The genome of an arbuscular mycorrhizal fungus provides insights into the oldest plant symbiosis. E Tisserant, M Malbreil, A Kuo, A Kohler, et al. Proceedings of the National Academy of Sciences

Significance

The arbuscular mycorrhizal symbiosis between fungi of the Glomeromycota phylum and plants involves more than two-thirds of all known plant species, including important crop species. This mutualistic symbiosis, involving one of the oldest fungal lineages, is arguably the most ecologically and agriculturally important symbiosis in terrestrial ecosystems. The Glomeromycota are unique in that their spores and coenocytic hyphae contain hundreds of nuclei in a common cytoplasm, which raises important questions about the natural selection, population genetics, and gene expression of these highly unusual organisms. Study of the genome of Rhizophagus irregularis provides insight into genes involved in obligate biotrophy and mycorrhizal symbioses and the evolution of an ancient asexual organism, and thus is of fundamental importance to the field of genome evolution.

Abstract

The mutualistic symbiosis involving Glomeromycota, a distinctive phylum of early diverging Fungi, is widely hypothesized to have promoted the evolution of land plants during the middle Paleozoic. These arbuscular mycorrhizal fungi (AMF) perform vital functions in the phosphorus cycle that are fundamental to sustainable crop plant productivity. The unusual biological features of AMF have long fascinated evolutionary biologists. The coenocytic hyphae host a community of hundreds of nuclei and reproduce clonally through large multinucleated spores. It has been suggested that the AMF maintain a stable assemblage of several different genomes during the life cycle, but this genomic organization has been questioned. Here we introduce the 153-Mb haploid genome of Rhizophagus irregularis and its repertoire of 28,232 genes. The observed low level of genome polymorphism (0.43 SNP per kb) is not consistent with the occurrence of multiple, highly diverged genomes. The expansion of mating-related genes suggests the existence of cryptic sex-related processes. A comparison of gene categories confirms that R. irregularis is close to the Mucoromycotina. The AMF obligate biotrophy is not explained by genome erosion or any related loss of metabolic complexity in central metabolism, but is marked by a lack of genes encoding plant cell wall-degrading enzymes and of genes involved in toxin and thiamine synthesis. A battery of mycorrhiza-induced secreted proteins is expressed in symbiotic tissues. The present comprehensive repertoire of R. irregularisgenes provides a basis for future research on symbiosis-related mechanisms in Glomeromycota.

Structure and function of bacterial communities in ageing soils: Insights from the Mendocino ecological staircase
S Uroz, JJ Tech, NA Sawaya, P Frey-Klett, JHJ Leveau
Soil Biology and Biochemistry

Highlights

• Soil and microbial characteristic were determined in the Mendocino site.
• Each terrace is derived from the same mineralogical parent material but differ in age.
• Soil and microbiological approaches were performed on the first three terraces.
• Bacterial communities appeared significantly different along the chronosequence.
• Nutrient availability affects the diversity and function of the bacterial communities.

Abstract

Diversification of Fungal Specific Class A Glutathione Transferases in Saprotrophic Fungi Yann Mathieu, Pascalita Prosper, Frédérique Favier, Luc Harvengt, Claude Didierjean, Jean-Pierre Jacquot, Mélanie Morel-Rouhier, Eric Gelhaye

Abstract

Glutathione transferases (GSTs) form a superfamily of multifunctional proteins with essential roles in cellular detoxification processes and endogenous metabolism. The distribution of fungal-specific class A GSTs was investigated in saprotrophic fungi revealing a recent diversification within this class. Biochemical characterization of eight GSTFuA isoforms fromPhanerochaete chrysosporium and Coprinus cinereus demonstrated functional diversity in saprotrophic fungi. The three-dimensional structures of three P. chrysosporium isoforms feature structural differences explaining the functional diversity of these enzymes. Competition experiments between fluorescent probes, and various molecules, showed that these GSTs function as ligandins with various small aromatic compounds, derived from lignin degradation or not, at a L-site overlapping the glutathione binding pocket. By combining genomic data with structural and biochemical determinations, we propose that this class of GST has evolved in response to environmental constraints induced by wood chemistry.

Density mapping of decaying wood using X-ray computed tomography. V Hervé, F Mothe, C Freyburger, E Gelhaye and P. Frey-Klett. International Biodeterioration and Biodegradation

Abstract

Evolution of a symbiotic receptor through gene duplications in the legume–rhizobium mutualism. De Mita S., A. Streng, T. Bisseling and R. Geurts. New phytologist

Abstract:

• The symbiosis between legumes and nitrogen-fixing rhizobia co-opted pre-existing endomycorrhizal features. In particular, both symbionts release lipo-chitooligosaccharides (LCOs) that are recognized by LysM-type receptor kinases. We investigated the evolutionary history of rhizobial LCO receptor genes MtLYK3–LjNFR1 to gain insight into the evolutionary origin of the rhizobial symbiosis.
• We performed a phylogenetic analysis integrating gene copies from nonlegumes and legumes, including the non-nodulating, phylogenetically basal legume Cercis chinensis. Signatures of differentiation between copies were investigated through patterns of molecular evolution.
• We show that two rounds of duplication preceded the evolution of the rhizobial symbiosis in legumes. Molecular evolution patterns indicate that the resulting three paralogous gene copies experienced different selective constraints. In particular, one copy maintained the ancestral function, and another specialized into perception of rhizobial LCOs. It has been suggested that legume LCO receptors evolved from a putative ancestral defense-related chitin receptor through the acquisition of two kinase motifs. However, the phylogenetic analysis shows that these domains are actually ancestral, suggesting that this scenario is unlikely.
• Our study underlines the evolutionary significance of gene duplication and subsequent neofunctionalization in MtLYK3-LjNFR1genes. We hypothesize that their ancestor was more likely a mycorrhizal LCO receptor, than a defense-related receptor kinase.

Monothiol glutaredoxin-BolA interactions: redox control of Arabidopsis thaliana BolA2 and SufE1

J Couturier, HC Wu, T Dhalleine, H Pégeot, D Sudre… – Molecular Plant, 2013.

Abstract

A functional relationship between monothiol glutaredoxins and BolA has been unravelled by genomic analyses and in several high-throughput studies. Phylogenetic analyses coupled to transient expression of GFP fusions indicated that, in addition to the sulfurtransferase SufE1, which contains a C-terminal BolA domain, three BolA isoforms exist inArabidopsis thaliana, BolA1 being plastidial, BolA2 nucleo-cytoplasmic and BolA4 dual-targeted to mitochondria and plastids. Binary yeast-two hybrid experiments demonstrated that all BolAs and SufE1, via its BolA domain, can interact with all monothiol glutaredoxins. Most interactions between protein couples of the same sub-cellular compartment have been confirmed by bimolecular fluorescence complementation. In vitroexperiments indicated that monothiol glutaredoxins could regulate the redox state of BolA2 and SufE1, both proteins possessing a single conserved reactive cysteine. Indeed, a glutathionylated form of SufE1 lost its capacity to activate the cysteine desulfurase, Nfs2, but it is reactivated by plastidial glutaredoxins. Besides, a monomeric glutathionylated form and a dimeric disulfide-bridged form of BolA2 can be preferentially reduced by the nucleo-cytoplasmic GrxS17. These results indicate that the glutaredoxin-BolA interaction occurs in several sub-cellular compartments and suggest that a redox regulation mechanism, disconnected from their capacity to form iron-sulfur cluster-bridged heterodimers, may be physiologically relevant for BolA2 and SufE1.