Infection assays in Arabidopsis reveal candidate effectors from the poplar rust fungus that promote susceptibility to bacteria and oomycete pathogens H Germain, DL Joly, C Mireault, MB Plourde, C Letanneur, D Stewart, … Molecular Plant Pathology

Abstract

Fungi of the Pucciniales order cause rust diseases, which altogether affect thousands of plant species worldwide and pose major threat to several crops. How rust effectors – virulence proteins delivered into infected tissues to modulate host functions – contribute to pathogen virulence remains poorly understood. Melampsora larici-populina is a devastating and widespread rust pathogen of poplars and its genome encodes 1,184 identified small secreted proteins that could potentially act as effectors. Here, following specific criteria we selected 16 candidate effector proteins and characterized their virulence activities and subcellular localizations in the leaf cells of Arabidopsis thaliana. Infection assays using bacterial (Pseudomonas syringae) and oomycete (Hyaloperonospora arabidopsidis) pathogens revealed subsets of candidate effectors that enhanced or decreased pathogen leaf colonization. Confocal imaging of GFP-tagged candidate effectors constitutively expressed in stable transgenic plants revealed that some protein fusions specifically accumulate in nuclei, chloroplasts, plasmodesmata and punctate cytosolic structures. Altogether, our analysis suggests that rust fungal candidate effectors target distinct cellular components in host cells to promote parasitic growth

Fungal and plant gene expression in the Tulasnella calospora–Serapias vomeracea symbiosis provides clues about nitrogen pathways in orchid mycorrhizas V Fochi, W Chitarra, A Kohler, S Voyron, VR Singan, EA Lindquist, …New Phytologist

Summary

• Orchids are highly dependent on their mycorrhizal fungal partners for nutrient supply, especially during early developmental stages. In addition to organic carbon, nitrogen (N) is probably a major nutrient transferred to the plant because orchid tissues are highly N-enriched. We know almost nothing about the N form preferentially transferred to the plant or about the key molecular determinants required for N uptake and transfer.
• We identified, in the genome of the orchid mycorrhizal fungus Tulasnella calospora, two functional ammonium transporters and several amino acid transporters but found no evidence of a nitrate assimilation system, in agreement with the N preference of the free-living mycelium grown on different N sources.
• Differential expression in symbiosis of a repertoire of fungal and plant genes involved in the transport and metabolism of N compounds suggested that organic N may be the main form transferred to the orchid host and that ammonium is taken up by the intracellular fungus from the apoplatic symbiotic interface.
• This is the first study addressing the genetic determinants of N uptake and transport in orchid mycorrhizas, and provides a model for nutrient exchanges at the symbiotic interface, which may guide future experiments.

Genetic bases of fungal white rot wood decay predicted by phylogenomic analysis of correlated gene-phenotype evolution LG Nagy, R Riley, PJ Bergmann, K Krizsán, FM Martin, IV Grigoriev, … Molecular Biology and Evolution, msw238

Abstract

Fungal decomposition of plant cell walls (PCW) is a complex process that has diverse industrial applications and huge impacts on the carbon cycle. White rot (WR) is a powerful mode of PCW decay in which lignin and carbohydrates are both degraded. Mechanistic studies of decay coupled with comparative genomic analyses have provided clues to the enzymatic components of WR systems and their evolutionary origins, but the complete suite of genes necessary for WR remains undetermined. Here, we use phylogenomic comparative methods, which we validate through simulations, to identify shifts in gene family diversification rates that are correlated with evolution of WR, using data from 62 fungal genomes. We detected 409 gene families that appear to be evolutionarily correlated with WR. The identified gene families encode well-characterized decay enzymes, e.g., fungal class II peroxidases and cellobiohydrolases, and enzymes involved in import and detoxification pathways, as well as 73 gene families that have no functional annotation. 310 of the 409 identified gene families are present in the genome of the model WR fungus Phanerochaete chrysosporium and 192 of these (62%) have been shown to be upregulated under ligninolytic culture conditions, which corroborates the phylogeny-based functional inferences. These results illuminate the complexity of WR and suggest that its evolution has involved a general elaboration of the decay apparatus, including numerous gene families with as-yet unknown exact functions.

Dithiol disulphide exchange in redox regulation of chloroplast enzymes in response to evolutionary and structural constraints DD Gütle, T Roret, A Hecker, R Reski, JP Jacquot. Plant Science

Abstract

Redox regulation of chloroplast enzymes via disulphide reduction is believed to control the rates of CO₂ fixation. The study of the thioredoxin reduction pathways and of various target enzymes lead to the following guidelines:

i)

Thioredoxin gene content is greatly higher in photosynthetic eukaryotes compared to prokaryotes;

ii)

Thioredoxin-reducing pathways have expanded in photosynthetic eukaryotes with four different thioredoxin reductases and the possibility to reduce some thioredoxins via glutaredoxins;

iii)

Some enzymes that were thought to be strictly linked to photosynthesis ferredoxin-thioredoxin reductase, phosphoribulokinase, ribulose-1,5-bisphosphate carboxylase/oxygenase, sedoheptulose-1,7-bisphosphatase are present in non-photosynthetic organisms;

iv)

Photosynthetic eukaryotes contain a genetic patchwork of sequences borrowed from prokaryotes including α–proteobacteria and archaea;

v)

The introduction of redox regulatory sequences did not occur at the same place for all targets. Some possess critical cysteines in cyanobacteria, for others the transition occurred rather at the green algae level;

vi)

Generally the regulatory sites of the target enzymes are distally located from the catalytic sites. The cysteine residues are generally not involved in catalysis. Following reduction, molecular movements open the active sites and make catalysis possible;

vii)

The regulatory sequences are located on surface-accessible loops. At least one instance they can be cut out and serve as signal peptides for inducing plant defence.

Unearthing the roots of ectomycorrhizal symbioses F Martin, A Kohler, C Murat, C Veneault-Fourrey, DS Hibbett Nature Reviews Microbiology

Abstract

During the diversification of Fungi and the rise of conifer-dominated and angiosperm- dominated forests, mutualistic symbioses developed between certain trees and ectomycorrhizal fungi that enabled these trees to colonize boreal and temperate regions. The evolutionary success of these symbioses is evident from phylogenomic analyses that suggest that ectomycorrhizal fungi have arisen in approximately 60 independent saprotrophic lineages, which has led to the wide range of ectomycorrhizal associations that exist today. In this Review, we discuss recent genomic studies that have revealed the adaptations that seem to be fundamental to the convergent evolution of ectomycorrhizal fungi, including the loss of some metabolic functions and the acquisition of effectors that facilitate mutualistic interactions with host plants. Finally, we consider how these insights can be integrated into a model of the development of ectomycorrhizal symbioses.

Molecular Mycorrhizal symbiosis

Martin, Francis, ed. Molecular Mycorrhizal Symbiosis. John Wiley & Sons, 2016.

Dissecting the metabolic role of mitochondria during developmental leaf senescence D Chrobok, SR Law, B Brouwer, P Lindén, A Ziolkowska, D Liebsch, … Plant Physiology, pp. 01463.2016

Abstract

The functions of mitochondria during leaf senescence, a type of programmed cell death aiming at the massive retrieval of nutrients from the senescing organ to the rest of the plant, remain elusive. Here, combining experimental and analytical approaches, we showed that mitochondrial integrity is conserved until the latest stages of leaf senescence, while their number drops by 30%. Adenylate phosphorylation state assays and mitochondrial respiratory measurements indicated that the leaf energy status is also maintained during this time period. Further, after establishing a curated list of genes coding for products targeted to mitochondria, we analysed in isolation their transcript profiles, focusing on several key mitochondrial functions such as the tricarboxylic acid cycle, mitochondrial electron transfer chain, iron-sulphur cluster biosynthesis, transporters as well as catabolic pathways. In tandem with a metabolomic approach, our data indicated that mitochondrial metabolism was reorganised to support the selective catabolism of both amino- and fatty acids. Such adjustments would ensure the replenishment of α-ketoglutarate and glutamate, which provide the carbon backbones for nitrogen remobilisation. Glutamate, being the substrate of the strongly up-regulated cytosolic glutamine synthase, is likely to become a metabolically limiting factor in the latest stages of developmental leaf senescence. Finally, an evolutionary age analysis revealed that while branched-chain amino acid and proline catabolism are very old mitochondrial functions particularly enriched at the latest stages of leaf senescence, auxin metabolism appeared rather newly acquired. In summation, our work shows that during developmental leaf senescence, mitochondria orchestrate catabolic processes by becoming increasingly central energy and metabolic hubs.

Trapping truffle production in holes: a promising technique for improving production and unravelling truffle life cycle C Murat, L Bonneau, H De La Varga, JM Olivier, S Fizzala,.. Italian Journal of Mycology 45, 47-53

Abstract

The Périgord black truffle, Tuber melanosporum Vittad., is an ectomycorrhizal fungus that forms edible hypogeous ascomata. It is now harvested in plantations and is recognized as an agricultural product by European policy. Empirical techniques without scientific demonstration of their efficiency are often used to improve the production of truffles in plantations. One of these techniques is “truffle trapping” which consists in practicing holes inside the potential productive area and to fill them with a substrate containing ascospores. We report an experiment in a truffle orchard where 784 holes were set under 196 trees. Two years after the installation of the holes, 95% of the truffles were found inside the holes corresponding to only 5% of the productive area. This study confirms the efficiency of this empirical technique and demonstrates new ways for in situ studies of the truffle life cycle.

Ecology of the forest microbiome: Highlights of temperate and boreal ecosystems S Uroz, M Buée, A Deveau, S Mieszkin, F Martin. Soil Biology and Biochemistry 103, 471-488

Abstract

Due to land use history, most of the current temperate and boreal forests are developed on nutrient-poor and rocky soils, keeping fertile soils for agriculture. Consequently, the conditions occurring in forest ecosystems strongly differ from those of other terrestrial environments, giving importance to the access of nutritive elements and their recycling for the long-lasting development of forest ecosystems. In this review, we present an overview of the recent findings on the relationships between bacterial and fungal communities and their tree hosts at both the taxonomic and functional levels. We highlighted the common and different deterministic drivers of these microbial communities, focusing on the tree species effect, the different interfaces existing between the trees and their environment, the impact of tree by-products (decaying wood and litter), the impact of soil and seasonal changes, and lastly, the consequences of forestry practices. Depicting both taxonomic and functional diversity based on cultivation-dependent and -independent analyses, we highlight the distribution patterns and the functional traits characterizing bacterial and fungal communities. We also discuss the importance of bridging environmental microbiology to genomics and how to integrate the interactions between microorganisms for a better understanding of tree growth and health.

Crystal Structure of Saccharomyces cerevisiae ECM4, a Xi-Class Glutathione Transferase that Reacts with Glutathionyl-(hydro) quinones M Schwartz, C Didierjean, A Hecker, JM Girardet, M Morel-Rouhier, … PLOS ONE 11 (10), e0164678

Abstract

Glutathionyl-hydroquinone reductases (GHRs) belong to the recently characterized Xi-class of glutathione transferases (GSTXs) according to unique structural properties and are present in all but animal kingdoms. The GHR ScECM4 from the yeast Saccharomyces cerevisiae has been studied since 1997 when it was found to be potentially involved in cell-wall biosynthesis. Up to now and in spite of biological studies made on this enzyme, its physiological role remains challenging. The work here reports its crystallographic study. In addition to exhibiting the general GSTX structural features, ScECM4 shows extensions including a huge loop which contributes to the quaternary assembly. These structural extensions are probably specific to Saccharomycetaceae. Soaking of ScECM4 crystals with GS-menadione results in a structure where glutathione forms a mixed disulfide bond with the cysteine 46. Solution studies confirm that ScECM4 has reductase activity for GS-menadione in presence of glutathione. Moreover, the high resolution structures allowed us to propose new roles of conserved residues of the active site to assist the cysteine 46 during the catalytic act.