The role of FHY3 and FAR1 in plant-microbial interaction in Arabidopsis thaliana

Research output: ThesisDoctoral Thesis

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The transposase-derived transcription factors FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and FAR-RED IMPAIRED RESPONSE 1 (FAR1) hold multifunctional roles in A. thaliana, such as in resetting the circadian clock, flowering and chloroplast division. This thesis aimed to investigate the cause of extensive leaf-lesion formation observed in fhy3 far1 mutants, reminiscent of the programmed cell death (PCD) associated with plant defence responses.
Global gene expression analysis suggested a constitutively activated defence response in
fhy3 far1 mutants causing the mutant’s leaf-lesions. However, defence marker gene expression associated with Salicylic Acid (SA)- and Jasmonic Acid (JA)/Ethylene (ET)-signalling, the two groups of signalling compounds that mediate defence response, was downregulated at the same time. Analysis of transcriptional changes upon biotic challenges suggested that this was the result of negative regulatory feedback in fhy3 far1 mutants.
A microarray analysis of key differentially expressed genes in fhy3 far1 mutants revealed an upregulation of the pro-PCD gene CYSTEINE-RICH RECEPTOR-LIKE PROTEIN KINASE 13 (CRK13) and a downregulation of the PCD-inhibiting METACASPASE 2 (MC2). The function of CRK13 and MC2 in PCD suggested that their misregulation in fhy3 far1 mutants could be part of the primary reason for increased leaf-lesion formation in double mutant plants. Transcriptional analysis of responses to biotic challenges in MC2 and CRK13 misexpression lines, however, revealed little similarity to the responses seen in fhy3 far1 mutants.
A constitutively activated defence response infers alterations of the associated microbiota. Initial investigations indicated that the fhy3 far1 mutant plant‘s phenotypical changes of extended leaf-lesion formation will be very likely to affect the phyllosphere, which prompted a next generation sequencing investigation of the phyllospheric microbiota. Its composition showed greatly increased species richness and a more even spectrum of abundances of bacterial species in fhy3 far1, a pattern that is commonly associated with continuing environmental disruption. The WT phyllosphere showed a stronger domination by a few species that were associated with the production of antimicrobials. In addition, the fungal community in fhy3 far1 mutant plants contained more pathogenic fungi in comparison to more saprotrophic fungi in WT. These findings support the suggestion that pathogen-protective properties of beneficial microbes in the phyllosphere are a community characteristic linked to microbial competition.
Original languageEnglish
Awarding Institution
  • Royal Holloway, University of London
  • Devlin, Paul, Supervisor
  • Gange, Alan, Advisor
Award date1 Oct 2017
Publication statusUnpublished - 2017


  • Arabidopsis, defence response, microbes

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