A novel bioinformatics pipeline to discover genes related to arbuscular mycorrhizal symbiosis based on their evolutionary conservation pattern among higher plants

Genes involved in arbuscular mycorrhizal (AM) symbiosis have been identified primarily by mutant screens, followed by identification of the mutated genes (forward genetics). In addition, a number of AM-related genes has been identified by their AM-related expression patterns, and their function has subsequently been elucidated by knock-down or knock-out approaches (reverse genetics). However, genes that are members of functionally redundant gene families, or genes that have a vital function and therefore result in lethal mutant phenotypes, are difficult to identify. If such genes are constitutively expressed and therefore escape differential expression analyses, they remain elusive. The goal of this study was to systematically search for AM-related genes with a bioinformatics strategy that is insensitive to these problems. The central element of our approach is based on the fact that many AM-related genes are conserved only among AM-competent species.Results: Our approach involves genome-wide comparisons at the proteome level of AM-competent host species with non-mycorrhizal species. Using a clustering method we first established orthologous/paralogous relationships and subsequently identified protein clusters that contain members only of the AM-competent species. Proteins of these clusters were then analyzed in an extended set of 16 plant species and ranked based on their relatedness among AM-competent monocot and dicot species, relative to non-mycorrhizal species. In addition, we combined the information on the protein-coding sequence with gene expression data and with promoter analysis. As a result we present a list of yet uncharacterized proteins that show a strongly AM-related pattern of sequence conservation, indicating that the respective genes may have been under selection for a function in AM. Among the top candidates are three genes that encode a small family of similar receptor-like kinases that are related to the S-locus receptor kinases involved in sporophytic self-incompatibility.Conclusions: We present a new systematic strategy of gene discovery based on conservation of the protein-coding sequence that complements classical forward and reverse genetics. This strategy can be applied to diverse other biological phenomena if species with established genome sequences fall into distinguished groups that differ in a defined functional trait of interest

A petunia GRAS transcription factor controls symbiotic gene expression and fungal morphogenesis in arbuscular mycorrhiza

Arbuscular mycorrhiza (AM) is a mutual symbiosis that involves a complex symbiotic interface over which nutrients are exchanged between the plant host and the AM fungus. Dozens of genes in the host are required for the establishment and functioning of the interaction, among them nutrient transporters that mediate the uptake of mineral nutrients delivered by the fungal arbuscules. We have isolated in a genetic mutant screen a petunia GRAS-type transcription factor, ATYPICAL ARBUSCULE (ATA), that acts as the central regulator of AM-related genes and is required for the morphogenesis of arbuscules. Forced mycorrhizal inoculations from neighbouring wild type plants revealed an additional role of ATA in restricting mycorrhizal colonization of the root meristem. The lack of ATA, which represents the orthologue of RAM1 in Medicago truncatula, renders the interaction completely ineffective, hence demonstrating the central role of AM-related genes for arbuscule development and function

VAPYRIN Marks an endosomal trafficking compartment involved in arbuscular mycorrhizal symbiosis

Arbuscular mycorrhiza (AM) is a symbiosis between plants and AM fungi that requires the intracellular accommodation of the fungal partner in the host. For reciprocal nutrient exchange, AM fungi form intracellular arbuscules that are surrounded by the peri-arbuscular membrane. This membrane, together with the fungal plasma membrane, and the space in between, constitute the symbiotic interface, over which nutrients are exchanged. Intracellular establishment of AM fungi requires the VAPYRIN protein which is induced in colonized cells, and which localizes to numerous small mobile structures of unknown identity (Vapyrin-bodies). In order to characterize the identity and function of the Vapyrin-bodies we pursued a dual strategy. First, we co-expressed fluorescently tagged VAPYRIN with a range of subcellular marker proteins, and secondly, we employed biochemical tools to identify interacting partner proteins of VAPYRIN. As an important tool for the quantitative analysis of confocal microscopic data sets from co-expression of fluorescent proteins, we developed a semi-automated image analysis pipeline that allows for precise spatio-temporal quantification of protein co-localization and of the dynamics of organelle association from movies. Taken together, these experiments revealed that Vapyrin-bodies have an endosomal identity with trans-Golgi features, and that VAPYRIN interacts with a symbiotic R-SNARE of the VAMP721 family, that localizes to the same compartment

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The current assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n=14) containing 32,928 and 36,697 protein-coding genes, respectively. The Petunia lineage has experienced at least two rounds of paleohexaploidization, the older gamma hexaploidy event, which is shared with other Eudicots, and the more recent Solanaceae paleohexaploidy event that is shared with tomato and other Solanaceae species. Transcription factors that were targets of selection during the shift from bee- to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral color patterns and pollination systems. The high quality genome sequences will enhance the value of Petunia as a model system for basic and applied research on a variety of unique biological phenomena

Insight into the evolution of the Solanaceae from the parental genomes of Petunia hybrida

Petunia hybrida is a popular bedding plant that has a long history as a genetic model system. We report the whole-genome sequencing and assembly of inbred derivatives of its two wild parents, P. axillaris N and P. inflata S6. The assemblies include 91.3% and 90.2% coverage of their diploid genomes (1.4 Gb; 2n = 14) containing 32,928 and 36,697 protein-coding genes, respectively. The genomes reveal that the Petunia lineage has experienced at least two rounds of hexaploidization: the older gamma event, which is shared with most Eudicots, and a more recent Solanaceae event that is shared with tomato and other solanaceous species. Transcription factors involved in the shift from bee to moth pollination reside in particularly dynamic regions of the genome, which may have been key to the remarkable diversity of floral colour patterns and pollination systems. The high-quality genome sequences will enhance the value of Petunia as a model system for research on unique biological phenomena such as small RNAs, symbiosis, self-incompatibility and circadian rhythms

Traitement et design des interfaces au sein des cellules solaires à base de pérovskites

Perovskite (HaP) solar cells are one of the emerging technologies of the last decade thanks to their expedient optoelectrical properties, low-cost materials, and a large range of applications, reaching 25.8% of PCE in 2023 However, PSCs suffer significantly from their instability caused mainly by the interface mismatch as the device is a heterojunction solar cell coupled with ion migration and subject to extrinsic factors like humidity or temperature. The main focus of my thesis was the interface design of the halide perovskite solar cell in NIP configuration through interface passivation. The main objective of my PhD thesis follows my work during my internship, which was to improve the stability of PSCs by protecting the sensitive layers in the device against humidity, and to increase the performance by reducing charge recombination at the interfaces. I attacked this objective from several angles during my thesis, from device fabrication to their full characterization. In my first project, we worked with adamantane and its derivatives, 1-adamantanamine and 1-adamantanamine hydrochloride. These molecules are hydrophobic. We wanted to produce a protective layer against humidity and possible favorable passivation. We successfully deposit a protective layer at the interface HaP/HTL, preserving HaP for a short-term period with 1ADAHCl. We did not observe an improvement in performance with as TiO2 an ETL. My second project was pursued in collaboration with ITODYS to develop aminocarboxylic acids and amidinocarboxylics acids as SAMs to improve the interface ETL/HaP. In the end, the SAM 4'- amidino -[1,1'-biphenyl]-4-carboxylic acid hydroiodide presented the highest performances compared to the other molecules as its specific docking groups help to promote perovskite film deposition. I pursued my third project with an intern, that I supervised, with the introduction of bilayer passivation of PSCs using the organic molecular layers PMMA and PCBM. The PMMA-only solution is optimized at 5 mg/mL at the interface HaP/HTL, whereas PMMA:PCBM was used at the interface ETL/HaP. In the end, surprisingly, the PMMA:PCBM did not play a favorable role in our configuration as it acted as a blocking layer.Les cellules solaires à pérovskite (HaPSC) sont l'une des technologies émergentes de la dernière décennie grâce à leurs propriétés optoélectriques opportunes, leurs matériaux à faible coût et une large gamme d'applications, atteignant 25,8% en 2023. Cependant, les PSC souffrent considérablement de leur instabilité dû a des facterus externes, comme l’humidité ou la température, et internes, comme les défauts d’interface conséquence du dispositif en hétérojuntion. L'objectif principal de ma thèse était d'améliorer la stabilité des PSC en protégeant les couches sensibles du dispositif contre l'humidité, et d'augmenter les performances en réduisant la recombinaison de charge aux interfaces. J'ai abordé cet objectif sous plusieurs angles au cours de ma thèse, de la fabrication des dispositifs à leur caractérisation complète. Dans mon premier projet, j’ai travaillé avec l'adamantane et ses dérivés, la 1-adamantanamine et l’1-adamantanamine hydrochlorydrate. Ces molécules étant hydrophobes, je voulais réaliser une couche protectrice contre humidité et éventuellement passivante, déposée à l’interface pérovskite (HaP)/HTL. Une préservation de la HaP est obtenu pendant une courte période avec 1ADAHCl. Nous n'avons pas observé d'amélioration des performances avec comme TiO2 un ETL. Mon deuxième projet était en collaboration avec ITODYSsur le développement d'acides aminocarboxyliques et d'acides amidinocarboxyliques comme couche de molécules auto-assemblées (SAM), afin d’améliorer l’interface ETL/HaP. Au final, sur 7 SAMs, l'iodhydrate d'acide 4'-amidino-[1,1'-biphényl]-4-carboxylique a présenté les performances les plus élevées grâce à ses groupes d'amarrage spécifiques favorisant le dépôt du film de pérovskite. J'ai poursuivi mon troisième projet avec mon stagiaire, avec l'introduction de la passivation en sandwich en utilisant du PMMA et PCBM. La solution PMMA est optimisée à 5 mg/mL à l'interface HaP/HTL, alors que PMMA:PCBM a été utilisé à l'interface ETL/HaP. Au final, nous constatons qu'étonnamment le PMMA:PCBM n'a pas joué un rôle favorable dans notre configuration car il agissait comme une couche bloquante à l’interface

How membranes shape plant symbioses: signaling and transport in nodulation and arbuscular mycorrhiza

As sessile organisms that cannot evade adverse environmental conditions, plants have evolved various adaptive strategies to cope with environmental stresses. One of the most successful adaptations is the formation of symbiotic associations with beneficial microbes. In these mutualistic interactions the partners exchange essential nutrients and improve their resistance to biotic and abiotic stresses. In arbuscular mycorrhiza (AM) and in root nodule symbiosis (RNS), AM fungi and rhizobia, respectively, penetrate roots and accommodate within the cells of the plant host. In these endosymbiotic associations, both partners keep their plasma membranes intact and use them to control the bidirectional exchange of signaling molecules and nutrients. Intracellular accommodation requires the exchange of symbiotic signals and the reprogramming of both interacting partners. This involves fundamental changes at the level of gene expression and of the cytoskeleton, as well as of organelles such as plastids, endoplasmic reticulum (ER), and the central vacuole. Symbiotic cells are highly compartmentalized and have a complex membrane system specialized for the diverse functions in molecular communication and nutrient exchange. Here, we discuss the roles of the different cellular membrane systems and their symbiosis-related proteins in AM and RNS, and we review recent progress in the analysis of membrane proteins involved in endosymbiosis