A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1
| dc.contributor.author | Yocgo, Rosita E | |
| dc.contributor.author | Geza, Ephifania | |
| dc.contributor.author | Chimusa, Emile R | |
| dc.contributor.author | Mazandu, Gaston K | |
| dc.date.accessioned | 2017-11-28T10:18:59Z | |
| dc.date.available | 2017-11-28T10:18:59Z | |
| dc.date.issued | 2017-11-23 | |
| dc.date.updated | 2017-11-26T04:57:25Z | |
| dc.description.abstract | Background: Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets. Moreover, elucidating biological mechanisms driving the induced disease resistance and influencing these observable disease phenotypes has never been systematically tackled, eliciting the need for an efficient model to characterize completely the gene target under consideration. Results: We developed a post-gene silencing bioinformatics (post-GSB) protocol which accounts for potential biases related to the disease phenotype datasets in assessing the contribution of the gene target to the plant defence response. The post-GSB protocol uses Gene Ontology semantic similarity and pathway dataset to generate enriched process regulatory network based on the functional degeneracy of the plant proteome to help understand the induced plant defence response. We applied this protocol to investigate the effect of the NPR1 gene silencing to changes in Arabidopsis thaliana plants following Pseudomonas syringae pathovar tomato strain DC3000 infection. Results indicated that the presence of a functionally active NPR1 reduced the plant’s susceptibility to the infection, with about 99% of variability in Pseudomonas spore growth between npr1 mutant and wild-type samples. Moreover, the post-GSB protocol has revealed the coordinate action of target-associated genes and pathways through an enriched process regulatory network, summarizing the potential target-based induced disease resistance mechanism. Conclusions: This protocol can improve the characterization of the gene target and, potentially, elucidate induced defence response by more effectively utilizing available phenotype information and plant proteome functional knowledge. | |
| dc.identifier.apacitation | Yocgo, R. E., Geza, E., Chimusa, E. R., & Mazandu, G. K. (2017). A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. <i>BMC Plant Biology</i>, http://hdl.handle.net/11427/26427 | en_ZA |
| dc.identifier.chicagocitation | Yocgo, Rosita E, Ephifania Geza, Emile R Chimusa, and Gaston K Mazandu "A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1." <i>BMC Plant Biology</i> (2017) http://hdl.handle.net/11427/26427 | en_ZA |
| dc.identifier.citation | Chimusa, E. R., Geza, E., Mazandu, G. K., & Yocgo, R. E. (2017). A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. BMC Plant Biology, 17(1), 218. | |
| dc.identifier.ris | TY - Journal Article AU - Yocgo, Rosita E AU - Geza, Ephifania AU - Chimusa, Emile R AU - Mazandu, Gaston K AB - Background: Advances in forward and reverse genetic techniques have enabled the discovery and identification of several plant defence genes based on quantifiable disease phenotypes in mutant populations. Existing models for testing the effect of gene inactivation or genes causing these phenotypes do not take into account eventual uncertainty of these datasets and potential noise inherent in the biological experiment used, which may mask downstream analysis and limit the use of these datasets. Moreover, elucidating biological mechanisms driving the induced disease resistance and influencing these observable disease phenotypes has never been systematically tackled, eliciting the need for an efficient model to characterize completely the gene target under consideration. Results: We developed a post-gene silencing bioinformatics (post-GSB) protocol which accounts for potential biases related to the disease phenotype datasets in assessing the contribution of the gene target to the plant defence response. The post-GSB protocol uses Gene Ontology semantic similarity and pathway dataset to generate enriched process regulatory network based on the functional degeneracy of the plant proteome to help understand the induced plant defence response. We applied this protocol to investigate the effect of the NPR1 gene silencing to changes in Arabidopsis thaliana plants following Pseudomonas syringae pathovar tomato strain DC3000 infection. Results indicated that the presence of a functionally active NPR1 reduced the plant’s susceptibility to the infection, with about 99% of variability in Pseudomonas spore growth between npr1 mutant and wild-type samples. Moreover, the post-GSB protocol has revealed the coordinate action of target-associated genes and pathways through an enriched process regulatory network, summarizing the potential target-based induced disease resistance mechanism. Conclusions: This protocol can improve the characterization of the gene target and, potentially, elucidate induced defence response by more effectively utilizing available phenotype information and plant proteome functional knowledge. DA - 2017-11-23 DB - OpenUCT DO - 10.1186/s12870-017-1151-y DP - University of Cape Town J1 - BMC Plant Biology LK - https://open.uct.ac.za PB - University of Cape Town PY - 2017 T1 - A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1 TI - A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1 UR - http://hdl.handle.net/11427/26427 ER - | en_ZA |
| dc.identifier.uri | http://dx.doi.org/10.1186/s12870-017-1151-y | |
| dc.identifier.uri | http://hdl.handle.net/11427/26427 | |
| dc.identifier.vancouvercitation | Yocgo RE, Geza E, Chimusa ER, Mazandu GK. A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1. BMC Plant Biology. 2017; http://hdl.handle.net/11427/26427. | en_ZA |
| dc.language.iso | en | |
| dc.publisher | BioMed Central | |
| dc.publisher.department | Institute of Infectious Disease and Molecular Medicine | en_ZA |
| dc.publisher.faculty | Faculty of Health Sciences | en_ZA |
| dc.publisher.institution | University of Cape Town | |
| dc.rights.holder | The Author(s) | |
| dc.source | BMC Plant Biology | |
| dc.source.uri | https://bmcplantbiol.biomedcentral.com/ | |
| dc.subject.other | Gene silencing | |
| dc.subject.other | Plant defence gene discovery | |
| dc.subject.other | Semantic similarity | |
| dc.subject.other | Arabidopsis thaliana | |
| dc.subject.other | Pseudomonas syringae | |
| dc.title | A post-gene silencing bioinformatics protocol for plant-defence gene validation and underlying process identification: case study of the Arabidopsis thaliana NPR1 | |
| dc.type | Journal Article | |
| uct.type.filetype | Text | |
| uct.type.filetype | Image |