Article: FEBS letters

Trametes versicolor Glutathione Transferase Xi 3, a dual Cys‐GST with catalytic specificities of both Xi and Omega classes M Schwartz, T Perrot, A Deroy, T Roret, M Morel‐Rouhier, G Mulliert, … FEBS letters

Abstract

Glutathione transferases (GSTs) from the Xi and Omega classes have a catalytic cysteine residue, which gives them reductase activities. Until now, they have been assigned distinct substrates. While Xi GSTs specifically reduce glutathionyl‐(hydro)quinones, Omega GSTs are specialized in the reduction of glutathionyl‐acetophenones. Here, we present the biochemical and structural analysis of TvGSTX1 and TvGSTX3 isoforms from the wood‐degrading fungus Trametes versicolor. TvGSTX1 reduces GS‐menadione as expected, while TvGSTX3 reduces both Xi and Omega substrates. An in‐depth structural analysis indicates a broader active site for TvGSTX3 due to specific differences in the nature of the residues situated in the C‐terminal helix α9. This feature could explain the catalytic duality of TvGSTX3. Based on phylogenetic analysis, we propose that this duality might exist in saprophytic fungi and ascomycetes.

Article: Applied and environmental microbiology

Multi-omic analyses of extensively decayed Pinus contorta reveal expression of diverse array of lignocellulose degrading enzymes C Hori, J Gaskell, D Cullen, G Sabat, PE Stewart, K Lail, Y Peng, K Barry, … Applied and environmental microbiology, AEM. 01133-18

ABSTRACT

Fungi play a key role cycling nutrients in forest ecosystems but the mechanisms remain uncertain. To clarify the enzymatic processes involved in wood decomposition, metatranscriptomics and metaproteomics of extensively decayed lodgepole pine were examined by RNAseq and LC-MS/MS, respectively. Following de novo metatranscriptome assembly, 52,011 contigs were searched for functional domains and homology to database entries. Contigs similar to to basidiomycete transcripts dominated and many of these were most closely related to ligninolytic white rot fungi or cellulolytic brown rot fungi. A diverse array of carbohydrate active enzymes (CAzymes) representing a total of 132 families or subfamilies were identified. Among these were 672 glycoside hydrolases including highly expressed cellulases or hemicellulases. The CAzymes also included 162 genes encoding redox enzymes classified within Auxiliary Activity (AA) families. Eighteen of these were manganese peroxidases, key components of ligninolytic white rot fungi. Expression of other redox enzymes supported the working of hydroquinone reduction cycles capable of generating reactive hydroxyl radical. The latter has been implicated as a diffusible oxidant responsible for cellulose depolymerization by brown rot fungi. Thus, enzyme diversity and the coexistence of brown and white rot fungi suggest complex interactions of fungal species and degradative strategies during the decay of logdepole pine.

Article: Journal of soil science

Tree genotype and seasonal effects on soil properties and biogeochemical functioning in Mediterranean pine forests. L Pérez‐Izquierdo, L Saint‐André, P Santenoise… – European Journal of Soil Science

Summary

In forests, intraspecific genetic variation in trees can affect the entire ecosystem, which in turn, depends on the different processes occurring through space and time in soil. We hypothesized that, in addition to the effect of the local site, tree genotype and season would have an effect on the properties and functions of the edaphic environment. We studied soils beneath different genotypes of Pinus pinaster Ait. (Atlantic, Mediterranean and African) in 45‐year old common gardens in spring and autumn. The pH, organic matter, nutrients and infrared spectroscopy together with enzyme activities were determined and used to evaluate the soil properties and biogeochemical functioning. In addition to strong site effects, tree genotype and seasonal effects were detected on soil properties and functions. Both were major controlling factors of microbially mediated functioning, especially processes related to the carbon (C) and nitrogen (N) cycles. In general, the soil environment beneath the Atlantic trees was different from that under the Mediterranean and African genotypes, with differences in raw infrared spectra and increased activities of enzymes involved in hemicellulose degradation and N mobilization. Regarding the season, the largest soil humidity (RH), electric conductivity (EC), and N and potassium (K) concentrations, coupled with the smallest phosphorus (P) concentration and C:N ratios were detected in autumn. Degradation of C peaked in autumn, while P and N mobilization usually peaked in spring. Our results showed that, beyond local site effects, there were detectable effects of tree genotype and season in Mediterranean forest soils, which governed microbially mediated processes that might have relevant functional consequences at the ecosystem level.

Article: Genome Announcements

Draft Genome Sequence of Tuber borchii Vittad., a Whitish Edible Truffle C Murat, A Kuo, KW Barry, A Clum, RB Dockter, L Fauchery, M Iotti, … Genome Announcements 6 (25), e00537-18

A B S T R A C T

The ascomycete Tuber borchii (Pezizomycetes) is a whitish edible truffle that establishes ectomycorrhizal symbiosis with trees and shrubs. This fungus is ubiqui- tous in Europe and is also cultivated outside Europe. Here, we present the draft genome sequence of T. borchii strain Tbo3840 (97.18 Mb in 969 scaffolds, with 12,346 predicted protein-coding genes).

Article: Nature Plants

Oak genome reveals facets of long lifespan C Plomion, JM Aury, J Amselem, T Leroy, F Murat, S Duplessis, S Faye, …Nature Plants, 1

Abstract

Oaks are an important part of our natural and cultural heritage. Not only are they ubiquitous in our most common landscapes1 but they have also supplied human societies with invaluable services, including food and shelter, since prehistoric times2. With 450 species spread throughout Asia, Europe and America3, oaks constitute a critical global renewable resource. The longevity of oaks (several hundred years) probably underlies their emblematic cultural and historical importance. Such long-lived sessile organisms must persist in the face of a wide range of abiotic and biotic threats over their lifespans. We investigated the genomic features associated with such a long lifespan by sequencing, assembling and annotating the oak genome. We then used the growing number of whole-genome sequences for plants (including tree and herbaceous species) to investigate the parallel evolution of genomic characteristics potentially underpinning tree longevity. A further consequence of the long lifespan of trees is their accumulation of somatic mutations during mitotic divisions of stem cells present in the shoot apical meristems. Empirical4 and modelling5 approaches have shown that intra-organismal genetic heterogeneity can be selected for6and provides direct fitness benefits in the arms race with short-lived pests and pathogens through a patchwork of intra-organismal phenotypes7. However, there is no clear proof that large-statured trees consist of a genetic mosaic of clonally distinct cell lineages within and between branches. Through this case study of oak, we demonstrate the accumulation and transmission of somatic mutations and the expansion of disease-resistance gene families in trees.

Article: Biochimica et Biophysica Acta

Conserved functions of Arabidopsis mitochondrial late-acting maturation factors in the trafficking of iron‑sulfur clusters MA Uzarska, J Przybyla-Toscano, F Spangar, F Zannini, R Lill, …Biochimica et Biophysica Acta (BBA)-Molecular Cell Research

Abstract

Numerous proteins require iron‑sulfur (Fe-S) clusters as cofactors for their function. Their biogenesis is a multi-step process occurring in the cytosol and mitochondria of all eukaryotes and additionally in plastids of photosynthetic eukaryotes. A basic model of Fe-S protein maturation in mitochondria has been obtained based on studies achieved in mammals and yeast, yet some molecular details, especially of the late steps, still require investigation. In particular, the late-acting biogenesis factors in plant mitochondria are poorly understood. In this study, we expressed the factors belonging to NFU, BOLA, SUFA/ISCA and IBA57 families in the respective yeast mutant strains. Expression of the Arabidopsis mitochondrial orthologs was usually sufficient to rescue the growth defects observed on specific media and/or to restore the abundance or activity of the defective Fe-S or lipoic acid-dependent enzymes. These data demonstrate that the plant mitochondrial counterparts, including duplicated isoforms, likely retained their ancestral functions. In contrast, the SUFA1 and IBA57.2 plastidial isoforms cannot rescue the lysine and glutamate auxotrophies of the respective isa1-isa2Δ and iba57Δ strains or of the isa1-isa2-iba57Δ triple mutant when expressed in combination. This suggests a specialization of the yeast mitochondrial and plant plastidial factors in these late steps of Fe-S protein biogenesis, possibly reflecting substrate-specific interactions in these different compartments.

Article: Fungal Genomics

Purification of Fungal High Molecular Weight Genomic DNA from Environmental Samples. L Fauchery, S Uroz, M Buée, A Kohler. Fungal Genomics, 21-35

Abstract

Sequencing of a high number of fungal genomes has become possible due to the development of next generation sequencing techniques (NGS). The most recent developments aim to sequence single-molecule long-reads in order to improve genome assemblies, but consequently needs higher quality (minimum >20 kbp) DNA as starting material. However, environmental-derived samples from soil, wood, or litter often contain phenolic compounds, pigments, and other molecules that can be inhibitors for reactions during sequencing library construction. In this chapter, we propose an optimized protocol allowing the preparation of high quality and long fragment DNA from different samples (mycelium, fruiting body, soil) compatible with the current sequencing requirements.

Article: Scientific reports

Molecular recognition of wood polyphenols by phase II detoxification enzymes of the white rot Trametes versicolor M Schwartz, T Perrot, E Aubert, S Dumarçay, F Favier, P Gérardin, …Scientific Reports 8 (1), 8472

Abstract

Wood decay fungi have complex detoxification systems that enable them to cope with secondary metabolites produced by plants. Although the number of genes encoding for glutathione transferases is especially expanded in lignolytic fungi, little is known about their target molecules. In this study, by combining biochemical, enzymatic and structural approaches, interactions between polyphenols and six glutathione transferases from the white-rot fungus Trametes versicolor have been demonstrated. Two isoforms, named TvGSTO3S and TvGSTO6S have been deeply studied at the structural level. Each isoform shows two distinct ligand-binding sites, a narrow L-site at the dimer interface and a peculiar deep hydrophobic H-site. In TvGSTO3S, the latter appears optimized for aromatic ligand binding such as hydroxybenzophenones. Affinity crystallography revealed that this H-site retains the flavonoid dihydrowogonin from a partially purified wild-cherry extract. Besides, TvGSTO6S binds two molecules of the flavonoid naringenin in the L-site. These data suggest that TvGSTO isoforms could interact with plant polyphenols released during wood degradation.

Article: The New Phytologist

Ericoid mycorrhizal fungi and their genomes: another side to the mycorrhizal symbiosis? S Perotto, S Daghino, E Martino. The New phytologist.

Summary

The genome of an organism bears the signature of its lifestyle, and organisms with similar life strategies are expected to share common genomic traits. Indeed, ectomycorrhizal and arbuscular mycorrhizal fungi share some genomic traits, such as the expansion of gene families encoding taxon‐specific small secreted proteins, which are candidate effectors in the symbiosis, and a very small repertoire of plant cell wall‐degrading enzymes. A large gene family coding for candidate effectors was also revealed in ascomycetous ericoid mycorrhizal (ERM) fungi, but these fungal genomes are characterised by a very high number of genes encoding degradative enzymes, mainly acting on plant cell wall components. We suggest that the genomic signature of ERM fungi mirrors a versatile life strategy, which allows them to occupy several ecological niches.

Article: Applied and Environmental Microbiology

Assessment of Passive Traps Combined with High-Throughput Sequencing To Study Airborne Fungal Communities J Aguayo, C Fourrier-Jeandel, C Husson, R Ioos. Applied and Environmental Microbiology 84 (11), e02637-17

ABSTRACT

Techniques based on high-throughput sequencing (HTS) of environmental DNA have provided a new way of studying fungal diversity. However, these techniques suffer from a number of methodological biases which may appear at any of the steps involved in a metabarcoding study. Air is one of the most important environments where fungi can be found, because it is the primary medium of dispersal for many species. Looking ahead to future developments, it was decided to test 20 protocols, including different passive spore traps, spore recovery procedures, DNA extraction kits, and barcode loci. HTS was performed with the Illumina MiSeq platform targeting two subloci of the fungal internal transcribed spacer. Multivariate analysis and generalized linear models showed that the type of passive spore trap, the spore recovery procedure, and the barcode all impact the description of fungal communities in terms of richness and diversity when assessed by HTS metabarcoding. In contrast, DNA extraction kits did not significantly impact these results. Although passive traps may be used to describe airborne fungal communities, a study using specific real-time PCR and a mock community showed that these kinds of traps are affected by environmental conditions that may induce losses of biological material, impacting diversity and community composition results.

IMPORTANCE The advent of high-throughput sequencing (HTS) methods, such as those offered by next-generation sequencing (NGS) techniques, has opened a new era in the study of fungal diversity in different environmental substrates. In this study, we show that an assessment of the diversity of airborne fungal communities can reliably be achieved by the use of simple and robust passive spore traps. However, a comparison of sample processing protocols showed that several methodological biases may impact the results of fungal diversity when assessed by metabarcoding. Our data suggest that identifying these biases is of paramount importance to enable a correct identification and relative quantification of community members.