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Comparative analysis of protein-protein interactions in the defense response of rice and wheat
BACKGROUND: Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat are still poorly understood. The complete sequence of the rice genome has prov...
Autores principales: | , , , , , , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2013
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602203/ https://www.ncbi.nlm.nih.gov/pubmed/23496930 http://dx.doi.org/10.1186/1471-2164-14-166 |
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author | Cantu, Dario Yang, Baoju Ruan, Randy Li, Kun Menzo, Virginia Fu, Daolin Chern, Mawsheng Ronald, Pamela C Dubcovsky, Jorge |
author_facet | Cantu, Dario Yang, Baoju Ruan, Randy Li, Kun Menzo, Virginia Fu, Daolin Chern, Mawsheng Ronald, Pamela C Dubcovsky, Jorge |
author_sort | Cantu, Dario |
collection | PubMed |
description | BACKGROUND: Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat are still poorly understood. The complete sequence of the rice genome has provided an extremely useful parallel road map for genetic and genomics studies in wheat. The recent construction of a defense response interactome in rice has the potential to further enhance the translation of advances in rice to wheat and other grasses. The objective of this study was to determine the degree of conservation in the protein-protein interactions in the rice and wheat defense response interactomes. As entry points we selected proteins that serve as key regulators of the rice defense response: the RAR1/SGT1/HSP90 protein complex, NPR1, XA21, and XB12 (XA21 interacting protein 12). RESULTS: Using available wheat sequence databases and phylogenetic analyses we identified and cloned the wheat orthologs of these four rice proteins, including recently duplicated paralogs, and their known direct interactors and tested 86 binary protein interactions using yeast-two-hybrid (Y2H) assays. All interactions between wheat proteins were further tested using in planta bimolecular fluorescence complementation (BiFC). Eighty three percent of the known rice interactions were confirmed when wheat proteins were tested with rice interactors and 76% were confirmed using wheat protein pairs. All interactions in the RAR1/SGT1/ HSP90, NPR1 and XB12 nodes were confirmed for the identified orthologous wheat proteins, whereas only forty four percent of the interactions were confirmed in the interactome node centered on XA21. We hypothesize that this reduction may be associated with a different sub-functionalization history of the multiple duplications that occurred in this gene family after the divergence of the wheat and rice lineages. CONCLUSIONS: The observed high conservation of interactions between proteins that serve as key regulators of the rice defense response suggests that the existing rice interactome can be used to predict interactions in wheat. Such predictions are less reliable for nodes that have undergone a different history of duplications and sub-functionalization in the two lineages. |
format | Online Article Text |
id | pubmed-3602203 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2013 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-36022032013-03-20 Comparative analysis of protein-protein interactions in the defense response of rice and wheat Cantu, Dario Yang, Baoju Ruan, Randy Li, Kun Menzo, Virginia Fu, Daolin Chern, Mawsheng Ronald, Pamela C Dubcovsky, Jorge BMC Genomics Research Article BACKGROUND: Despite the importance of wheat as a major staple crop and the negative impact of diseases on its production worldwide, the genetic mechanisms and gene interactions involved in the resistance response in wheat are still poorly understood. The complete sequence of the rice genome has provided an extremely useful parallel road map for genetic and genomics studies in wheat. The recent construction of a defense response interactome in rice has the potential to further enhance the translation of advances in rice to wheat and other grasses. The objective of this study was to determine the degree of conservation in the protein-protein interactions in the rice and wheat defense response interactomes. As entry points we selected proteins that serve as key regulators of the rice defense response: the RAR1/SGT1/HSP90 protein complex, NPR1, XA21, and XB12 (XA21 interacting protein 12). RESULTS: Using available wheat sequence databases and phylogenetic analyses we identified and cloned the wheat orthologs of these four rice proteins, including recently duplicated paralogs, and their known direct interactors and tested 86 binary protein interactions using yeast-two-hybrid (Y2H) assays. All interactions between wheat proteins were further tested using in planta bimolecular fluorescence complementation (BiFC). Eighty three percent of the known rice interactions were confirmed when wheat proteins were tested with rice interactors and 76% were confirmed using wheat protein pairs. All interactions in the RAR1/SGT1/ HSP90, NPR1 and XB12 nodes were confirmed for the identified orthologous wheat proteins, whereas only forty four percent of the interactions were confirmed in the interactome node centered on XA21. We hypothesize that this reduction may be associated with a different sub-functionalization history of the multiple duplications that occurred in this gene family after the divergence of the wheat and rice lineages. CONCLUSIONS: The observed high conservation of interactions between proteins that serve as key regulators of the rice defense response suggests that the existing rice interactome can be used to predict interactions in wheat. Such predictions are less reliable for nodes that have undergone a different history of duplications and sub-functionalization in the two lineages. BioMed Central 2013-03-12 /pmc/articles/PMC3602203/ /pubmed/23496930 http://dx.doi.org/10.1186/1471-2164-14-166 Text en Copyright ©2013 Cantu et al.; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Research Article Cantu, Dario Yang, Baoju Ruan, Randy Li, Kun Menzo, Virginia Fu, Daolin Chern, Mawsheng Ronald, Pamela C Dubcovsky, Jorge Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title | Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title_full | Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title_fullStr | Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title_full_unstemmed | Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title_short | Comparative analysis of protein-protein interactions in the defense response of rice and wheat |
title_sort | comparative analysis of protein-protein interactions in the defense response of rice and wheat |
topic | Research Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3602203/ https://www.ncbi.nlm.nih.gov/pubmed/23496930 http://dx.doi.org/10.1186/1471-2164-14-166 |
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