Article: New Phytologist

Comparative genomics and transcriptomics depict ericoid mycorrhizal fungi as versatile saprotrophs and plant mutualists. E Martino, E Morin, GA Grelet, A Kuo, A Kohler, S Daghino, KW Barry, … New Phytologist

Abstract

  • Some soil fungi in the Leotiomycetes form ericoid mycorrhizal (ERM) symbioses with Ericaceae. In the harsh habitats in which they occur, ERM plant survival relies on nutrient mobilization from soil organic matter (SOM) by their fungal partners. The characterization of the fungal genetic machinery underpinning both the symbiotic lifestyle and SOM degradation is needed to understand ERM symbiosis functioning and evolution, and its impact on soil carbon (C) turnover.
  • We sequenced the genomes of the ERM fungi Meliniomyces bicolor, M. variabilis,Oidiodendron maius and Rhizoscyphus ericae, and compared their gene repertoires with those of fungi with different lifestyles (ecto- and orchid mycorrhiza, endophytes, saprotrophs, pathogens). We also identified fungal transcripts induced in symbiosis.
  • The ERM fungal gene contents for polysaccharide-degrading enzymes, lipases, proteases and enzymes involved in secondary metabolism are closer to those of saprotrophs and pathogens than to those of ectomycorrhizal symbionts. The fungal genes most highly upregulated in symbiosis are those coding for fungal and plant cell wall-degrading enzymes (CWDEs), lipases, proteases, transporters and mycorrhiza-induced small secreted proteins (MiSSPs).
  • The ERM fungal gene repertoire reveals a capacity for a dual saprotrophic and biotrophic lifestyle. This may reflect an incomplete transition from saprotrophy to the mycorrhizal habit, or a versatile life strategy similar to fungal endophytes.

Article: The Plant Journal

Know your Enemy, Embrace your Friend: Using omics to understand how plants respond differently to pathogenic and mutualistic microorganisms JM Plett, FM Martin. The Plant Journal

Summary

Micro-organisms, or ‘microbes’, have formed intimate associations with plants throughout the length of their evolutionary history. In extant plant systems microbes still remain an integral part of the ecological landscape impacting plant health, productivity, and long-term fitness. Therefore, to properly understand the genetic wiring of plants, we must first determine what perception systems plants have evolved to parse beneficial from commensal from pathogenic microbes. In this review, we consider some of the most recent advances in how plants respond at the molecular level to different microbial lifestyles. Further, we cover some of the means by which microbes are able to manipulate plant signaling pathways through altered destructiveness and nutrient sinks as well as the use of effector proteins and miRNA’s. We conclude by highlighting some of the major questions still to be answered in the field of plant-microbe research and suggest some of key areas that most need further research investment. The results of these proposed studies will have impacts in a wide range of plant research disciplines and will, ultimately, translate into stronger agronomic crops and forestry stock whose immune perception and response system is bred to foster beneficial microbial symbioses while repudiating pathogenic symbioses.

Article: BMC Biology

Erv1 of Arabidopsis thaliana can directly oxidize mitochondrial intermembrane space proteins in the absence of redox-active Mia40 V Peleh, F Zannini, S Backes, N Rouhier, JM Herrmann. BMC biology 15 (1), 106

Background

Many proteins of the mitochondrial intermembrane space (IMS) contain structural disulfide bonds formed by the mitochondrial disulfide relay. In fungi and animals, the sulfhydryl oxidase Erv1 ‘generates’ disulfide bonds that are passed on to the oxidoreductase Mia40, which oxidizes substrate proteins. A different structural organization of plant Erv1 proteins compared to that of animal and fungal orthologs was proposed to explain its inability to complement the corresponding yeast mutant.

Results

Herein, we have revisited the biochemical and functional properties of Arabidopsis thaliana Erv1 by both in vitro reconstituted activity assays and complementation of erv1and mia40 yeast mutants. These mutants were viable, however, they showed severe defects in the biogenesis of IMS proteins. The plant Erv1 was unable to oxidize yeast Mia40 and rather even blocked its activity. Nevertheless, it was able to mediate the import and folding of mitochondrial proteins.

Conclusions

We observed that plant Erv1, unlike its homologs in fungi and animals, can promote protein import and oxidative protein folding in the IMS independently of the oxidoreductase Mia40. In accordance to the absence of Mia40 in many protists, our study suggests that the mitochondrial disulfide relay evolved in a stepwise reaction from an Erv1-only system to which Mia40 was added in order to improve substrate specificity.

Article: Advances in Genetics

Phylogenetics and Phylogenomics of Rust Fungi MC Aime, AR McTaggart, SJ Mondo, S Duplessis. Advances in Genetics

Abstract

Rust fungi (Pucciniales) are the most speciose and the most complex group of plant pathogens. Historically, rust taxonomy was largely influenced by host and phenotypic characters, which are potentially plastic. Molecular systematic studies suggest that the extant diversity of this group was largely shaped by host jumps and subsequent shifts. However, it has been challenging to reconstruct the evolutionary history for the order, especially at deeper (family-level) nodes. Phylogenomics offer a potentially powerful tool to reconstruct the Pucciniales tree of life, although researchers working at this vanguard still face unprecedented challenges working with nonculturable organisms that possess some of the largest and most repetitive genomes now known in kingdom fungi. In this chapter, we provide an overview of the current status and special challenges of rust genomics, and we highlight how phylogenomics may provide new perspectives and answer long-standing questions regarding the biology of rust fungi.

Article: Microbiology spectrum

The Fungal Tree of Life: from Molecular Systematics to Genome-Scale Phylogenies. JW Spatafora, MC Aime, IV Grigoriev, F Martin, JE Stajich, M Blackwell. Microbiology spectrum 5 (5)

Abstract:

The kingdom Fungi is one of the more diverse clades of eukaryotes in terrestrial ecosystems, where they provide numerous ecological services ranging from decomposition of organic matter and nutrient cycling to beneficial and antagonistic associations with plants and animals. The evolutionary relationships of the kingdom have represented some of the more recalcitrant problems in systematics and phylogenetics. The advent of molecular phylogenetics, and more recently phylogenomics, has greatly advanced our understanding of the patterns and processes associated with fungal evolution, however. In this article, we review the major phyla, subphyla, and classes of the kingdom Fungi and provide brief summaries of ecologies, morphologies, and exemplar taxa. We also provide examples of how molecular phylogenetics and evolutionary genomics have advanced our understanding of fungal evolution within each of the phyla and some of the major classes. In the current classification we recognize 8 phyla, 12 subphyla, and 46 classes within the kingdom. The ancestor of fungi is inferred to be zoosporic, and zoosporic fungi comprise three lineages that are paraphyletic to the remainder of fungi. Fungi historically classified as zygomycetes do not form a monophyletic group and are paraphyletic to Ascomycota and Basidiomycota. Ascomycota and Basidiomycota are each monophyletic and collectively form the subkingdom Dikarya.

Article: BMC genomics

Regulatory networks underlying mycorrhizal development delineated by genome-wide expression profiling and functional analysis of the transcription factor repertoire of the plant symbiotic fungus Laccaria bicolor. Y Daguerre, E Levati, J Ruytinx, E Tisserant, E Morin, A Kohler, … BMC genomics 18 (1), 737

Abstract

Background

Ectomycorrhizal (ECM) fungi develop a mutualistic symbiotic interaction with the roots of their host plants. During this process, they undergo a series of developmental transitions from the running hyphae in the rhizosphere to the coenocytic hyphae forming finger-like structures within the root apoplastic space. These transitions, which involve profound, symbiosis-associated metabolic changes, also entail a substantial transcriptome reprogramming with coordinated waves of differentially expressed genes. To date, little is known about the key transcriptional regulators driving these changes, and the aim of the present study was to delineate and functionally characterize the transcription factor (TF) repertoire of the model ECM fungus Laccaria bicolor.

Results

We curated the L. bicolor gene models coding for transcription factors and assessed their expression and regulation in Poplar and Douglas fir ectomycorrhizae. We identified 285 TFs, 191 of which share a significant similarity with known transcriptional regulators. Expression profiling of the corresponding transcripts identified TF-encoding fungal genes differentially expressed in the ECM root tips of both host plants. The L. bicolor core set of differentially expressed TFs consists of 12 and 22 genes that are, respectively, upregulated and downregulated in symbiotic tissues. These TFs resemble known fungal regulators involved in the control of fungal invasive growth, fungal cell wall integrity, carbon and nitrogen metabolism, invasive stress response and fruiting-body development. However, this core set of mycorrhiza-regulated TFs seems to be characteristic of L. bicolor and our data suggest that each mycorrhizal fungus has evolved its own set of ECM development regulators. A subset of the above TFs was functionally validated with the use of a heterologous, transcription activation assay in yeast, which also allowed the identification of previously unknown, transcriptionally active yet secreted polypeptides designated as Secreted Transcriptional Activator Proteins (STAPs).

Conclusions

Transcriptional regulators required for ECM symbiosis development in L. bicolor have been uncovered and classified through genome-wide analysis. This study also identifies the STAPs as a new class of potential ECM effectors, highly expressed in mycorrhizae, which may be involved in the control of the symbiotic root transcriptome.

Article: Soil Biology and Biochemistry

Tree roots select specific bacterial communities in the subsurface critical zone O Nicolitch, Y Colin, MP Turpault, L Fauchery, S Uroz. Soil Biology and Biochemistry 115, 109-123

Abstract

In soils characterized by nutrient-poor conditions trees have developed strategies to maximize the exploration of the environment through their root system. Notably, in shallow soils, trees adopt a deep-rooting strategy to access appropriate levels of water and nutrients from the bedrock. Despite the critical importance of microorganisms in nutrient access in topsoil, understanding their involvement in subsoil was rarely addressed. Our study provides the first comprehensive picture of the bacterial communities colonizing deep roots at the bedrock interface. Particularly, we aimed at deciphering if the subsoil edaphic conditions allowed the enrichment of specific bacterial communities in the rhizosphere. To answer such questioning, we focused on a shallow soil dominated by deep-rooting beech trees (Fagus sylvatica). The taxonomic and functional structures of bacterial communities were investigated through 16S rRNA-pyrosequencing analyses and in vitro bioassays on culturable representatives isolated from the saprolite, the limestone rocks and the roots penetrating those two compartments at the bedrock interface. Our taxonomic analyses revealed a rhizosphere effect, with no difference between the limestone- and saprolite-rhizosphere bacterial communities. Notably, our functional assays highlighted a significant enrichment of bacteria effective at mineral weathering in the limestone-rhizosphere compared to the surrounding environment, whereas organic matter decomposing bacteria were exclusively enriched in the saprolite-rhizosphere. Altogether our results suggest that tree roots select specific bacterial communities in subsoil as potential allies to improve nutrient availability and tree nutrition.

Article: J Plant Biochem Physiol

Covalent and Non-Covalent Associations Mediate MED28 Homo J Shaikhali, N Rouhier, A Hecker, K Brännström, G Wingsle.  J Plant Biochem Physiol 5:189. doi:10.4172/2329-9029.1000189

Abstract

The Mediator is a multi-protein complex that plays a key role in modulating gene expression. Our previous studies suggested that the MED10a, MED28, MED32 complex subunits could be subject to redox regulation. In this study we tested the capacity of different thioredoxins (TRXs) from poplar (TRX-H3 and TRX-H5) and Arabidopsis thaliana (TPR repeat-containing thioredoxin, TDX) as well as glutaredoxins (GRXs) from poplar (GRX-C3 and GRX-C4) to reduce MED28 oligomers in vitro and found that these proteins were less efficient than the the previously tested poplar TRX-H1 and Arabidopsis GRX-C1. Concerning the susceptibility of MED28 to oxidation, both hydrogen peroxide (H2O2) and glutathione disulfide (GSSG) are efficiently mediating the formation of intermolecular disulfides. In fact, MED28 forms homo- oligomers in vivo as assessed by yeast two-hybrid experiments but also in vitro in solution as shown by size-exclusion chromatography, the latter also demonstrated the formation of non- covalent homo-oligomers. These findings suggest that both the redox-dependent and – independent MED28 oligomerization could regulate its biological activities, could it be linked or not to the Mediator. In particular, it would be important to assess MED28 oligomerization state during senescence considering the previously observed phenotype of med28 plants.

Article: Photorespiration

In Vitro Alkylation Methods for Assessing the Protein Redox State. F Zannini, J Couturier, O Keech, N Rouhier. Photorespiration, 51-64

Abstract

Cysteines are important residues for protein structure, function, and regulation. Owing to their modified reactivity, some cysteines can undergo very diverse redox posttranslational modifications, including the reversible formation of disulfide bonds, a widespread protein regulatory process as well exemplified in plant chloroplasts for Calvin-Benson cycle enzymes. Both core- and peripheral-photorespiratory enzymes possess conserved cysteines, some of which have been identified as being subject to oxidative modifications. This is not surprising considering their presence in subcellular compartments where the production of reactive species can be important. However, in most cases, the types of modifications and their biochemical effect on protein activity have not been validated, meaning that the possible impact of these modifications in a complex physiological context, such as photorespiration, remains obscure.

We here describe a detailed set of protocols for alkylation methods that have been used so far to (1) study the protein cysteine redox state either in vitro by submitting purified recombinant proteins to reducing/oxidation treatments or in vivo by western blots on protein extracts from plants subject to environmental constraints, and its dependency on the two major reducing systems in the cell, i.e., the thioredoxin and glutathione/glutaredoxin systems, and (2) determine two key redox parameters, i.e., the cysteine pKa and the redox midpoint potential.

Article: Plant, Cell & Environment

Involvement of Arabidopsis glutaredoxin S14 in the maintenance of chlorophyll content P Rey, N Becuwe, S Tourrette, N Rouhier Plant, Cell & Environment

Abstract

Plant class-II glutaredoxins (GRXs) are oxidoreductases carrying a CGFS active site signature and are able to bind iron-sulfur clusters in vitro. In order to explore the physiological functions of the two plastidial class-II isoforms, GRXS14 and GRXS16, we generated knockdown and overexpression Arabidopsis thaliana lines and characterized their phenotypes using physiological and biochemical approaches. Plants deficient in one GRX did not display any growth defect, whereas the growth of plants lacking both was slowed. Plants overexpressing GRXS14 exhibited reduced chlorophyll content in control, high light and high salt conditions. However, when exposed to prolonged darkness, plants lacking GRXS14 showed accelerated chlorophyll loss compared to WT and overexpression lines. We observed that the GRXS14 abundance and the proportion of reduced form were modified in WT upon darkness and high salt. The dark treatment also resulted in decreased abundance of proteins involved in the maturation of iron-sulfur proteins. We propose that the phenotype of GRXS14-modified lines results from its participation in the control of chlorophyll content in relation with light and osmotic conditions, possibly through a dual action e.g. regulating the redox status of biosynthetic enzymes and contributing to the biogenesis of iron-sulfur clusters, which are essential cofactors in chlorophyll metabolism.