Effector proteins of rust fungi
B Petre, DL Joly, S Duplessis
Frontiers in Plant Science 22, 23

Abstract

Rust fungi include many species that are devastating crop pathogens. To develop resistant plants, a better understanding of rust virulence factors, or effector proteins, is needed. Thus far, only six rust effector proteins have been described: AvrP123, AvrP4, AvrL567, AvrM, RTP1 and PGTAUSPE-10-1. Although some are well established model proteins used to investigate mechanisms of immune receptor activation (avirulence activities) or entry into plant cells, how they work inside host tissues to promote fungal growth remains unknown. The genome sequences of four rust fungi (two Melampsoraceae and two Pucciniaceae) have been analyzed so far. Genome-wide analyses of these species, as well as transcriptomics performed on a broader range of rust fungi, revealed hundreds of small secreted proteins considered as rust candidate secreted effector proteins (CSEPs). The rust community now needs high-throughput approaches (effectoromics) to accelerate effector discovery/characterization and to better understand how they function in planta. However, this task is challenging due to the non-amenability of rust pathosystems (obligate biotrophs infecting crop plants) to traditional molecular genetic approaches mainly due to difficulties in culturing these species in vitro. The use of heterologous approaches should be promoted in the future.

Pairwise Transcriptomic Analysis of the Interactions Between the Ectomycorrhizal Fungus Laccaria bicolor S238N and Three Beneficial, Neutral and Antagonistic Soil Bacteria
A Deveau, M Barret, AG Diedhiou, J Leveau, W de Boer, F Martin, … Microbial ecology, 1-14

Abstract

Cross Kingdom Functional Conservation of the Core Universally Conserved Threonylcarbamoyladenosine tRNA Synthesis Enzymes
PC Thiaville, B El Yacoubi, L Perrochia, A Hecker, M Prigent, JJ Thiaville, …
Eukaryotic Cell, EC. 00147-14

Abstract

Threonylcarbamoyladenosine (t⁶A) is a universal modification located in the anticodon stem loop of tRNAs. In yeast, both cytoplasmic and mitochondrial tRNAs are modified. The cytoplasmic t⁶A synthesis pathway was elucidated and requires Sua5p, Kae1p and four other KEOPS complex proteins. Recent in vitrowork suggested that the mitochondrial t⁶A machinery of S. cerevisiae is composed of only two proteins, Sua5p and Qri7p, a member of Kae1p/TsaD family. Sua5p catalyzes the first step leading to the threonyl-carbamoyl-AMP intermediate (TC-AMP) while Qri7 transfers the threonyl-carbamoyl moiety from TC-AMP to tRNA to form t⁶A. Qri7p localizes to the mitochondria, but Sua5p was reported to be cytoplasmic. We show that Sua5p is targeted both to the cytoplasm and to the mitochondria through the use of alternative start sites. Import of Sua5p into the mitochondria is required for this organelle to be functional since the TC-AMP intermediate produced by Sua5p in the cytoplasm is not transported into the mitochondria in sufficient amounts. The conservation of this minimal t⁶A pathway was characterized in vitro and, for the first time, in vivoby heterologous complementation studies in E. coli. The data revealed a potential for TC-AMP channeling in the t⁶A pathway as co-expression of Qri7p and Sua5p is required to complement the essentiality of E. coli tsaD^–. Our results firmly established that Qri7p and Sua5p constitute the mitochondrial pathway for the biosynthesis of t⁶A and bring additional advancement in our understanding of the reaction mechanism.

Latent homology and convergent regulatory evolution underlies the repeated emergence of yeasts
LG Nagy, RA Ohm, GM Kovács, D Floudas, R Riley, A Gácser, M Sipiczki, …
Nature Communications 5

Abstract

Convergent evolution is common throughout the tree of life, but the molecular mechanisms causing similar phenotypes to appear repeatedly are obscure. Yeasts have arisen in multiple fungal clades, but the genetic causes and consequences of their evolutionary origins are unknown. Here we show that the potential to develop yeast forms arose early in fungal evolution and became dominant independently in multiple clades, most likely via parallel diversification of Zn-cluster transcription factors, a fungal-specific family involved in regulating yeast–filamentous switches. Our results imply that convergent evolution can happen by the repeated deployment of a conserved genetic toolkit for the same function in distinct clades via regulatory evolution. We suggest that this mechanism might be a common source of evolutionary convergence even at large time scales.

On the current status of Phakopsora pachyrhizi genome sequencing

M Loehrer, A Vogel, B Huettel, R Reinhardt, V Benes, S Duplessis, … Frontiers in Plant Science 5, 377

Abstract:

Recent advances in the field of sequencing technologies and bioinformatics allow a more rapid access to genomes of non-model organisms at sinking costs. Accordingly, draft genomes of several economically important cereal rust fungi have been released in the last three years. Aside from the very recent flax rust and poplar rust draft assemblies there are  genomic data available for other dicot-infecting rust fungi. In this article we outline rust fungus sequencing efforts and comment on the current status of Phakopsora pachyrhizi (Asian soybean rust) genome sequencing.

Structural and spectroscopic insights into BolA-glutaredoxin complexes
T Roret, P Tsan, J Couturier, B Zhang, MK Johnson, N Rouhier, …
Journal of Biological Chemistry, jbc. M114. 572701

Abstract

BolA proteins are defined as stress-responsive transcriptional regulators but they also participate to iron metabolism. Although they can form [2Fe-2S]-containing complexes with monothiol glutaredoxins (Grx), structural details are lacking. Three Arabidopsis thaliana BolA structures were solved. They differ primarily by the size of a loop referred to as the variable [H/C] loop which contains an important cysteine (BolA_C group) or histidine (BolA_H group) residue. From 3D modeling and spectroscopic analyses of A. thaliana GrxS14-BolA1 holo-heterodimer (BolA_H), we provide evidence for the coordination of a Rieske-type [2Fe-2S] cluster. For BolA_C members, the cysteine could replace the histidine as a ligand. NMR interaction experiments using apo-proteins indicate that a completely different heterodimer was formed, involving the nucleic acid binding site of BolA and the C-terminal tail of Grx. The possible biological importance of these complexes is discussed considering the physiological functions previously assigned to BolA and to Grx-BolA or Grx-Grx complexes.

Genomics of arbuscular mycorrhizal fungi: out of the shadows. M Malbreil, E Tisserant, F Martin, C Roux, FM Martin. Advances in Botanical Research 70, 259-290

Abstract

Arbuscular mycorrhizal (AM) symbiosis is the most widespread mutualistic association. It concerns 80% of land plants and involves fungi belonging to the phylum Glomeromycota. Benefits to the host plants due to this symbiosis range from nutrient supply to protection against pathogens. AM fungi are important components of the soil microbiome and are of great interest for managing sustainable agriculture, provided that their life cycle is better understood. Recently, major advances in the genomics of the model AM fungus Rhizophagus irregularis DAOM197198 have been published, offering new tools to investigate the biology of this symbiosis. In this chapter, we provide an overview of the efforts that were necessary to reach these results, from the discovery of these fungi and the description of their mutualistic incidence to their in vitro cultivation and on to genomics. The genome of DAOM197198 is estimated at ca. 150 Mb. It is haploid and less polymorphic than expected. Although it is an obligate biotrophic fungus, very little gene loss was observed. We put the Rhizophagus gene repertoire in perspective with previous investigations performed on the physiology of AM fungi: germination, early signalling with host plants, plant invasion, metabolism (phosphorous, carbon and nitrogen) and sexuality. Clearly, the publication of the genome of R. irregularis DAOM197198 is a turning point in the study of AM fungi, and large areas of their biology that still remain to be elucidated will now become accessible for investigation.

Forty years of inoculating seedlings with truffle fungi: past and future perspectives

C Murat, Mycorrhiza July 2014

Abstract

Leaf and Root-Associated Fungal Assemblages Do Not Follow Similar Elevational Diversity Patterns.

A Coince, T Cordier, J Lengellé, E Defossez, C Vacher, C Robin, M Buée, … PLOS ONE 9 (6), e100668.

Abstract

The diversity of fungi along environmental gradients has been little explored in contrast to plants and animals. Consequently, environmental factors influencing the composition of fungal assemblages are poorly understood. The aim of this study was to determine whether the diversity and composition of leaf and root-associated fungal assemblages vary with elevation and to investigate potential explanatory variables. High-throughput sequencing of the Internal Transcribed Spacer 1 region was used to explore fungal assemblages along three elevation gradients, located in French mountainous regions. Beech forest was selected as a study system to minimise the host effect. The variation in species richness and specific composition was investigated for ascomycetes and basidiomycetes assemblages with a particular focus on root-associated ectomycorrhizal fungi. The richness of fungal communities associated with leaves or roots did not significantly relate to any of the tested environmental drivers, i.e.elevation, mean temperature, precipitation or edaphic variables such as soil pH or the ratio carbon:nitrogen. Nevertheless, the ascomycete species richness peaked at mid-temperature, illustrating a mid-domain effect model. We found that leaf and root-associated fungal assemblages did not follow similar patterns of composition with elevation. While the composition of the leaf-associated fungal assemblage correlated primarily with the mean annual temperature, the composition of root-associated fungal assemblage was explained equally by soil pH and by temperature. The ectomycorrhizal composition was also related to these variables. Our results therefore suggest that above and below-ground fungal assemblages are not controlled by the same main environmental variables. This may be due to the larger amplitude of climatic variables in the tree foliage compared to the soil environment.

Extensive sampling of basidiomycete genomes demonstrates inadequacy of the white-rot/brown-rot paradigm for wood decay fungi

Significance

Wood decay fungi have historically been characterized as either white rot, which degrade all components of plant cell walls, including lignin, or brown rot, which leave lignin largely intact. Genomic analyses have shown that white-rot species possess multiple lignin-degrading peroxidases (PODs) and expanded suites of enzymes attacking crystalline cellulose. To test the adequacy of the white/brown-rot categories, we analyzed 33 fungal genomes. Some species lack PODs, and thus resemble brown-rot fungi, but possess the cellulose-degrading apparatus typical of white-rot fungi. Moreover, they appear to degrade lignin, based on decay analyses on wood wafers. Our results indicate that the prevailing paradigm of white rot vs. brown rot does not capture the diversity of fungal wood decay mechanisms.

Abstract

Basidiomycota (basidiomycetes) make up 32% of the described fungi and include most wood-decaying species, as well as pathogens and mutualistic symbionts. Wood-decaying basidiomycetes have typically been classified as either white rot or brown rot, based on the ability (in white rot only) to degrade lignin along with cellulose and hemicellulose. Prior genomic comparisons suggested that the two decay modes can be distinguished based on the presence or absence of ligninolytic class II peroxidases (PODs), as well as the abundance of enzymes acting directly on crystalline cellulose (reduced in brown rot). To assess the generality of the white-rot/brown-rot classification paradigm, we compared the genomes of 33 basidiomycetes, including four newly sequenced wood decayers, and performed phylogenetically informed principal-components analysis (PCA) of a broad range of gene families encoding plant biomass-degrading enzymes. The newly sequenced Botryobasidium botryosum and Jaapia argillacea genomes lack PODs but possess diverse enzymes acting on crystalline cellulose, and they group close to the model white-rot species Phanerochaete chrysosporium in the PCA. Furthermore, laboratory assays showed that both B. botryosum and J. argillaceacan degrade all polymeric components of woody plant cell walls, a characteristic of white rot. We also found expansions in reducing polyketide synthase genes specific to the brown-rot fungi. Our results suggest a continuum rather than a dichotomy between the white-rot and brown-rot modes of wood decay. A more nuanced categorization of rot types is needed, based on an improved understanding of the genomics and biochemistry of wood decay.