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Title: Using cell type specific transcriptomics to understand how Arabidopsis roots respond to Sinorhizobium meliloti
Author: Hulsmans, Jo
ISNI:       0000 0004 6350 6041
Awarding Body: University of Warwick
Current Institution: University of Warwick
Date of Award: 2014
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Roots are key organs for the uptake of nutrients in plants. Leguminous plants form nodules, providing a niche for symbiotic nitrogen-fixing bacteria, enabling plants to colonize nitrogen depleted soils. Lateral root formation shares genetic regulation, as well as developmental features, with nodulation. This led us to investigate whether shared genetic control can be revealed in lateral root development responses of Arabidopsis thaliana to rhizobia. The phenotypic response of Arabidopsis to Sinorhizobium meliloti was analyzed. Arabidopsis lateral root length was found to be shorter, indicating a potential link between bacterial perception and lateral root development, even in a non symbiotic host plant. To gain more insight, a transcriptome time series was carried out. The response of Arabidopsis to Sinorhizobium inoculation compared to the response of nitrogen treatment were analyzed. In order to identify highly localized, yet important minimal regulatory cues and maximize the spatial specificity of the data, this analysis was carried out in isolated cortical and pericycle cells. Combined, in response to the two treatments approximately a 20% of the Arabidopsis genome is differentially expressed during the first 48 hours. Bioinformatic tools (clustering and network inference) were used to obtain a chronology of different responses, highlighting which metabolic processes change over time and identify potential gene regulatory mechanisms. The data and approach presented here present a unique analysis of the response to Sinorhizobium and nitrogen treatment and open the way to further tissue specific analysis of transcriptional regulation in plants. The similarities and differences between the response to Sinorhizobium (a potentially neutral bacteria) and Ralstonia (a pathogen of Arabidopsis roots) were evaluated using an analysis of gene expression at two early time points after inoculation. There was significant overlap in transcriptional response to both treatments, as well as striking differences: we find pathogen defense genes in the response to Sinorhizobium, rather than Ralstonia. We also find a core of 11 auxin responsive genes that have similar differential expression between treatments. Our results show that Rhizobium has a distinct transcriptional and phenotypic effect on Arabidopsis roots that is distinct from a pathogenic interaction. Several network hub genes are proposed as potential targets for further studying this effect.
Supervisor: Not available Sponsor: Not available
Qualification Name: Thesis (Ph.D.) Qualification Level: Doctoral
EThOS ID:  DOI: Not available
Keywords: SB Plant culture