Role of the Nodule Inception promoter in the evolutionary gain of the nitrogen-fixing root nodule symbiosis

Cathebras, Chloé (2022): Role of the Nodule Inception promoter in the evolutionary gain of the nitrogen-fixing root nodule symbiosis. Dissertation, LMU München: Fakultät für Biologie

Abstract

To overcome nutrient limitations, plants engage in two main types of root endosymbioses with beneficial microbes. Arbuscular mycorrhiza (AM) is an ancient symbiosis formed by about 70-90 % of land plants and phosphate-acquiring fungi of the phylum Glomeromycota. By contrast, root nodule symbiosis (RNS) with nitrogen-fixing bacteria is evolutionary much younger and is phylogenetically restricted to a single clade of flowering plants comprising only four orders, the Fabales, Fagales, Cucurbitales and Rosales (FaFaCuRo). AM and RNS require a common set of plant genes – the common symbiosis genes – and it is believed that genes that evolved for AM development have been recruited during the evolution of RNS to enable intracellular uptake and accommodation of bacteria. Moreover, RNS is characterised by the formation of a novel organ, the root nodule, and it was hypothesised that part of the lateral root (LR) developmental program was co-opted for nodule formation. The restricted occurrence of RNS calls for yet unidentified trait acquisitions and genetic changes in the last common ancestor of the FaFaCuRo clade. Using a phylogenomic approach, a cis-regulatory element (PACE) was discovered to be exclusively present in the promoter of the transcription factor gene Nodule Inception (NIN) of FaFaCuRo member species. NIN is positioned at the top of a RNS-specific transcriptional regulatory cascade and is indispensable for RNS. We found that PACE is essential for restoring infection threads (ITs) in Lotus japonicus nin mutants. PACE sequence variants from RNS-competent species appear functionally equivalent. Evolutionary loss or mutation of PACE is associated with loss of this symbiosis. PACE dictates gene expression in cortical cells forming IT and PACE-driven NIN expression restores the formation of cortical ITs, also when engineered into the NIN promoter of tomato. Our data pinpoint PACE as a key evolutionary invention that connected NIN to a pre-existing signal transduction cascade that governs the intracellular accommodation of AM fungi. This connection enabled bacterial uptake into plant cells via ITs, a unique and unifying feature of this symbiosis. Symbiosis signalling and LR development are tightly interconnected and treatment with lipochito-oligosaccharide molecules produced by AM fungi and rhizobia induce LR formation. To gain insight into the molecular players that connect these two distinct signalling programs, we studied the role of three common symbiosis genes Symbiosis Receptor Kinase (SymRK), Calcium Calmodulin-dependent kinase (CCaMK) and Cyclops, and of NIN in the formation of LRs. We reported that deregulated versions of SymRK, CCaMK, and Cyclops significantly increase the number of LRs in L. japonicus in a NIN-dependent manner and that ectopic expression of NIN likewise results in a significant increase in LR numbers. Additionally, NIN is necessary for LR induction mediated by both AM fungi and rhizobia bacteria. Our data reveal NIN as a key ranscriptional regulator that does not only employ parts of the LR evelopmental program for nodule organogenesis but also directly activates the development of LRs in a symbiotic context. Taken together, our data underpin the essential role of NIN in the evolutionary gain of RNS.

• Dokumententyp: Dissertationen (Dissertation, LMU München)
• Themengebiete: 500 Naturwissenschaften und Mathematik ; 500 Naturwissenschaften und Mathematik > 570 Biowissenschaften, Biologie
• Fakultäten: Fakultät für Biologie
• Sprache der Hochschulschrift: Englisch
• Datum der mündlichen Prüfung: 4. Oktober 2022
• 1. Bericht­erstatter:in: Parniske, Martin