Expanding Genomics of Mycorrhizal Symbiosis

Abstract

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant and soil health, and carbon and nutrient cycles. The symbiosis evolved repeatedly and independently as multiple morphological types (e.g. arbuscular [AM], ectomycorrhizal [ECM]) in multiple fungal clades (e.g. phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and culturability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first 3 mycorrhizal fungal genomes, representing 3 fungal phyla and 2 mycorrhizal types. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant-degrading enzymes (PDEs) and expansion of lineage-specific gene families, including short secreted protein (SSP) effectors and other symbiosis genes. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of gene families in contrast to Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other 2 fungi, the symbiosis can involve similar solutions as loss of PDEs and mycorrhiza-induced SSPs. The mycorrhizal community is building on these studies with 3 large-scale initiatives. The Mycorrhizal Genomics Initiative (MGI) is sequencing 35 genomes of multiple fungal clades and mycorrhizal types for phylogenomic and population analyses. 17 MGI species whose symbiosis is reconstitutable in vitro are targeted for comprehensive transcriptomics of mycorrhiza formation. MGI genomes are seeding a set of 50+ reference fungal genomes for annotating metatranscriptomes sampled from 7 diverse well-described soil sites. These 3 projects address fundamental questions about the nature and role of a vital mutualism.

The roles of glutaredoxins ligating Fe-S clusters: Sensing, transfer or repair functions?

J Couturier, J Przybyla-Toscano, T Roret, C Didierjean, N Rouhier

Biochimica et Biophysica Acta (BBA)-Molecular Cell Research

Abstract

Glutaredoxins (Grxs) are major oxidoreductases involved in the reduction of glutathionylated proteins. Owing to the capacity of several class I Grxs and likely all class II Grxs to incorporate iron–sulfur (Fe–S) clusters, they are also linked to iron metabolism. Most Grxs bind [2Fe–2S] clusters which are oxidatively- and reductively-labile and have identical ligation, involving notably external glutathione. However, subtle differences in the structural organization explain that class II Fe–S Grxs, having more labile and solvent-exposed clusters, can accept Fe–S clusters and transfer them to client proteins, whereas class I Fe–S Grxs usually do not. From the observed glutathione disulfide-mediated Fe–S cluster degradation, the current view is that the more stable Fe–S clusters found in class I Fe–S Grxs might constitute a sensor of oxidative stress conditions by modulating their activity. Indeed, in response to an oxidative signal, inactive holoforms i.e., without disulfide reductase activity, should be converted to active apoforms. Among class II Fe–S Grxs, monodomain Grxs likely serve as carrier proteins for the delivery of preassembled Fe–S clusters to acceptor proteins in organelles. Another proposed function is the repair of Fe–S clusters. From their cytoplasmic and/or nuclear localization, multidomain Grxs function in signalling pathways. In particular, they regulate iron homeostasis in yeast species by modulating the activity of transcription factors and eventually forming heterocomplexes with BolA-like proteins in response to the cellular iron status. We provide an overview of the biochemical and structural properties of Fe–S cluster-loaded Grxs in relation to their hypothetical or confirmed associated functions. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.

OmGOGAT disruption in the ericoid mycorrhizal fungus Oidiodendron maius induces reorganization of the N pathway and reduces tolerance to heavy-metals. HR Khouja, S Daghino, S Abbà, F Boutaraa, M Chalot, D Blaudez, …Fungal Genetics and Biology

Abstract

Mycorrhizal fungi are key mediators of soil-to-plant movement of mineral nutrients, including essential and non-essential metals. In soil conditions that facilitate mobilization of metal ions, potentially toxic metals can interfere with nitrogen metabolism in both plants and microorganisms. Less is known about possible relationships between nitrogen metabolism and responses to heavy metals. Aim of this study was to investigate this aspect in the ericoid mycorrhizal fungus Oidiodendron maius strain Zn, a metal tolerant ascomycete. Growth of O. maius Zn on zinc and cadmium containing media was significantly affected by the nitrogen source. Screening of a library of O. maius Zn random genetic transformants for sensitivity to heavy metals (zinc and cadmium) and oxidative stress (menadione) yielded a mutant strain that carried a partial deletion of the glutamate synthase (NADH-GOGAT EC 1.4.1.14) gene and its adjacent gene, the APC15subunit of the anaphase promoting complex. Comparison of WT and OmGOGAT-OmAPC15 mutant strains indicated an impaired N-metabolism and altered stress tolerance, and assays on the OmAPC15-recomplemented strains ascribed the observed phenotypes to the deletion in the OmGOGAT gene.OmGOGAT disruption modified the nitrogen pathway, with a strong reduction of the associated glutamine synthetase (GS, EC 6.3.1.2) activity and an up-regulation of the alternative NADP-glutamate dehydrogenase (NADP-GDH, EC 1.4.1.4) pathway for glutamate biosynthesis. Unless they were supplemented with glutamine, O. maius Zn transformants lacking OmGOGAT were very sensitive to zinc. These results highlight the importance of nitrogen metabolism not only for nitrogen assimilation and transformation, but also for stress tolerance. For mycorrhizal fungi, such as O. maius, this may bear consequences not only to the fungus, but also to the host plant.

X-ray structures of Nfs2, the plastidial cysteine desulfurase from Arabidopsis thaliana

Abstract:

The chloroplastic Arabidopsis thaliana Nfs2 (AtNfs2) is a group II pyridoxal 5′-phosphate-dependent cysteine desulfurase that is involved in the initial steps of iron-sulfur cluster biogenesis. The group II cysteine desulfurases require the presence of sulfurtransferases such as SufE proteins for optimal activity. Compared with group I cysteine desulfurases, proteins of this group contains a smaller extended lobe harbouring the catalytic cysteine and have a -hairpin constraining the active site. Here, two crystal structures of AtNfs2 are reported: a wild-type form with the catalytic cysteine in a persulfide-intermediate state and a C384S variant mimicking the resting state of the enzyme. In both structures the well conserved Lys241 covalently binds pyridoxal 5′-phosphate, forming an internal aldimine. Based on available homologous bacterial complexes, a model of a complex between AtNfs2 and the SufE domain of its biological partner AtSufE1 is proposed, revealing the nature of the binding sites.

Genomic and transcriptomic analysis of Laccaria bicolor CAZome reveals insights into polysaccharides remodelling during symbiosis establishment C Veneault-Fourrey, C Commun, A Kohler, E Morin, R Balestrini, J Plett, …

Genome-wide patterns of segregation and linkage disequilibrium: the construction of a linkage genetic map of the poplar rust fungus Melampsora larici-populina

Patterns of genomic variation in the poplar rust fungus Melampsora larici-populina identify pathogenesis-related factors A Persoons, E Morin, C Delaruelle, T Payen, F Halkett, P Frey, S De Mita, … Plant-Microbe Interaction 5, 450

The still mysterious roles of cysteine-containing glutathione transferases in plants
P Lallement, B Brouwer, O Keech, A Hecker, N Rouhier
Experimental Pharmacology and Drug Discovery 5, 192

Abstract

Glutathione transferases (GSTs) represent a widespread multigenic enzyme family able to modify a broad range of molecules. These notably include secondary metabolites and exogenous substrates often referred to as xenobiotics, usually for their detoxification, subsequent transport or export. To achieve this, these enzymes can bind non-substrate ligands (ligandin function) and/or catalyze the conjugation of glutathione onto the targeted molecules, the latter activity being exhibited by GSTs having a serine or a tyrosine as catalytic residues. Besides, other GST members possess a catalytic cysteine residue, a substitution that radically changes enzyme properties. Instead of promoting GSH-conjugation reactions, cysteine-containing GSTs (Cys-GSTs) are able to perform deglutathionylation reactions similarly to glutaredoxins but the targets are usually different since glutaredoxin substrates are mostly oxidized proteins and Cys-GST substrates are metabolites. The Cys-GSTs are found in most organisms and form several classes. While Beta and Omega GSTs and chloride intracellular channel proteins (CLICs) are not found in plants, these organisms possess microsomal ProstaGlandin E-Synthase type 2, glutathionyl hydroquinone reductases, Lambda, Iota and Hemerythrin GSTs and dehydroascorbate reductases (DHARs); the four last classes being restricted to the green lineage. In plants, whereas the role of DHARs is clearly associated to the reduction of dehydroascorbate to ascorbate, the physiological roles of other Cys-GSTs remain largely unknown. In this context, a genomic and phylogenetic analysis of Cys-GSTs in photosynthetic organisms provides an updated classification that is discussed in the light of the recent literature about the functional and structural properties of Cys-GSTs. Considering the antioxidant potencies of phenolic compounds and more generally of secondary metabolites, the connection of GSTs with secondary metabolism may be interesting from a pharmacological perspective.

Transcriptomic responses of Phanerochaete chrysosporium to oak acetonic extracts: focus on a new glutathione transferase. A Thuillier, K Chibani, G Belli, E Herrero, S Dumarçay, P Gérardin, … Applied and Environmental Microbiology, AEM. 02103-14

Abstract

The first steps of wood degradation by fungi lead to the release of toxic compounds known as extractives. To better understand how lignolytic fungi cope with the toxicity of these molecules, a transcriptomic analysis of Phanerochaete chrysosporium genes was performed in presence of oak acetonic extracts. It reveals that in complement to the extracellular machinery of degradation, intracellular antioxidant and detoxification systems contribute to the lignolytic capabilities of fungi presumably by preventing cellular damages and maintaining fungal health. Focusing on these systems, a glutathione transferase (PcGTT2.1) has been selected for functional characterization. This enzyme, not characterized so far in basidiomycetes, has been first classified as a GTT2 in comparison to theSaccharomyces cerevisiae isoform. However, a deeper analysis shows that GTT2.1 isoform has functionally evolved to reduce lipid peroxidation by recognizing high-molecular weight peroxides as substrates. Moreover, the GTT2.1 gene has been lost in some non-wood decay fungi. This example suggests that the intracellular detoxification system could have evolved concomitantly with the extracellular ligninolytic machinery in relation to the capacity of fungi to degrade wood.

The black truffle methylome: non-exhaustive DNA methylation-mediated transposon silencing in a complex fungal genome with massive repeat element content B Montanini, PY Chen, M Morselli, A Jaroszewicz, D Lopez, F Martin, … Genome Biology 15 (7), 411

Abstract