Category Archives: Academic productions

Article: Annals of Forest Science

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Certainties and uncertainties about the life cycle of the Périgord black truffle (Tuber melanosporum Vittad.) F. LeTacon, A Rubini, C Murat, C. Riccioni, C Robin… Annals of Forest Science

Abstract

• Key message

Several aspects of the life cycle of the Périgord black truffle have been elucidated only recently, while others remain either controversial or unstudied. In this paper, we present a revised life cycle of this fungus and highlight key aspects that have yet to be addressed or require further understanding.

• Context

The hypogeous sporophores of several Tuber species, renowned for their aromatic and gustatory qualities, are widely commercialized. One of the most valuable species is Tuber melanosporumVittad., the Périgord black truffle also known as “the black diamond”. However, many aspects of T. melanosporum life cycle remain unsolved.

• Aims

In this work, we examine past and recent findings on the life cycle of T. melanosporum, currently regarded as a model system for Tuber species, with the view of highlighting aspects of its life cycle which remain unsolved.

• Results

Several aspects of its life cycle have recently been elucidated (i.e. characterization of two mating type genes, heterothallism, prevalence of sexual reproduction on vegetative propagation, exclusion of one mating type by its opposite on ectomycorrhizas, dependency of ascocarps on their host for carbon allocation), while others remain unaddressed.

• Conclusion

Numerous additional aspects of the T. melanosporum life cycle remain unsolved, such as exclusion or competition mechanisms between ectomycorrhizal mating types, factors involved in ascocarp initiation, the nature of the connection linking ascocarps and mycorrhizas and atmospheric nitrogen fixation.

Article: Biochimica et Biophysica Acta

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Involvement of thiol-based mechanisms in plant development. N Rouhier, D Cerveau, J Couturier, JP Reichheld, P Rey Biochimica et Biophysica Acta (BBA)-General Subjects

Abstract

Background

Increasing knowledge has been recently gained regarding the redox regulation of plant developmental stages.

Scope of view

The current state of knowledge concerning the involvement of glutathione, glutaredoxins and thioredoxins in plant development is reviewed.

Major conclusions

The control of the thiol redox status is mainly ensured by glutathione (GSH), a cysteine-containing tripeptide and by reductases sharing redox-active cysteines, glutaredoxins (GRXs) and thioredoxins (TRXs). Indeed, thiol groups present in many regulatory proteins and metabolic enzymes are prone to oxidation, ultimately leading to post-translational modifications such as disulfide bond formation or glutathionylation. This review focuses on the involvement of GSH, GRXs and TRXs in plant development. Recent studies showed that the proper functioning of root and shoot apical meristems depends on glutathione content and redox status, which regulate, among others, cell cycle and hormone-related processes. A critical role of GRXs in the formation of floral organs has been uncovered, likely through the redox regulation of TGA transcription factor activity. TRXs fulfill many functions in plant development via the regulation of embryo formation, the control of cell-to-cell communication, the mobilization of seed reserves, the biogenesis of chloroplastic structures, the metabolism of carbon and the maintenance of cell redox homeostasis. This review also highlights the tight relationships between thiols, hormones and carbon metabolism, allowing a proper development of plants in relation with the varying environment and the energy availability.

Article: Molecular Plant-Microbe Interactions

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Candidate Effector Proteins of the Rust Pathogen Melampsora Larici-Populina Target Diverse Plant Cell Compartments

B Petre, DGO Saunders, J Sklenar, C Lorrain, J Win, S Duplessis, …
Molecular Plant-Microbe Interactions
Summary
Rust fungi are devastating crop pathogens that deliver effector proteins into infected tissues to modulate plant functions and promote parasitic growth. The genome of the poplar leaf rust fungus Melampsora larici-populina revealed a large catalogue of secreted proteins, some of which have been considered candidate effectors. Unravelling how these proteins function in host cells is key to understanding pathogenicity mechanisms and developing resistant plants. In this study, we used an effectoromics pipeline to select, clone, and express 20 candidate effectors in Nicotiana benthamiana leaf cells to determine their subcellular localisation and identify the plant proteins they interact with. Confocal microscopy revealed that six candidate effectors target the nucleus, nucleoli, chloroplasts, mitochondria and discrete cellular bodies. We also used coimmunoprecipitation and mass spectrometry to identify 606 N. benthamiana proteins that associate with the candidate effectors. Five candidate effectors specifically associated with a small set of plant proteins that may represent biologically relevant interactors. We confirmed the interaction between the candidate effector MLP124017 and the TOPLESS-Related Protein 4 from poplar by in planta coimmunoprecipitation. Altogether, our data enable us to validate effector proteins from M. larici-populina and reveal that these proteins may target multiple compartments and processes in plant cells. It also shows that N. benthamiana can be a powerful heterologous system to study effectors of obligate biotrophic pathogens.

Article: New Phytologist

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Evolving insights to understanding mycorrhizas. IA Dickie, I Alexander, S Lennon, M Öpik, MA Selosse, MGA Heijden, … New Phytologist 205 (4), 1369-1374

Mycorrhizal ecology and evolution: the past, the present, and the future MGA Heijden, FM Martin, MA Selosse, IR Sanders. New Phytologist

Summary

Almost all land plants form symbiotic associations with mycorrhizal fungi. These below-ground fungi play a key role in terrestrial ecosystems as they regulate nutrient and carbon cycles, and influence soil structure and ecosystem multifunctionality. Up to 80% of plant N and P is provided by mycorrhizal fungi and many plant species depend on these symbionts for growth and survival. Estimates suggest that there are c. 50 000 fungal species that form mycorrhizal associations with c. 250 000 plant species. The development of high-throughput molecular tools has helped us to better understand the biology, evolution, and biodiversity of mycorrhizal associations. Nuclear genome assemblies and gene annotations of 33 mycorrhizal fungal species are now available providing fascinating opportunities to deepen our understanding of the mycorrhizal lifestyle, the metabolic capabilities of these plant symbionts, the molecular dialogue between symbionts, and evolutionary adaptations across a range of mycorrhizal associations. Large-scale molecular surveys have provided novel insights into the diversity, spatial and temporal dynamics of mycorrhizal fungal communities. At the ecological level, network theory makes it possible to analyze interactions between plant–fungal partners as complex underground multi-species networks. Our analysis suggests that nestedness, modularity and specificity of mycorrhizal networks vary and depend on mycorrhizal type. Mechanistic models explaining partner choice, resource exchange, and coevolution in mycorrhizal associations have been developed and are being tested. This review ends with major frontiers for further research.

Article: Annals of Forest Science

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Structural and functional characterization of tree proteins involved in redox regulation: a new frontier in forest science

JP Jacquot, J Couturier, C Didierjean, E Gelhaye, M Morel-Rouhier, …
Annals of Forest Science, 1-16

Abstract

Key message

This paper describes how the combination of genomics, genetic engineering, and 3D structural characterization has helped clarify the redox regulatory networks in poplar with consequences not only in system biology in plants but also in bacteria and mammalian systems.

Context

Tree genomes are increasingly available with a large number of orphan genes coding for proteins, the function of which is still unknown.

Aims and methods

Modern techniques of genome analysis coupled with recombinant protein technology and massive 3D structural determination of tree proteins should help elucidate the function of many of the proteins encoded by orphan genes. X-ray crystallography and NMR will be the methods of choice for protein structure determination.

Results

In this review, we provide examples illustrating how the above-mentioned techniques improved our understanding of redox regulatory circuits in poplar, the first forest tree species sequenced. We showed that poplar peroxiredoxins use either thioredoxin or glutaredoxin as electron donors to reduce hydrogen peroxide. That glutaredoxin could be a reductant was unknown at the time of this discovery even in other biological organisms and was later confirmed notably by the observation that the two genes are fused in some bacteria and by the resolution of the structure of the bacterial hybrid protein. Similarly, genome analysis coupled to in vitro analysis of enzymatic properties led to the discovery that some plant methionine sulfoxide reductases can also use both thioredoxins and glutaredoxins as electron donors. Besides their disulfide reductase activity, it has been demonstrated that some poplar glutaredoxins are also involved in iron-sulfur center biogenesis and assembly. The original 3D structure determination has been made with poplar glutaredoxin C1 and then confirmed in a variety of other biological organisms including human. Our work also showed that in plants, so-called glutathione peroxidases use thioredoxins and not glutathione as electron donors. This is true for all non-selenocysteine-containing glutathione peroxidases. Finally, connections between the thioredoxin and glutaredoxin systems have been elucidated through the study of atypical poplar thioredoxins.

Conclusion

Altogether, these data illustrate how the combination of genetic engineering and structural biology improves our understanding of biological processes and helps fuel systems biology for trees and other biological species.

Article: FEBS letters

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Glutathionyl-hydroquinone reductases from poplar are plastidial proteins that deglutathionylate both reduced and oxidized quinones

PA Lallement, E Meux, JM Gualberto, S Dumarcay, F Favier, C Didierjean, … FEBS Letters

Abstract

Glutathionyl-hydroquinone reductases (GHRs) catalyze the deglutathionylation of quinones via a catalytic cysteine. The two GHR genes in the Populus trichocarpa genome, Pt-GHR1 and Pt-GHR2, are primarily expressed in reproductive organs. Both proteins are localized in plastids. More specifically, Pt-GHR2 localizes in nucleoids. At the structural level, Pt-GHR1 adopts a typical GHR fold, with a dimerization interface comparable to that of the bacterial and fungal GHR counterparts. Pt-GHR1 catalyzes the deglutathionylation of both reduced and oxidized glutathionylated quinones, but the enzyme is more catalytically efficient with the reduced forms.

Article: Frontiers in plant science

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The poplar phi class glutathione transferase: expression, activity and structure of GSTF1

H Pégeot, C Koh, B Petre, S Mathiot, S Duplessis, A Hecker, C Didierjean, …
Name: Frontiers in Plant Science 5, 712
Abstract

Glutathione transferases (GSTs) constitute a superfamily of enzymes with essential roles in cellular detoxification and secondary metabolism in plants as in other organisms. Several plant GSTs, including those of the Phi class (GSTFs), require a conserved catalytic serine residue to perform glutathione (GSH)-conjugation reactions. Genomic analyses revealed that errestrial plants have around 10 GSTFs, 8 in the Populus trichocarpa genome, but their physiological functions and substrates are mostly unknown. Transcript expression analyses showed a predominant expression of all genes both in reproductive (female flowers, fruits, floral buds) and vegetative organs (leaves, petioles). Here, we show that the recombinant poplar GSTF1 (PttGSTF1) possesses peroxidase activity towards cumene hydroperoxide and GSH-conjugation activity towards model substrates such as 2,4-dinitrochlorobenzene, benzyl and phenetyl isothiocyanate, 4-nitrophenyl butyrate and 4-hydroxy-2-nonenal but interestingly not on previously identified GSTF-class substrates. In accordance to analytical gel filtration data, crystal structure of PttGSTF1 showed a canonical dimeric organization with bound GSH or MES molecules. The structure of these protein-substrate complexes allowed delineating the residues contributing to both the G and H sites that form the active site cavity. In sum, the presence of GSTF1 transcripts and proteins in most poplar organs especially those rich in secondary metabolites such as flowers and fruits, together with its GSH-conjugation activity and its documented stress-responsive expression suggest that its function is associated with the catalytic transformation of metabolites and/or peroxide removal rather than with ligandin properties as previously reported for other GSTFs.

Article: New Phytologist

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The effect of elevated carbon dioxide on the interaction between Eucalyptus grandis and diverse isolates of Pisolithus sp. is associated with a complex shift in the root transcriptome

JM Plett, A Kohler, A Khachane, K Keniry, KL Plett, F Martin, IC Anderson. New Phytologist

Abstract

  • Using the newly available genome for Eucalyptus grandis, we sought to determine the genome-wide traits that enable this host to form mutualistic interactions with ectomycorrhizal (ECM) Pisolithus sp. and to determine how future predicted concentrations of atmospheric carbon dioxide (CO2) will affect this relationship.
  • We analyzed the physiological and transcriptomic responses of E. grandis during colonization by different Pisolithus sp. isolates under conditions of ambient (400 ppm) and elevated (650 ppm) CO2 to tease out the gene expression profiles associated with colonization status.
  • We demonstrate that E. grandis varies in its susceptibility to colonization by different Pisolithus isolates in a manner that is not predictable by geographic origin or the internal transcribed spacer (ITS)-based phylogeny of the fungal partner. Elevated concentrations of CO2 alter the receptivity of E. grandis to Pisolithus, a change that is correlated to a dramatic shift in the transcriptomic profile of the root.
  • These data provide a starting point for understanding how future environmental change may alter the signaling between plants and their ECM partners and is a step towards determining the mechanism behind previously observed shifts in Eucalypt-associated fungal communities exposed to elevated concentrations of atmospheric CO2.

Article: Applied Microbiology and Biotechnology

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Occurrence of lignin degradation genotypes and phenotypes among prokaryotes

JH Tian, AM Pourcher, T Bouchez, E Gelhaye, P Peu
Applied Microbiology and Biotechnology, 1-18

Abstract

A number of prokaryotes actively contribute to lignin degradation in nature and their activity could be of interest for many applications including the production of biogas/biofuel from lignocellulosic biomass and biopulping. This review compares the reliability and efficiency of the culture-dependent screening methods currently used for the isolation of ligninolytic prokaryotes. Isolated prokaryotes exhibiting lignin-degrading potential are presented according to their phylogenetic groups. With the development of bioinformatics, culture-independent techniques are emerging that allow larger-scale data mining for ligninolytic prokaryotic functions but today, these techniques still have some limits. In this work, two phylogenetic affiliations of isolated prokaryotes exhibiting ligninolytic potential and laccase-encoding prokaryotes were determined on the basis of 16S rDNAsequences, providing a comparative view of results obtained by the two types of screening techniques. The combination of laboratory culture and bioinformatics approaches is a promising way to explore lignin-degrading prokaryotes.

Article: Molecular Plant-Microbe Interactions

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The mutualist Laccaria bicolor expresses a core gene regulon during the colonization of diverse host plants and a variable regulon to counteract host-specific defenses

JM Plett, E Tisserant, A Brun, E Morin, IV Grigoriev, A Kuo, FM Martin, …

Molecular Plant-Microbe Interactions

Abstract
The coordinated transcriptomic responses of both mutualistic ectomycorrhizal (ECM) fungi and their hosts during the establishment of symbiosis are not well understood. This study characterizes the transcriptomic alterations of the ECM fungus Laccaria bicolor during different colonization stages on two hosts (Populus trichocarpa and Pseudotsuga menziesii) and compares this to the transcriptomic variations of P. trichocarpa across the same time-points. A large number of L. bicolor genes (>8,000) were significantly regulated at the transcriptional level in at least one stage of colonization. From our data we identify 1,249 genes that we hypothesize is the “core” gene regulon necessary for the mutualistic interaction between L. biolor and its host plants. We further identify a group of 1,210 genes that are regulated in a host-specific manner. This variable regulon encodes a number of genes coding for proteases and xenobiotic efflux transporters that we hypothesize act to counter chemical based defenses simultaneously activated at the transcriptomic level in P. trichocarpa. The transcriptional response of the host plant P. trichocarpa consisted of differential waves of gene regulation related to signaling perception and transduction, defense response and the induction of nutrient transfer in P. trichocarpa tissues. This study, therefore, gives fresh insight into the shifting transcriptomic landscape in both the colonizing fungus and their hosts and the different strategies employed by both partners in orchestrating a mutualistic