Datum der Datenerfassung
- 2015
- Titel
- Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis.
- Sub types
- Research Support, Non-U.S. Gov't
- research-article
- Journal Article
- Ausgabe der Zeitschrift
- 10
Files
https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0136234&type=printable https://europepmc.org/articles/PMC4546398?pdf=render
Data source: Europe PubMed Central
- Abstract
- Most land plants live in a symbiotic association with arbuscular mycorrhizal fungi (AMF) that belong to the phylum Glomeromycota. Although a number of plant genes involved in the plant-AMF interactions have been identified by analyzing mutants, the ability to rapidly manipulate gene expression to study the potential functions of new candidate genes remains unrealized. We analyzed changes in gene expression of wild tobacco roots (Nicotiana attenuata) after infection with mycorrhizal fungi (Rhizophagus irregularis) by serial analysis of gene expression (SuperSAGE) combined with next generation sequencing, and established a virus-induced gene-silencing protocol to study the function of candidate genes in the interaction. From 92,434 SuperSAGE Tag sequences, 32,808 (35%) matched with our in-house Nicotiana attenuata transcriptome database and 3,698 (4%) matched to Rhizophagus genes. In total, 11,194 Tags showed a significant change in expression (p<0.05, >2-fold change) after infection. When comparing the functions of highly up-regulated annotated Tags in this study with those of two previous large-scale gene expression studies, 18 gene functions were found to be up-regulated in all three studies mainly playing roles related to phytohormone metabolism, catabolism and defense. To validate the function of identified candidate genes, we used the technique of virus-induced gene silencing (VIGS) to silence the expression of three putative N. attenuata genes: germin-like protein, indole-3-acetic acid-amido synthetase GH3.9 and, as a proof-of-principle, calcium and calmodulin-dependent protein kinase (CCaMK). The silencing of the three plant genes in roots was successful, but only CCaMK silencing had a significant effect on the interaction with R. irregularis. Interestingly, when a highly activated inoculum was used for plant inoculation, the effect of CCaMK silencing on fungal colonization was masked, probably due to trans-complementation. This study demonstrates that large-scale gene expression studies across different species induce of a core set of genes of similar functions. However, additional factors seem to influence the overall pattern of gene expression, resulting in high variability among independent studies with different hosts. We conclude that VIGS is a powerful tool with which to investigate the function of genes involved in plant-AMF interactions but that inoculum strength can strongly influence the outcome of the interaction.
- Date of acceptance
- 2015
- Autoren
- Karin Groten
- Nabin T Pahari
- Shuqing Xu
- Maja Miloradovic van Doorn
- Ian T Baldwin
- Autoren-URL
- https://www.ncbi.nlm.nih.gov/pubmed/26291081
- DOI
- 10.1371/journal.pone.0136234
- eISSN
- 1932-6203
- Externe Identifier
- PubMed Central ID: PMC4546398
- Ausgabe der Veröffentlichung
- 8
- Zeitschrift
- PLoS One
- Schlüsselwörter
- Gene Expression Regulation, Fungal
- Gene Expression Regulation, Plant
- Gene Ontology
- Gene Silencing
- Genes, Plant
- Glomeromycota
- Mycorrhizae
- Plant Roots
- Plant Viruses
- Real-Time Polymerase Chain Reaction
- Sequence Homology
- Nicotiana
- Sprache
- eng
- Country
- United States
- Paginierung
- e0136234
- PII
- PONE-D-15-18880
- Datum der Veröffentlichung
- 2015
- Status
- Published online
- Datum, an dem der Datensatz öffentlich gemacht wurde
- 2016
- Titel
- Virus-Induced Gene Silencing Using Tobacco Rattle Virus as a Tool to Study the Interaction between Nicotiana attenuata and Rhizophagus irregularis.
- Sub types
- Journal Article
- Research Support, Non-U.S. Gov't
- Ausgabe der Zeitschrift
- 10
Data source: PubMed
- Beziehungen:
- Property of