The Role of Non-­Coding RNA in Plant Stress

Handle URI:
http://hdl.handle.net/10754/255072
Title:
The Role of Non-­Coding RNA in Plant Stress
Authors:
MacPherson, Cameron R.
Abstract:
Post-transcriptional gene silencing (PTGS) is a powerful mechanism that can be adapted to genetically modify crop plants. PTGS operates in many plant signaling pathways including those mediating stress responses. Given the small number of miRNAs known, research on the characterization of stress-related micro-RNA (miRNA) and their targets could provide the basis for engineering stress tolerant traits in crops. Indeed, several examples of miRNA mediated crop tolerance have been reported. In the research presented here, we aimed to analyze the role of small non-coding RNA (smRNA) pathways involved in plant stress. In particular, we focused on miRNA-mediated PTGS in phosphate (Pi) starvation. The analysis was split into two research projects. First, to identify potential miRNA targets we began by analyzing the response and recovery of coding and long non-coding RNAs (lncRNA) to Pi starvation in shoot and root. The results obtained were the first genome-wide description of the root’s Pi starvation response and recovery. We found that the root's response involved a widely different set of genes than that of the shoot. In the second research project, the results of the first project were correlated with the responses of miRNA and trans-acting small-interfering RNA (tasiRNA) during Pi starvation. Many miRNA circuits have been predicted before, however, tasiRNA circuits are not as well defined. Therefore, we made use of the double-stranded RNA-binding protein 4 (DRB4) smRNA libraries to enhance our prediction of tasiRNAs. Altogether, we provided evidence to support the following miRNA-mRNA pairs that may function in Pi starvation: IPS1:miR399:PHO2; miR399:RS4; miR399:NF-YA10; miR398:CSD1/2; miR2111:TPS11; miR164:NAC6; miR157:TMO7; miR157:PSB28; RPS2:miR169:IPS2; miR397:LAC2; TAS4:PAP1; NR1:PAP1; and Chr3_1967672:TMO7. In general, we found that non-miR399 related circuits were active only during the root’s recovery from Pi starvation. The functional roles of the genes targeted by these PTGS circuits suggested that the local root response to Pi starvation was influenced by the plant's systemic response pathways via PHR1-mediated PTGS. Finally, since many PTGS targets function to modulate concentrations of reactive oxygen species and sucrose, we hypothesized that the candidate PTGS circuits found in our research mediate a general stress recovery process by modulating metabolites involved in signaling pathways.
Advisors:
Bajic, Vladimir B. ( 0000-0001-5435-4750 )
Committee Member:
Chua, Nam-Hai; Fedoroff, Nina V.; Magistretti, Pierre
KAUST Department:
Biological and Environmental Sciences and Engineering (BESE) Division
Program:
Bioscience
Issue Date:
Dec-2012
Type:
Dissertation
Appears in Collections:
Bioscience Program; Dissertations; Biological and Environmental Sciences and Engineering (BESE) Division

Full metadata record

DC FieldValue Language
dc.contributor.advisorBajic, Vladimir B.en
dc.contributor.authorMacPherson, Cameron R.en
dc.date.accessioned2012-12-10T08:29:57Z-
dc.date.available2012-12-10T08:29:57Z-
dc.date.issued2012-12en
dc.identifier.urihttp://hdl.handle.net/10754/255072en
dc.description.abstractPost-transcriptional gene silencing (PTGS) is a powerful mechanism that can be adapted to genetically modify crop plants. PTGS operates in many plant signaling pathways including those mediating stress responses. Given the small number of miRNAs known, research on the characterization of stress-related micro-RNA (miRNA) and their targets could provide the basis for engineering stress tolerant traits in crops. Indeed, several examples of miRNA mediated crop tolerance have been reported. In the research presented here, we aimed to analyze the role of small non-coding RNA (smRNA) pathways involved in plant stress. In particular, we focused on miRNA-mediated PTGS in phosphate (Pi) starvation. The analysis was split into two research projects. First, to identify potential miRNA targets we began by analyzing the response and recovery of coding and long non-coding RNAs (lncRNA) to Pi starvation in shoot and root. The results obtained were the first genome-wide description of the root’s Pi starvation response and recovery. We found that the root's response involved a widely different set of genes than that of the shoot. In the second research project, the results of the first project were correlated with the responses of miRNA and trans-acting small-interfering RNA (tasiRNA) during Pi starvation. Many miRNA circuits have been predicted before, however, tasiRNA circuits are not as well defined. Therefore, we made use of the double-stranded RNA-binding protein 4 (DRB4) smRNA libraries to enhance our prediction of tasiRNAs. Altogether, we provided evidence to support the following miRNA-mRNA pairs that may function in Pi starvation: IPS1:miR399:PHO2; miR399:RS4; miR399:NF-YA10; miR398:CSD1/2; miR2111:TPS11; miR164:NAC6; miR157:TMO7; miR157:PSB28; RPS2:miR169:IPS2; miR397:LAC2; TAS4:PAP1; NR1:PAP1; and Chr3_1967672:TMO7. In general, we found that non-miR399 related circuits were active only during the root’s recovery from Pi starvation. The functional roles of the genes targeted by these PTGS circuits suggested that the local root response to Pi starvation was influenced by the plant's systemic response pathways via PHR1-mediated PTGS. Finally, since many PTGS targets function to modulate concentrations of reactive oxygen species and sucrose, we hypothesized that the candidate PTGS circuits found in our research mediate a general stress recovery process by modulating metabolites involved in signaling pathways.en
dc.language.isoenen
dc.subjectNon-coding RNAen
dc.subjectPlant stressen
dc.subjectPhosphate starvationen
dc.titleThe Role of Non-­Coding RNA in Plant Stressen
dc.typeDissertationen
dc.contributor.departmentBiological and Environmental Sciences and Engineering (BESE) Divisionen
thesis.degree.grantorKing Abdullah University of Science and Technologyen_GB
dc.contributor.committeememberChua, Nam-Haien
dc.contributor.committeememberFedoroff, Nina V.en
dc.contributor.committeememberMagistretti, Pierreen
thesis.degree.disciplineBioscienceen
thesis.degree.nameDoctor of Philosophyen
dc.person.id107204en
All Items in KAUST are protected by copyright, with all rights reserved, unless otherwise indicated.