Functional genomic studies of novel players in innate immunity and classification of promoter activation patterns of the AtPROPEP genes and their corresponding receptors in the model plant : "arabidopsis thaliana"

The first layer of innate immunity in plants is initiated through the perception of microbe-associated molecular patterns (MAMPs) or damage-associated molecular patterns (DAMPs) by pattern recognition receptors. MAMP/DAMP perception initiates downstream defense responses, a process which ultimately leads to pattern triggered immunity, as reviewed in the first chapter of this thesis. In the second chapter of this thesis, based on a deep-sequencing expression profiling approach, a number of hitherto overlooked genes have been identified that are induced in wild type Arabidopsis seedlings upon treatment with both the MAMP, flg22, and the DAMP, AtPep1. This implies the possible involvement of the corresponding gene products in innate immunity. Four of them, named PP2-B13, ACLP1, SERP1 and GRP89, respectively, were studied in more detail. Homozygous mutant lines for the genes encoding these proteins were obtained and analyzed. The mutants pp2-b13, aclp1, serp1 and grp89 exhibited an increased susceptibility to infection by the virulent pathogen P. syringae pv. tomato DC3000 and also by its avirulent hrcC mutant. Furthermore, it was observed that the aclp1 mutant was deficient in ethylene production upon flg22 treatment, while the mutants pp2-b13, serp1 and grp89 were deficient in reactive oxygen species production. As mentioned, in addition to MAMPs, plants can sense and recognize DAMPs, i.e. endogenous elicitors which activate the immune system in response to biotic and also abiotic stimuli. So far, eight peptides have been described as DAMPs or endogenous danger peptides in Arabidopsis thaliana, named AtPeps1-8. These peptides are derived from precursor proteins called the AtPROPEPs. The leucine-rich-repeat receptor kinases, AtPEPR1 and AtPEPR2, act as the receptors for the AtPep peptides. In the third chapter of this thesis, promoter-GUS reporter constructs were used to study the expression pattern of the genes encoding the AtPROPEPs as well as the AtPEPRs under biotic and abiotic stress, including AtPep1, flg22, Methyl jasmonate, and NaCl treatments. We found that the genes for the two AtPEPR receptors were differentially regulated in response to MAMPs (flg22) and DAMPs (AtPEP1). In addition, we showed that the activation pattern of the genes encoding the eight AtPROPEPs was totally different, despite the similarity of the members of the Pep family. This allowed us to classify the activity of the AtPROPEP promoters, based on their differential response to biotic and abiotic stimuli