Author Archives: eric

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

Article: Frontiers in Microbiology

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Expanding Genomics of Mycorrhizal Symbiosis

A Kuo, A Kohler, FM Martin, IV Grigoriev – Microbial Symbioses, 2014
 

Abstract

The mycorrhizal symbiosis between soil fungi and plant roots is a ubiquitous mutualism that plays key roles in plant and soil health, and carbon and nutrient cycles. The symbiosis evolved repeatedly and independently as multiple morphological types (e.g. arbuscular [AM], ectomycorrhizal [ECM]) in multiple fungal clades (e.g. phyla Glomeromycota, Ascomycota, Basidiomycota). The accessibility and culturability of many mycorrhizal partners make them ideal models for symbiosis studies. Alongside molecular, physiological, and ecological investigations, sequencing led to the first 3 mycorrhizal fungal genomes, representing 3 fungal phyla and 2 mycorrhizal types. The genome of the ECM basidiomycete Laccaria bicolor showed that the mycorrhizal lifestyle can evolve through loss of plant-degrading enzymes (PDEs) and expansion of lineage-specific gene families, including short secreted protein (SSP) effectors and other symbiosis genes. The genome of the ECM ascomycete Tuber melanosporum showed that the ECM type can evolve without expansion of gene families in contrast to Laccaria, and thus a different set of symbiosis genes. The genome of the AM glomeromycete Rhizophagus irregularis showed that despite enormous phylogenetic distance and morphological difference from the other 2 fungi, the symbiosis can involve similar solutions as loss of PDEs and mycorrhiza-induced SSPs. The mycorrhizal community is building on these studies with 3 large-scale initiatives. The Mycorrhizal Genomics Initiative (MGI) is sequencing 35 genomes of multiple fungal clades and mycorrhizal types for phylogenomic and population analyses. 17 MGI species whose symbiosis is reconstitutable in vitro are targeted for comprehensive transcriptomics of mycorrhiza formation. MGI genomes are seeding a set of 50+ reference fungal genomes for annotating metatranscriptomes sampled from 7 diverse well-described soil sites. These 3 projects address fundamental questions about the nature and role of a vital mutualism.

Seminar: Wendish V.

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The  seminar of Pr. Volker Wendisch (Bielefeld University, Germany) entitled  « Production of diamines and carotenoids from alternative carbon sources by microbial cell factories » will be held Friday 10th October .
The seminar will start at 13.00 pm in the meeting room Bat B, 7th floor FST.

Seminar: Skrede I.

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The  seminar of Inger Skrede (Mirobial Evolution Research Group, University of Oslo, Norvège) entiteld « Speciation processes and comparative genomics in the brown rot fungus Serpula » will be held Friday 10th October (LGEF meeting room/visio UL).
The seminar will start at 11.00 am in the LGEF meeting room.

Seminar: Sophie Mieskin

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The seminar of the week (Friday 3th October) will be given by Sophie Mieskin, lecturer who recently joined our unit. Sophie will present the work she performed during her PhD and Post-doc:
“Molecular diagnosis of the origin of faecal contaminations in coastal environment – Development of host-specific Bacteroidales markers”
Post-doc: “Does a bacterial biofilm influence the settlement and the adhesion strength of marine algae? »
The seminar will start at 1.30pm in the LGEF meeting room.

Article: Biochimica et Biophysica Acta

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The roles of glutaredoxins ligating Fe-S clusters: Sensing, transfer or repair functions?
J Couturier, J Przybyla-Toscano, T Roret, C Didierjean, N Rouhier
Biochimica et Biophysica Acta (BBA)-Molecular Cell Research

Abstract

Glutaredoxins (Grxs) are major oxidoreductases involved in the reduction of glutathionylated proteins. Owing to the capacity of several class I Grxs and likely all class II Grxs to incorporate iron–sulfur (Fe–S) clusters, they are also linked to iron metabolism. Most Grxs bind [2Fe–2S] clusters which are oxidatively- and reductively-labile and have identical ligation, involving notably external glutathione. However, subtle differences in the structural organization explain that class II Fe–S Grxs, having more labile and solvent-exposed clusters, can accept Fe–S clusters and transfer them to client proteins, whereas class I Fe–S Grxs usually do not. From the observed glutathione disulfide-mediated Fe–S cluster degradation, the current view is that the more stable Fe–S clusters found in class I Fe–S Grxs might constitute a sensor of oxidative stress conditions by modulating their activity. Indeed, in response to an oxidative signal, inactive holoforms i.e., without disulfide reductase activity, should be converted to active apoforms. Among class II Fe–S Grxs, monodomain Grxs likely serve as carrier proteins for the delivery of preassembled Fe–S clusters to acceptor proteins in organelles. Another proposed function is the repair of Fe–S clusters. From their cytoplasmic and/or nuclear localization, multidomain Grxs function in signalling pathways. In particular, they regulate iron homeostasis in yeast species by modulating the activity of transcription factors and eventually forming heterocomplexes with BolA-like proteins in response to the cellular iron status. We provide an overview of the biochemical and structural properties of Fe–S cluster-loaded Grxs in relation to their hypothetical or confirmed associated functions. This article is part of a Special Issue entitled: Fe/S proteins: Analysis, structure, function, biogenesis and diseases.