Molecular characterization, function and regulation of ammonium transporters (Amt) and ammonium-metabolizing enzymes (GS, NADP-GDH) in the ectomycorrhizal fungus Hebeloma cylindrosporum

Identification and functional characterization of ammonium transporters in Penicilliumpurpurogenum

The filamentous fungus Penicillium purpurogenum IAM15392 produces a nitrogen-containing azaphilone pigment, (10Z)-12-carboxyl-monascorubramine (PP-V), which is a potentially valuable natural food colorant. Because ammonium is used as a nitrogen source, and because ammonium uptake is the first step in the synthesis of PP-V, ammonium transporters of P. purpurogenum were identified and characterized. The P. purpurogenum genome was found to contain four putative ammonium transporter genes, designated amtA, amtB, amtC, and amtD, which encode 11 transmembrane proteins of 479, 567, 452, and 475 amino acid residues, respectively. These genes were tested for their ability to complement mutations in the ammonium transporter genes of the fission yeast Schizosaccharomyces pombe. The phenotypes of mutants included defects in growth on low ammonium medium, methylammonium sensitivity, ammonium uptake from the culture medium, and ammonium limitation-induced invasive growth. Furthermore, the transcription of the amt genes was examined in P. purpurogenum grown under different ammonium concentrations. The results suggest that AmtB plays a major role in growth using ammonium as a nitrogen source, whereas AmtA and possibly AmtD function at low ammonium concentrations. Because a medium used for the production of PP-V contains a high concentration of ammonium, our functional characterization of the P. purpurogenum ammonium transporters suggests that AmtB is a potential target of bioengineering for increased PP-V production.

Biological ammonium transporters: evolution and diversification

Although ammonium is the preferred nitrogen source for microbes and plants, in animal cells it is a toxic product of nitrogen metabolism that needs to be excreted. Thus, ammonium movement across biological membranes, whether for uptake or excretion, is a fundamental and ubiquitous biological process catalysed by the superfamily of the Amt/Mep/Rh transporters. A remarkable feature of the Amt/Mep/Rh family is that they are ubiquitous and, despite sharing low amino acid sequence identity, are highly structurally conserved. Despite sharing a common structure, these proteins have become involved in a diverse range of physiological process spanning all domains of life, with reports describing their involvement in diverse biological processes being published regularly. In this context, we exhaustively present their range of biological roles across the domains of life and after explore current hypotheses concerning their evolution to help to understand how and why the conserved structure fulfils diverse physiological functions.

Genome-Wide Identification and Characterization of Ammonium Transporter (AMT) Genes in Chlamydomonas reinhardtii

Ammonium transporters (AMTs) are vital plasma membrane proteins facilitating NH4+ uptake and transport, crucial for plant growth. The identification of favorable AMT genes is the main goal of improving ammonium-tolerant algas. However, there have been no reports on the systematic identification and expression analysis of Chlamydomonas reinhardtii (C. reinhardtii) AMT genes. This study comprehensively identified eight CrAMT genes, distributed across eight chromosomes, all containing more than 10 transmembrane structures. Phylogenetic analysis revealed that all CrAMTs belonged to the AMT1 subfamily. The conserved motifs and domains of CrAMTs were similar to those of the AMT1 members of OsAMTs and AtAMTs. Notably, the gene fragments of CrAMTs are longer and contain more introns compared to those of AtAMTs and OsAMTs. And the promoter regions of CrAMTs are enriched with cis-elements associated with plant hormones and light response. Under NH4+ treatment, CrAMT1;1 and CrAMT1;3 were significantly upregulated, while CrAMT1;2, CrAMT1;4, and CrAMT1;6 saw a notable decrease. CrAMT1;7 and CrAMT1;8 also experienced a decline, albeit less pronounced. Transgenic algas with overexpressed CrAMT1;7 did not show a significant difference in growth compared to CC-125, while transgenic algas with CrAMT1;7 knockdown exhibited growth inhibition. Transgenic algas with overexpressed or knocked-down CrAMT1;8 displayed reduced growth compared to CC-125, which also resulted in the suppression of other CrAMT genes. None of the transgenic algas showed better growth than CC-125 at high ammonium levels. In summary, our study has unveiled the potential role of CrAMT genes in high-ammonium environments and can serve as a foundational research platform for investigating ammonium-tolerant algal species.

Biological ammonium transporters from the Amt/Mep/Rh superfamily: mechanism, energetics, and technical limitations

The exchange of ammonium across cellular membranes is a fundamental process in all domains of life and is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. Remarkably, despite a high structural conservation in all domains of life, these proteins have gained various biological functions during evolution. It is tempting to hypothesise that the physiological functions gained by these proteins may be explained at least in part by differences in the energetics of their translocation mechanisms. Therefore, in this review, we will explore our current knowledge of energetics of the Amt/Mep/Rh family, discuss variations in observations between different organisms, and highlight some technical drawbacks which have hampered effects at mechanistic characterisation. Through the review, we aim to provide a comprehensive overview of current understanding of the mechanism of transport of this unique and extraordinary Amt/Mep/Rh superfamily of ammonium transporters.

Mycorrhizal C/N ratio determines plant-derived carbon and nitrogen allocation to symbiosis

Carbon allocation of trees to ectomycorrhizas is thought to shape forest nutrient cycling, but the sink activities of different fungal taxa for host resources are unknown. Here, we investigate fungal taxon-specific differences in naturally composed ectomycorrhizal (EM) communities for plant-derived carbon and nitrogen. After aboveground dual labeling of young beech with 15N and 13C, ectomycorrhizas formed with different fungal taxa exhibit strong differences in label enrichment. Secondary Ion Mass Spectrometry (SIMS) imaging of nitrogen in cross sections of ectomycorrhizas demonstrates plant-derived 15N in both root and fungal structures. Isotope enrichment in ectomycorrhizas correlates with that in the corresponding ectomycorrhiza-attached lateral root, supporting fungal taxon-specific N and C fluxes in ectomycorrhizas. The enrichments with 13C and 15N in the symbiosis decrease with increasing C/N ratio of ectomycorrhizas, converging to zero at high C/N. The relative abundances of EM fungal species on roots are positively correlated with 13C enrichment, demonstrating higher fitness of stronger than of less C-demanding symbioses. Overall, our results support that differences among the C/N ratios in ectomycorrhizas formed with different fungal species regulate the supply of the symbioses with host-derived carbon and provide insights on functional traits of ectomycorrhizas, which are important for major ecosystem processes.

Prokaryotic ammonium transporters: what has three decades of research revealed?

The exchange of ammonium across cellular membranes is a fundamental process in all domains of life. In plants, bacteria and fungi, ammonium represents a vital source of nitrogen, which is scavenged from the external environment. In contrast, in animal cells ammonium is a cytotoxic metabolic waste product and must be excreted to prevent cell death. Transport of ammonium is facilitated by the ubiquitous Amt/Mep/Rh transporter superfamily. In addition to their function as transporters, Amt/Mep/Rh proteins play roles in a diverse array of biological processes and human physiopathology. Despite this clear physiological importance and medical relevance, the molecular mechanism of Amt/Mep/Rh proteins has remained elusive. Crystal structures of bacterial Amt/Rh proteins suggest electroneutral transport, whilst functional evidence supports an electrogenic mechanism. Here, focusing on bacterial members of the family, we summarize the structure of Amt/Rh proteins and what three decades of research tells us concerning the general mechanisms of ammonium translocation, in particular the possibility that the transport mechanism might differ in various members of the Amt/Mep/Rh superfamily.

Transcriptome analysis reveals the regulatory mode by which NAA promotes the growth of Armillaria gallica

A symbiotic relationship is observed between Armillaria and the Chinese herbal medicine Gastrodia elata (G. elata). Armillaria is a nutrient source for the growth of G. elata, and its nutrient metabolism efficiency affects the growth and development of G. elata. Auxin has been reported to stimulate Armillaria species, but the molecular mechanism remains unknown. We found that naphthalene acetic acid (NAA) can also promote the growth of A. gallica. Moreover, we identified a total of 2071 differentially expressed genes (DEGs) by analyzing the transcriptome sequencing data of A. gallica at 5 and 10 hour of NAA treatment. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analyses showed that these unigenes were significantly enriched in the metabolism pathways of arginine, proline, propanoate, phenylalanine and tryptophan. The expression levels of the general amino acid permease (Gap), ammonium transporter (AMT), glutamate dehydrogenase (GDH), glutamine synthetase (GS), Zn(II) 2Cys6 and C2H2 transcription factor genes were upregulated. Our transcriptome analysis showed that the amino acid and nitrogen metabolism pathways in Armillaria were rapidly induced within hours after NAA treatment. These results provide valuable insights into the molecular mechanisms by which NAA promotes the growth of Armillaria species.

The Exploring Functional Role of Ammonium Transporters of Aspergillus oryzae in Nitrogen Metabolism: Challenges towards Cell Biomass Production

Ammonium is a source of fermentable inorganic nitrogen essential for the growth and development of filamentous fungi. It is involved in several cellular metabolic pathways underlying nitrogen transport and assimilation. Ammonium can be transferred into the cell by an ammonium transporter. This study explored the role of ammonium transporters in nitrogen metabolism and cell biomass production in Aspergillus oryzae strain BCC 7051. Specific sequences encoding ammonium transporters (Amts) in A. oryzae were identified using genomic analysis. Four of the identified ammonium transporter genes, aoamt1-aoamt4, showed similarity in deduced amino acid sequences to the proteins in the ammonium transporter/methylammonium permease (AMT/MEP) family. Transcriptional analysis showed that the expression of aoamt2 and aoamt3 was ammonium-dependent, and was highly upregulated under ammonium-limited conditions. Their functional roles are characterized by genetic perturbations. The gene disruption and overexpression of aoamt3 indicated that the protein encoded by it was a crucial ammonium transporter associated with nitrogen metabolism and was required for filamentous growth. Compared with the wild type, the aoamt3-overexpressing strain showed superior growth performance, high biomass yield, and low glucose consumption. These results shed light on further improvements in the production of potent bioproducts by A. oryzae by manipulating the ammonium uptake capacity and nitrogen metabolism.

Transcriptional Landscape of Ectomycorrhizal Fungi and Their Host Provides Insight into N Uptake from Forest Soil

Mineral nitrogen (N) is a major nutrient showing strong fluctuations in the environment due to anthropogenic activities. The acquisition and translocation of N to forest trees are achieved mainly by highly diverse ectomycorrhizal fungi (EMF) living in symbioses with their host roots. Here, we examined colonized root tips to characterize the entire root-associated fungal community by DNA metabarcoding-Illumina sequencing of the fungal internal transcribed spacer 2 (ITS2) molecular marker and used RNA sequencing to target metabolically active fungi and the plant transcriptome after N application. The study was conducted with beech (Fagus sylvatica L.), a dominant tree species in central Europe, grown in native forest soil. We demonstrate strong enrichment of 15N from nitrate or ammonium in the ectomycorrhizal roots by stable-isotope labeling. The relative abundance of the EMF members in the fungal community was correlated with their transcriptional abundances. The fungal metatranscriptome covered Kyoto Encyclopedia of Genes and Genomes (KEGG) and Eukaryotic Orthologous Groups (KOG) categories similar to those of model fungi and did not reveal significant changes related to N metabolization but revealed species-specific transcription patterns, supporting trait stability. In contrast to the resistance of the fungal metatranscriptome, the transcriptome of the host exhibited dedicated nitrate- or ammonium-responsive changes with the upregulation of transporters and enzymes required for nitrate reduction and a drastic enhancement of glutamine synthetase transcript levels, indicating the channeling of ammonium into the pathway for plant protein biosynthesis. Our results support that naturally assembled fungal communities living in association with the tree roots buffer nutritional signals in their own metabolism but do not shield plants from high environmental N levels. IMPORTANCE Although EMF are well known for their role in supporting tree N nutrition, the molecular mechanisms underlying N flux from the soil solution into the host through the ectomycorrhizal pathway remain widely unknown. Furthermore, ammonium and nitrate availability in the soil solution is subject to frequent oscillations that create a dynamic environment for the tree roots and associated microbes during N acquisition. Therefore, it is important to understand how root-associated mycobiomes and the tree roots handle these fluctuations. We studied the responses of the symbiotic partners by screening their transcriptomes after a sudden environmental flux of nitrate or ammonium. We show that the fungi and the host respond asynchronously, with the fungi displaying resistance to increased nitrate or ammonium and the host dynamically metabolizing the supplied N sources. This study provides insights into the molecular mechanisms of the symbiotic partners operating under N enrichment in a multidimensional symbiotic system.

Digging Deeper: In Search of the Mechanisms of Carbon and Nitrogen Exchange in Ectomycorrhizal Symbioses

Symbiosis with ectomycorrhizal (ECM) fungi is an advantageous partnership for trees in nutrient-limited environments. Ectomycorrhizal fungi colonize the roots of their hosts and improve their access to nutrients, usually nitrogen (N) and, in exchange, trees deliver a significant portion of their photosynthetic carbon (C) to the fungi. This nutrient exchange affects key soil processes and nutrient cycling, as well as plant health, and is therefore central to forest ecosystem functioning. Due to their ecological importance, there is a need to more accurately understand ECM fungal mediated C and N movement within forest ecosystems such that we can better model and predict their role in soil processes both now and under future climate scenarios. There are a number of hurdles that we must overcome, however, before this is achievable such as understanding how the evolutionary history of ECM fungi and their inter- and intra- species variability affect their function. Further, there is currently no generally accepted universal mechanism that appears to govern the flux of nutrients between fungal and plant partners. Here, we consider the current state of knowledge on N acquisition and transport by ECM fungi and how C and N exchange may be related or affected by environmental conditions such as N availability. We emphasize the role that modern genomic analysis, molecular biology techniques and more comprehensive and standardized experimental designs may have in bringing cohesion to the numerous ecological studies in this area and assist us in better understanding this important symbiosis. These approaches will help to build unified models of nutrient exchange and develop diagnostic tools to study these fungi at various scales and environments.

Metarhizium robertsii ammonium permeases (MepC and Mep2) contribute to rhizoplane colonization and modulates the transfer of insect derived nitrogen to plants

The endophytic insect pathogenic fungi (EIPF) Metarhizium promotes plant growth through symbiotic association and the transfer of insect-derived nitrogen. However, little is known about the genes involved in this association and the transfer of nitrogen. In this study, we assessed the involvement of six Metarhizium robertsii genes in endophytic, rhizoplane and rhizospheric colonization with barley roots. Two ammonium permeases (MepC and Mep2) and a urease, were selected since homologous genes in arbuscular mycorrhizal fungi were reported to play a pivotal role in nitrogen mobilization during plant root colonization. Three other genes were selected on the basis on RNA-Seq data that showed high expression levels on bean roots, and these encoded a hydrophobin (Hyd3), a subtilisin-like serine protease (Pr1A) and a hypothetical protein. The root colonization assays revealed that the deletion of urease, hydrophobin, subtilisin-like serine protease and hypothetical protein genes had no impact on endophytic, rhizoplane and rhizospheric colonization at 10 or 20 days. However, the deletion of MepC resulted in significantly increased rhizoplane colonization at 10 days whereas ΔMep2 showed increased rhizoplane colonization at 20 days. In addition, the nitrogen transporter mutants also showed significantly higher 15N incorporation of insect derived nitrogen in barley leaves in the presence of nutrients. Insect pathogenesis assay revealed that disruption of MepC, Mep2, urease did not reduce virulence toward insects. The enhanced rhizoplane colonization of ΔMep2 and ΔMepC and insect derived nitrogen transfer to plant hosts suggests the role of MepC and Mep2 in Metarhizium-plant symbiosis.

Development of an attenuated oral vaccine strain of tilapia Group B Streptococci serotype Ia by gene knockout technology

Our previous studies demonstrated that the deletion of D2 fragment in tilapia Streptococcus agalactiae(GBS) attenuated strain YM001 is the main reason for the loss of virulence to tilapia. In this study, a Δ2 mutant that deletion of D2 fragment in parental virulent strain HN016 was constructed, and the safety, stability, immunogenicity, and growth characteristics, as well as the virulence mechanism of Δ2 mutant were evaluated. The results showed that Δ2 mutant was not pathogenic to tilapia, and the virulent revertants were not observed after 50 generations of passage. The RPS reached 96.11% at 15 days and 93.05% at 30 days, respectively, after intraperitoneal injection, while RPS reached 74.80% at 15 days and 53.16% at 30 days, respectively, after oral immunization. The growth of Δ2 mutant was significantly faster than YM001, and genes that were enriched in the nitrogen metabolism and arginine biosynthesis signaling pathway (arc, glnA, and gdhA) were identified as important candidate genes responsible for growth rate of S. agalactiae. The absence of D2 fragment affected the expression of Sip, therefore influencing the bacterial virulence. Altogether, this study demonstrated that deletion of D2 fragment in HN016 causes the loss of virulence to tilapia, and Δ2 mutant is a promising, better attenuated oral vaccine strain of S. agalactiae compared to YM001.

Scavenging organic nitrogen and remodelling lipid metabolism are key survival strategies adopted by the endophytic fungi, Serendipita vermifera and Serendipita bescii to alleviate nitrogen and phosphorous starvation in vitro

Serendipitaceae represents a diverse fungal group in the Basidiomycota that includes endophytes and lineages that repeatedly evolved ericoid, orchid and ectomycorrhizal lifestyle. Plants rely upon both nitrogen and phosphorous, for essential growth processes, and are often provided by mycorrhizal fungi. In this study, we investigated the cellular proteome of Serendipita vermifera MAFF305830 and closely related Serendipita vermifera subsp. bescii NFPB0129 grown in vitro under (N) ammonium and (P) phosphate starvation conditions. Mycelial growth pattern was documented under these conditions to correlate growth-specific responses to nutrient starvation. We found that N-starvation accelerated hyphal radial growth, whereas P-starvation accelerated hyphal branching. Additionally, P-starvation triggers an integrated starvation response leading to remodelling of lipid metabolism. Higher abundance of an ammonium transporter known to serve as both an ammonium sensor and stimulator of hyphal growth was detected under N-starvation. Additionally, N-starvation led to strong up-regulation of nitrate, amino acid, peptide, and urea transporters, along with several proteins predicted to have peptidase activity. Taken together, our finding suggests S. bescii and S. vermifera have the metabolic capacity for nitrogen assimilation from organic forms of N compounds. We hypothesize that the nitrogen metabolite repression is a key regulator of such organic N assimilation.

Influence of Ammonium on Formation of Mineral-Associated Organic Carbon by an Ectomycorrhizal Fungus

The interactions between dissolved organic matter (DOM) and mineral particles are critical for the stabilization of soil organic matter (SOM) in terrestrial ecosystems. The processing of DOM by ectomycorrhizal fungi contributes to the formation of mineral-stabilized SOM by two contrasting pathways: the extracellular transformation of DOM (ex vivo pathway) and the secretion of mineral-surface-reactive metabolites (in vivo pathway). In this study, we examined how changes in nitrogen (N) availability affected the formation of mineral-associated carbon (C) from these two pathways. DOM was extracted from forest soils. The processing of this DOM by the ectomycorrhizal fungus Paxillus involutus was examined in laboratory-scale studies with different levels of ammonium. At low levels of ammonium (i.e., under N-limited conditions), the DOM components were slightly oxidized, and fungal C metabolites with iron-reducing activity were secreted. Ammonium amendments decreased the amount of C metabolites, and no additional oxidation of the organic matter was detected. In contrast, the hydrolytic activity and the secretion of N-containing compounds increased, particularly when high levels of ammonium were added. Under these conditions, C, but not N, limited fungal growth. Although the overall production of mineral-associated organic C was not affected by ammonium concentrations, the observed shifts in the activities of the ex vivo and in vivo pathways affected the composition of organic matter adsorbed onto the mineral particles. Such changes will affect the properties of organic matter-mineral associations and, thus, ultimately, the stabilization of SOM.IMPORTANCE Nitrogen (N) availability plays a critical role in the cycling and storage of soil organic matter (SOM). However, large uncertainties remain in predicting the net effect of N addition on soil organic carbon (C) storage due to the complex interactions between organic matter, microbial activity, and mineral particles that determine the formation of stable SOM. Here, we attempted to disentangle the effects of ammonium on these interactions in controlled microcosm experiments including the ectomycorrhizal fungus P.involutus and dissolved organic matter extracted from forest soils. Increased ammonium levels affected the fungal processing of the organic material as well as the secretion of extracellular metabolites. Although ammonium additions did not increase the net production of mineral-adsorbed C, changes in the decomposition and secretion pathways altered the composition of the adsorbed organic matter. These changes may influence the properties of the organic matter-mineral associations and, thus, the stabilization of SOM.

Nitrogen and phosphate metabolism in ectomycorrhizas

1047 I. Introduction 1047 II. Mobilization of soil N/P by ECM fungi 1048 III. N/P uptake 1048 IV. N/P assimilation 1049 V. N/P storage and remobilization 1049 VI. Hyphal N/P efflux at the plant-fungus interface 1052 VII. Conclusion and research needs 1054 Acknowledgements 1055 References 1055 SUMMARY: Nutrient homeostasis is essential for fungal cells and thus tightly adapted to the local demand in a mycelium with hyphal specialization. Based on selected ectomycorrhizal (ECM) fungal models, we outlined current concepts of nitrogen and phosphate nutrition and their limitations, and included knowledge from Baker's yeast when major gaps had to be filled. We covered the entire pathway from nutrient mobilization, import and local storage, distribution within the mycelium and export at the plant-fungus interface. Even when nutrient import and assimilation were broad issues for ECM fungi, we focused mainly on nitrate and organic phosphorus uptake, as other nitrogen/phosphorus (N/P) sources have been covered by recent reviews. Vacuolar N/P storage and mobilization represented another focus point of this review. Vacuoles are integrated into cellular homeostasis and central for an ECM mycelium at two locations: soil-growing hyphae and hyphae of the plant-fungus interface. Vacuoles are also involved in long-distance transport. We further discussed potential mechanisms of bidirectional long-distance nutrient transport (distances from millimetres to metres). A final focus of the review was N/P export at the plant-fungus interface, where we compared potential efflux mechanisms and pathways, and discussed their prerequisites.

Fenton reaction facilitates organic nitrogen acquisition by an ectomycorrhizal fungus

Boreal trees rely on their ectomycorrhizal fungal symbionts to acquire growth-limiting nutrients, such as nitrogen (N), which mainly occurs as proteins complexed in soil organic matter (SOM). The mechanisms for liberating this N are unclear as ectomycorrhizal fungi have lost many genes encoding lignocellulose-degrading enzymes present in their saprotrophic ancestors. We hypothesized that hydroxyl radicals (^˙ OH), produced by the ectomycorrhizal fungus Paxillus involutus during growth on SOM, are involved in liberating organic N. Paxillus involutus was grown for 7 d on N-containing or N-free substrates that represent major organic compounds of SOM. ^˙ OH production, ammonium assimilation, and proteolytic activity were measured daily. ^˙ OH production was strongly induced when P. involutus switched from ammonium to protein as the main N source. Extracellular proteolytic activity was initiated shortly after the oxidation. Oxidized protein substrates induced higher proteolytic activity than unmodified proteins. Dynamic modeling predicted that ^˙ OH production occurs in a burst, regulated mainly by ammonium and ferric iron concentrations. We propose that the production of ^˙ OH and extracellular proteolytic enzymes are regulated by similar nutritional signals. Oxidation works in concert with proteolysis, improving N liberation from proteins in SOM. Organic N mining by ectomycorrhizal fungi has, until now, only been attributed to proteolysis.

Multiple Transceptors for Macro- and Micro-Nutrients Control Diverse Cellular Properties Through the PKA Pathway in Yeast: A Paradigm for the Rapidly Expanding World of Eukaryotic Nutrient Transceptors Up to Those in Human Cells

The nutrient composition of the medium has dramatic effects on many cellular properties in the yeast Saccharomyces cerevisiae. In addition to the well-known specific responses to starvation for an essential nutrient, like nitrogen or phosphate, the presence of fermentable sugar or a respirative carbon source leads to predominance of fermentation or respiration, respectively. Fermenting and respiring cells also show strong differences in other properties, like storage carbohydrate levels, general stress tolerance and cellular growth rate. However, the main glucose repression pathway, which controls the switch between respiration and fermentation, is not involved in control of these properties. They are controlled by the protein kinase A (PKA) pathway. Addition of glucose to respiring yeast cells triggers cAMP synthesis, activation of PKA and rapid modification of its targets, like storage carbohydrate levels, general stress tolerance and growth rate. However, starvation of fermenting cells in a glucose medium for any essential macro- or micro-nutrient counteracts this effect, leading to downregulation of PKA and its targets concomitant with growth arrest and entrance into G0. Re-addition of the lacking nutrient triggers rapid activation of the PKA pathway, without involvement of cAMP as second messenger. Investigation of the sensing mechanism has revealed that the specific high-affinity nutrient transporter(s) induced during starvation function as transporter-receptors or transceptors for rapid activation of PKA upon re-addition of the missing substrate. In this way, transceptors have been identified for amino acids, ammonium, phosphate, sulfate, iron, and zinc. We propose a hypothesis for regulation of PKA activity by nutrient transceptors to serve as a conceptual framework for future experimentation. Many properties of transceptors appear to be similar to those of classical receptors and nutrient transceptors may constitute intermediate forms in the development of receptors from nutrient transporters during evolution. The nutrient-sensing transceptor system in yeast for activation of the PKA pathway has served as a paradigm for similar studies on candidate nutrient transceptors in other eukaryotes and we succinctly discuss the many examples of transceptors that have already been documented in other yeast species, filamentous fungi, plants, and animals, including the examples in human cells.

Nutrient Sensing at the Plasma Membrane of Fungal Cells

To respond to the changing environment, cells must be able to sense external conditions. This is important for many processes including growth, mating, the expression of virulence factors, and several other regulatory effects. Nutrient sensing at the plasma membrane is mediated by different classes of membrane proteins that activate downstream signaling pathways: nontransporting receptors, transceptors, classical and nonclassical G-protein-coupled receptors, and the newly defined extracellular mucin receptors. Nontransporting receptors have the same structure as transport proteins, but have lost the capacity to transport while gaining a receptor function. Transceptors are transporters that also function as a receptor, because they can rapidly activate downstream signaling pathways. In this review, we focus on these four types of fungal membrane proteins. We mainly discuss the sensing mechanisms relating to sugars, ammonium, and amino acids. Mechanisms for other nutrients, such as phosphate and sulfate, are discussed briefly. Because the model yeast Saccharomyces cerevisiae has been the most studied, especially regarding these nutrient-sensing systems, each subsection will commence with what is known in this species.

Take a Trip Through the Plant and Fungal Transportome of Mycorrhiza

Soil nutrient acquisition and exchanges through symbiotic plant-fungus interactions in the rhizosphere are key features for the current agricultural and environmental challenges. Improved crop yield and plant mineral nutrition through a fungal symbiont has been widely described. In return, the host plant supplies carbon substrates to its fungal partner. We review here recent progress on molecular players of membrane transport involved in nutritional exchanges between mycorrhizal plants and fungi. We cover the transportome, from the transport proteins involved in sugar fluxes from plants towards fungi, to the uptake from the soil and exchange of nitrogen, phosphate, potassium, sulfate, and water. Together, these advances in the comprehension of the mycorrhizal transportome will help in developing the future engineering of new agro-ecological systems.

GintAMT3 - a Low-Affinity Ammonium Transporter of the Arbuscular Mycorrhizal Rhizophagus irregularis

Nutrient acquisition and transfer are essential steps in the arbuscular mycorrhizal (AM) symbiosis, which is formed by the majority of land plants. Mineral nutrients are taken up by AM fungi from the soil and transferred to the plant partner. Within the cortical plant root cells the fungal hyphae form tree-like structures (arbuscules) where the nutrients are released to the plant-fungal interface, i.e., to the periarbuscular space, before being taken up by the plant. In exchange, the AM fungi receive carbohydrates from the plant host. Besides the well-studied uptake of phosphorus (P), the uptake and transfer of nitrogen (N) plays a crucial role in this mutualistic interaction. In the AM fungus Rhizophagus irregularis (formerly called Glomus intraradices), two ammonium transporters (AMT) were previously described, namely GintAMT1 and GintAMT2. Here, we report the identification and characterization of a newly identified R. irregularis AMT, GintAMT3. Phylogenetic analyses revealed high sequence similarity to previously identified AM fungal AMTs and a clear separation from other fungal AMTs. Topological analysis indicated GintAMT3 to be a membrane bound pore forming protein, and GFP tagging showed it to be highly expressed in the intraradical mycelium of a fully established AM symbiosis. Expression of GintAMT3 in yeast successfully complemented the yeast AMT triple deletion mutant (MATa ura3 mep1Δ mep2Δ::LEU2 mep3Δ::KanMX2). GintAMT3 is characterized as a low affinity transport system with an apparent Km of 1.8 mM and a V max of 240 nmol(-1) min(-1) 10(8) cells(-1), which is regulated by substrate concentration and carbon supply.

Structural basis for Mep2 ammonium transceptor activation by phosphorylation

Mep2 proteins are fungal transceptors that play an important role as ammonium sensors in fungal development. Mep2 activity is tightly regulated by phosphorylation, but how this is achieved at the molecular level is not clear. Here we report X-ray crystal structures of the Mep2 orthologues from Saccharomyces cerevisiae and Candida albicans and show that under nitrogen-sufficient conditions the transporters are not phosphorylated and present in closed, inactive conformations. Relative to the open bacterial ammonium transporters, non-phosphorylated Mep2 exhibits shifts in cytoplasmic loops and the C-terminal region (CTR) to occlude the cytoplasmic exit of the channel and to interact with His2 of the twin-His motif. The phosphorylation site in the CTR is solvent accessible and located in a negatively charged pocket ∼30 Å away from the channel exit. The crystal structure of phosphorylation-mimicking Mep2 variants from C. albicans show large conformational changes in a conserved and functionally important region of the CTR. The results allow us to propose a model for regulation of eukaryotic ammonium transport by phosphorylation.

Comprehensive Transcriptome Profiling Reveals Long Noncoding RNA Expression and Alternative Splicing Regulation during Fruit Development and Ripening in Kiwifruit (Actinidia chinensis)

Genomic and transcriptomic data on kiwifruit (Actinidia chinensis) in public databases are very limited despite its nutritional and economic value. Previously, we have constructed and sequenced nine fruit RNA-Seq libraries of A. chinensis "Hongyang" at immature, mature, and postharvest ripening stages of fruit development, and generated over 66.2 million paired-end and 24.4 million single-end reads. From this dataset, here we have identified 7051 long noncoding RNAs (lncRNAs), 29,327 alternative splicing (AS) events and 2980 novel protein-coding genes that were not annotated in the draft genome of "Hongyang." AS events were demonstrated in genes involved in the synthesis of nutritional metabolites in fruit, such as ascorbic acids, carotenoids, anthocyanins, and chlorophylls, and also in genes in the ethylene signaling pathway, which plays an indispensable role in fruit ripening. Additionally, transcriptome profiles and the contents of sugars, organic and main amino acids were compared between immature, mature, and postharvest ripening stages in kiwifruits. A total of 5931 differentially expressed genes were identified, including those associated with the metabolism of sugar, organic acid, and main amino acids. The data generated in this study provide a foundation for further studies of fruit development and ripening in kiwifruit, and identify candidate genes and regulatory elements that could serve as targets for improving important agronomic traits through marker assisted breeding and biotechnology.

Nutrient transfer in plant-fungal symbioses

Almost all plant species form symbioses with soil fungi, and nutrient transfer to plants is largely mediated through this partnership. Studies of fungal nutrient transfer to plants have largely focused on the transfer of limiting soil nutrients, such as nitrogen and phosphorous, by mycorrhizal fungi. However, certain fungal endophytes, such as Metarhizium and Beauveria, are also able to transfer nitrogen to their plant hosts. Here, we review recent studies that have identified genes and their encoded transporters involved in the movement of nitrogen, phosphorous, and nonlimiting soil nutrients between symbionts. These recent advances in our understanding could lead to applications in agricultural and horticultural settings, and to the development of model fungal systems that could further elucidate the role of fungi in these symbioses.

Biotrophic transportome in mutualistic plant-fungal interactions

Understanding the mechanisms that underlie nutrient use efficiency and carbon allocation along with mycorrhizal interactions is critical for managing croplands and forests soundly. Indeed, nutrient availability, uptake and exchange in biotrophic interactions drive plant growth and modulate biomass allocation. These parameters are crucial for plant yield, a major issue in the context of high biomass production. Transport processes across the polarized membrane interfaces are of major importance in the functioning of the established mycorrhizal association as the symbiotic relationship is based on a 'fair trade' between the fungus and the host plant. Nutrient and/or metabolite uptake and exchanges, at biotrophic interfaces, are controlled by membrane transporters whose regulation patterns are essential for determining the outcome of plant-fungus interactions and adapting to changes in soil nutrient quantity and/or quality. In the present review, we summarize the current state of the art regarding transport systems in the two major forms of mycorrhiza, namely ecto- and arbuscular mycorrhiza.

Carbon availability triggers the decomposition of plant litter and assimilation of nitrogen by an ectomycorrhizal fungus

The majority of nitrogen in forest soils is found in organic matter-protein complexes. Ectomycorrhizal fungi (EMF) are thought to have a key role in decomposing and mobilizing nitrogen from such complexes. However, little is known about the mechanisms governing these processes, how they are regulated by the carbon in the host plant and the availability of more easily available forms of nitrogen sources. Here we used spectroscopic analyses and transcriptome profiling to examine how the presence or absence of glucose and/or ammonium regulates decomposition of litter material and nitrogen mobilization by the ectomycorrhizal fungus Paxillus involutus. We found that the assimilation of nitrogen and the decomposition of the litter material are triggered by the addition of glucose. Glucose addition also resulted in upregulation of the expression of genes encoding enzymes involved in oxidative degradation of polysaccharides and polyphenols, peptidases, nitrogen transporters and enzymes in pathways of the nitrogen and carbon metabolism. In contrast, the addition of ammonium to organic matter had relatively minor effects on the expression of transcripts and the decomposition of litter material, occurring only when glucose was present. On the basis of spectroscopic analyses, three major types of chemical modifications of the litter material were observed, each correlated with the expression of specific sets of genes encoding extracellular enzymes. Our data suggest that the expression of the decomposition and nitrogen assimilation processes of EMF can be tightly regulated by the host carbon supply and that the availability of inorganic nitrogen as such has limited effects on saprotrophic activities.

Host-related metabolic cues affect colonization strategies of a root endophyte

The mechanisms underpinning broad compatibility in root symbiosis are largely unexplored. The generalist root endophyte Piriformospora indica establishes long-lasting interactions with morphologically and biochemically different hosts, stimulating their growth, alleviating salt stress, and inducing local and systemic resistance to pathogens. Cytological studies and global investigations of fungal transcriptional responses to colonization of barley and Arabidopsis at different symbiotic stages identified host-dependent colonization strategies and host-specifically induced effector candidates. Here, we show that in Arabidopsis, P. indica establishes and maintains biotrophic nutrition within living epidermal cells, whereas in barley the symbiont undergoes a nutritional switch to saprotrophy that is associated with the production of secondary thinner hyphae in dead cortex cells. Consistent with a diversified trophic behavior and with the occurrence of nitrogen deficiency at the onset of saprotrophy in barley, fungal genes encoding hydrolytic enzymes and nutrient transporters were highly induced in this host but not in Arabidopsis. Silencing of the high-affinity ammonium transporter PiAMT1 gene, whose transcripts are accumulating during nitrogen starvation and in barley, resulted in enhanced colonization of this host, whereas it had no effect on the colonization of Arabidopsis. Increased levels of free amino acids and reduced enzymatic activity for the cell-death marker VPE (vacuolar-processing enzyme) in colonized barley roots coincided with an extended biotrophic lifestyle of P. indica upon silencing of PiAMT1. This suggests that PiAmt1 functions as a nitrogen sensor mediating the signal that triggers the in planta activation of the saprotrophic program. Thus, host-related metabolic cues affect the expression of P. indica's alternative lifestyles.

Differential activation of ammonium transporters during the accumulation of ammonia by Colletotrichum gloeosporioides and its effect on appressoria formation and pathogenicity

Ammonium secreted by the post-harvest pathogen Colletotrichum gloeosporioides during host colonization accumulates in the host environment due to enhanced fungal nitrogen metabolism. Two types of ammonium transporter-encoding genes, AMET and MEP, are expressed during pathogenicity. Gene disruption of AMET, a gene modulating ammonia secretion, showed twofold reduced ammonia secretion and 45% less colonization on avocado fruit, suggesting a contribution to pathogenicity. MEPB, a gene modulating ammonium transport, is expressed by C. gloeosporioides during pathogenicity and starvation conditions in culture. Gene disruption of MEPB, the most highly expressed gene of the MEP family, resulted in twofold overexpression of MEPA and MEPC but reduced colonization, suggesting MEPB expression's contribution to pathogenicity. Analysis of internal and external ammonia accumulation by ΔmepB strains in mycelia and germinated spores showed rapid uptake and accumulation, and reduced secretion of ammonia in the mutant versus wild-type (WT) strains. Ammonia uptake by the WT germinating spores but not by the ΔmepB strain with compromised ammonium transport activated cAMP and transcription of PKA subunits PKAR and PKA2. ΔmepB mutants showed 75% less appressorium formation and colonization than the WT, which was partially restored by 10 mM exogenous ammonia. Thus, whereas both AMET and MEPB genes modulate ammonia secretion, only MEPB contributes to ammonia accumulation by mycelia and germinating spores that activate the cAMP pathways, inducing the morphogenetic processes contributing to C. gloeosporioides pathogenicity.

Regulation of genes involved in nitrogen utilization on different C/N ratios and nitrogen sources in the model ectomycorrhizal fungus Hebeloma cylindrosporum

Nitrogen (N) utilization by ectomycorrhizal fungi is an essential aspect of their ecosystem function. N deposition changes both the N pools and the carbon/nitrogen (C/N) ratio of the substrates where ectomycorrhizal fungi are found, and it is important to understand how these changes affect the N forms used by ectomycorrhizal fungi. To overcome the difficulties of studying ectomycorrhizal fungi in situ, we investigated all known N genes in the model fungus, Hebeloma cylindrosporum in a culture study. In addition to studying the regulation of all known N utilization genes, we aimed to understand whether there are gene clusters that undergo similar regulation. Lastly we studied how C/N ratio, N transporter type, and N source affected relative gene expression levels. We grew the D2 strain of H. cylindrosporum on a range of inorganic and organic N sources under low, medium, and high C/N ratios. We found three gene clusters that were regulated in a similar pattern. Lastly, we found C/N ratio, N source and N transporter type all affected gene expression levels. Relative expression levels were highest on the high C/N ratio, BSA and diLeucine N sources, and inorganic N transporters were always expressed at higher levels than organic N transporters. These results suggest that inorganic N sources may always the default preference for H. cylindrosporum, regardless of both the N sources and the C/N ratio of the substrate.

Kinetics of NH (4) (+) uptake by the arbuscular mycorrhizal fungus Rhizophagus irregularis

The kinetics and energetics of (15)NH (4) (+) uptake by the extraradical mycelium of the arbuscular mycorrhizal fungus Rhizophagus irregularis were investigated. (15)NH (4) (+) uptake increased with increasing substrate concentration over the concentration range of 0.002 to 25 mM. Eadie-Hofstee plots showed that ammonium (NH (4) (+) ) uptake over this range was biphasic. At concentrations below 100 μM, NH (4) (+) uptake fits a Michaelis-Menten curve, typical of the activity of a saturable high-affinity transport system (HATS). At concentrations above 1 mM, NH (4) (+) influx showed a linear response typical of a nonsaturable low-affinity transport system (LATS). Both transport systems were dependent on external pH. The HATS and, to a lesser extent, the LATS were inhibited by the ionophore carbonylcyanide m-chlorophenylhydrazone (CCCP) and the ATP-synthesis inhibitor 2,4-dinitrophenol. These data indicate that the two NH (4) (+) transport systems of R. irregularis are dependent on metabolic energy and on the electrochemical H(+) gradient. The HATS- and the LATS-mediated (15)NH (4) (+) influxes were also regulated by acetate. This first report of the existence of active high- and low-affinity NH4(+) transport systems in the extraradical mycelium of an arbuscular mycorrhizal fungus and provides novel information on the mechanisms underlying mycosymbiont uptake of nitrogen from the soil environment.

The arbuscular mycorrhizal status has an impact on the transcriptome profile and amino acid composition of tomato fruit

BACKGROUND

Arbuscular mycorrhizal (AM) symbiosis is the most widespread association between plant roots and fungi in natural and agricultural ecosystems. This work investigated the influence of mycorrhization on the economically relevant part of the tomato plant, by analyzing its impact on the physiology of the fruit. To this aim, a combination of phenological observations, transcriptomics (Microarrays and qRT-PCR) and biochemical analyses was used to unravel the changes that occur on fruits from Micro-Tom tomato plants colonized by the AM fungus Glomus mosseae.

RESULTS

Mycorrhization accelerated the flowering and fruit development and increased the fruit yield. Eleven transcripts were differentially regulated in the fruit upon mycorrhization, and the mycorrhiza-responsive genes resulted to be involved in nitrogen and carbohydrate metabolism as well as in regulation and signal transduction. Mycorrhization has increased the amino acid abundance in the fruit from mycorrhizal plants, with glutamine and asparagine being the most responsive amino acids.

CONCLUSIONS

The obtained results offer novel data on the systemic changes that are induced by the establishment of AM symbiosis in the plant, and confirm the work hypothesis that AM fungi may extend their influence from the root to the fruit.

Fungi in roots of nursery grown Pinus sylvestris: ectomycorrhizal colonisation, genetic diversity and spatial distribution

The aims of this study were to investigate patterns of ectomycorrhizal (ECM) colonisation and community structure on nursery grown seedlings of Pinus sylvestris, spatial distribution of ECMs in the nursery plot and genetic diversity of commonly isolated ECM basidiomycete Hebeloma cavipes. One hundred seedlings were sampled in 225 m(2) area using a systematic grid design. For each seedling, 20 individual root tips were randomly collected, morphotyped, and surface sterilised for fungal isolation in pure culture. Results showed that ECM community was comprised of nine distinct morphotypes among which Thelephora terrestris (39.7%), Hebeloma sp. (17.8%) and Suillus luteus (6.1%) were the most abundant. Spatial distribution of ECMs in the nursery plot was determined by their relative abundance: even in common ECMs and random in rare ones. Fungal isolation yielded 606 pure cultures, representing 71 distinct taxa. The most commonly isolated fungi were the ascomycetes Neonectria macrodidyma (20.3%), Phialocephala fortinii (13.5%), Neonectria radicicola (6.3%) and the ECM basidiomycete H. cavipes (4.5%). Intraspecific genetic diversity within 27 H. cavipes isolates was studied using two methods: restriction digestion of the amplified intergenic spacer of nuclear ribosomal DNA and genealogical concordance of five genetic markers. Five and eight genotypes were revealed by each respective method, but both of those were largely consistent, in particular, in determining the largest genotype (A) composed of 18 isolates. Mapping positions for each H. cavipes isolate and genotype in the field showed that isolates of the A genotype covered a large part of the nursery plot. This suggests that H. cavipes is largely disseminated by vegetative means of local genotypes and that nursery cultivation practices are likely to contribute to the dissemination of this species in the forest nursery soils.

Regulation of the nitrogen transfer pathway in the arbuscular mycorrhizal symbiosis: gene characterization and the coordination of expression with nitrogen flux

The arbuscular mycorrhiza (AM) brings together the roots of over 80% of land plant species and fungi of the phylum Glomeromycota and greatly benefits plants through improved uptake of mineral nutrients. AM fungi can take up both nitrate and ammonium from the soil and transfer nitrogen (N) to host roots in nutritionally substantial quantities. The current model of N handling in the AM symbiosis includes the synthesis of arginine in the extraradical mycelium and the transfer of arginine to the intraradical mycelium, where it is broken down to release N for transfer to the host plant. To understand the mechanisms and regulation of N transfer from the fungus to the plant, 11 fungal genes putatively involved in the pathway were identified from Glomus intraradices, and for six of them the full-length coding sequence was functionally characterized by yeast complementation. Two glutamine synthetase isoforms were found to have different substrate affinities and expression patterns, suggesting different roles in N assimilation. The spatial and temporal expression of plant and fungal N metabolism genes were followed after nitrate was added to the extraradical mycelium under N-limited growth conditions using hairy root cultures. In parallel experiments with (15)N, the levels and labeling of free amino acids were measured to follow transport and metabolism. The gene expression pattern and profiling of metabolites involved in the N pathway support the idea that the rapid uptake, translocation, and transfer of N by the fungus successively trigger metabolic gene expression responses in the extraradical mycelium, intraradical mycelium, and host plant.

Glutamine, arginine and the amino acid transporter Pt-CAT11 play important roles during senescence in poplar

BACKGROUND AND AIMS

Nitrogen (N) availability in the forest soil is extremely low and N economy has a special importance in woody plants that are able to cope with seasonal periods of growth and development over many years. Here we report on the analysis of amino acid pools and expression of key genes in the perennial species Populus trichocarpa during autumn senescence.

METHODS

Amino acid pools were measured throughout senescence. Expression analysis of arginine synthesis genes and cationic amino acid transporter (CAT) genes during senescence was performed. Heterologous expression in yeast mutants was performed to study Pt-CAT11 function in detail.

KEY RESULTS

Analysis of amino acid pools showed an increase of glutamine in leaves and an accumulation of arginine in stems during senescence. Expression of arginine biosynthesis genes suggests that arginine was preferentially synthesized from glutamine in perennial tissues. Pt-CAT11 expression increased in senescing leaves and functional characterization demonstrated that Pt-CAT11 transports glutamine.

CONCLUSIONS

The present study established a relationship between glutamine synthesized in leaves and arginine synthesized in stems during senescence, arginine being accumulated as an N storage compound in perennial tissues such as stems. In this context, Pt-CAT11 may have a key role in N remobilization during senescence in poplar, by facilitating glutamine loading into phloem vessels.

PtAAP11, a high affinity amino acid transporter specifically expressed in differentiating xylem cells of poplar

Amino acids are the currency of nitrogen exchange between source and sink tissues in plants and constitute a major source of the components used for cellular growth and differentiation. The characterization of a new amino acid transporter belonging to the amino acid permease (AAP) family, AAP11, expressed in the perennial species Populus trichocarpa is reported here. PtAAP11 expression analysis was performed by semi-quantitative RT-PCR and GUS activity after poplar transformation. PtAAP11 function was studied in detail by heterologous expression in yeast. The poplar genome contains 14 putative AAPs which is quite similar to other species analysed except Arabidopsis. PtAAP11 was mostly expressed in differentiating xylem cells in different organs. Functional characterization demonstrated that PtAAP11 was a high affinity amino acid transporter, more particularly for proline. Compared with other plant amino acid transporters, PtAAP11 represents a novel high-affinity system for proline. Thus, the functional characterization and expression studies suggest that PtAAP11 may play a major role in xylogenesis by providing proline required for xylem cell wall proteins. The present study provides important information highlighting the role of a specific amino acid transporter in xylogenesis in poplar.

Mutational analysis of the Candida albicans ammonium permease Mep2p reveals residues required for ammonium transport and signaling

The ammonium permease Mep2p mediates ammonium uptake and also induces filamentous growth in the human-pathogenic yeast Candida albicans in response to nitrogen limitation. The C-terminal cytoplasmic tail of Mep2p contains a signaling domain that is not required for ammonium transport but is essential for Mep2p-dependent morphogenesis. Progressive C-terminal truncations showed Y433 to be the last amino acid that is essential for the induction of filamentous growth, thereby delimiting the Mep2p signaling domain. To understand in more detail how the signaling activity of Mep2p is regulated by ammonium availability and transport, we mutated conserved amino acid residues that have been implicated in ammonium binding or uptake. Mutation of D180, which has been proposed to mediate initial contact with extracellular ammonium, or the pore-lining residues H188 and H342 abolished Mep2p expression, indicating that these residues are important for protein stability. Mutation of F239, which together with F126 is thought to form an extracytosolic gate to the conductance channel, abolished both ammonium uptake and Mep2p-dependent filament formation, despite proper localization of the protein. On the other hand, mutation of W167, which is assumed to participate with Y122, F126, and S243 in the recruitment and coordination of the ammonium ion at the extracytosolic side of the cell membrane, also abolished filament formation without having a strong impact on ammonium transport, demonstrating that extracellular alterations in Mep2p can affect intracellular signaling. Mutation of Y122 reduced ammonium uptake much more strongly than mutation of W167 but still allowed efficient filament formation, indicating that the signaling activity of Mep2p is not directly correlated with its transport activity. These results provide important insights into ammonium transport and control of morphogenesis by Mep2p in C. albicans.

Gene transcription in Lactarius quietus-Quercus petraea ectomycorrhizas from a forest soil

Extracting fungal mRNA from ectomycorrhizas (ECMs) and forest soil samples for monitoring in situ metabolic activities is a significant challenge when studying the role of ECMs in biogeochemical cycles. A robust, simple, rapid, and effective method was developed for extracting RNA from rhizospheric soil and ECMs by adapting previous grinding and lysis methods. The quality and yield of the extracted RNA were sufficient to be used for reverse transcription. RNA extracted from ECMs of Lactarius quietus in a 100-year-old oak stand was used to construct a cDNA library and sequence expressed sequence tags. The transcripts of many genes involved in primary metabolism and in the degradation of organic matter were found. The transcription levels of four targeted fungal genes (glutamine synthase, a general amino acid transporter, a tyrosinase, and N-acetylhexosaminidase) were measured by quantitative reverse transcription-PCR in ECMs and in the ectomycorrhizospheric soil (the soil surrounding the ECMs containing the extraradical mycelium) in forest samples. On average, levels of gene expression for the L. quietus ECM root tips were similar to those for the extraradical mycelium, although gene expression varied up to 10-fold among the samples. This study demonstrates that gene expression from ECMs and soil can be analyzed. These results provide new perspectives for investigating the role of ectomycorrhizal fungi in the functioning of forest ecosystems.

Identification of nitrogen mineralization enzymes, L-amino acid oxidases, from the ectomycorrhizal fungi Hebeloma spp. and Laccaria bicolor

Amino acids are major nitrogen sources in soils and they harbour a central position in the nitrogen metabolism of cells. We determined whether Hebeloma spp. and Laccaria bicolor expressed the enzyme L-amino acid oxidase (LAO), which catalyses the oxidative deamination of the alpha-amino group of L-amino acids. We measured LAO activities from the mycelial extracts of seven laboratory-grown fungal strains with three methods, and we measured how LAO activities were expressed in one Hebeloma sp. strain grown on four nitrogen sources. Hebeloma spp. and L. bicolor converted L-phenylalanine, but not D-phenylalanine, to hydrogen peroxide, 2-oxoacid, and ammonia, suggesting that they expressed LAO enzymes. The enzymes utilized five out of seven tested L-amino acids as substrates. LAO activities were maximal at pH 8, where Michaelis constant (Km) values were 2-5mm. The LAO of Hebeloma sp. was expressed on every nitrogen source analysed, and the activities were the highest in mycelia grown in nitrogen-rich conditions. We suggest that LAO is a mechanism for cellular amino acid catabolism in Hebeloma spp. and L. bicolor. Many soil bacteria and fungi also express LAO enzymes that have broad substrate specificities. Therefore, LAO is a potential candidate for a mechanism that catalyses nitrogen mineralization from amino acids at the ecosystem level.

A Mep2-dependent transcriptional profile links permease function to gene expression during pseudohyphal growth in Saccharomyces cerevisiae

The ammonium permease Mep2 is required for the induction of pseudohyphal growth, a process in Saccharomyces cerevisiae that occurs in response to nutrient limitation. Mep2 has both a transport and a regulatory function, supporting models in which Mep2 acts as a sensor of ammonium availability. Potentially similar ammonium permease-dependent regulatory cascades operate in other fungi, and they may also function in animals via the homologous Rh proteins; however, little is known about the molecular mechanisms that mediate ammonium sensing. We show that Mep2 is localized to the cell surface during pseudohyphal growth, and it is required for both filamentous and invasive growth. Analysis of site-directed Mep2 mutants in residues lining the ammonia-conducting channel reveal separation of function alleles (transport and signaling defective; transport-proficient/signaling defective), indicating transport is necessary but not sufficient to sense ammonia. Furthermore, Mep2 overexpression enhances differentiation under normally repressive conditions and induces a transcriptional profile that is consistent with activation of the mitogen-activated protein (MAP) kinase pathway. This finding is supported by epistasis analysis establishing that the known role of the MAP kinase pathway in pseudohyphal growth is linked to Mep2 function. Together, these data strengthen the model that Mep2-like proteins are nutrient sensing transceptors that govern cellular differentiation.

Characterization and regulation of PiDur3, a permease involved in the acquisition of urea by the ectomycorrhizal fungus Paxillus involutus

Urea, which is known to be a source of nitrogen for the growth of many organisms, represents an important fertilizer in forest soils. Since most trees form symbiotic associations with ectomycorrhizal fungi, the capacities of these symbionts to take up and assimilate urea would determine the efficiency of urea nitrogen salvaging by plants. We showed that Paxillusinvolutus, an ectomycorrhizal basidiomycete, is capable of using urea as sole nitrogen source. We report the molecular characterization of an active urea transporter (PiDur3) isolated from this fungus. We demonstrated that the import of urea is a minor event on ammonium condition, since the expression of PiDUR3 is repressed by the high intracellular glutamine pool. Interestingly, on urea nutritive condition, the uptake of urea is rather mediated by the intracellular urea pool and particularly by urease efficiency.

A gene repertoire for nitrogen transporters in Laccaria bicolor

Ectomycorrhizal interactions established between the root systems of terrestrial plants and hyphae from soil-borne fungi are the most ecologically widespread plant symbioses. The efficient uptake of a broad range of nitrogen (N) compounds by the fungal symbiont and their further transfer to the host plant is a major feature of this symbiosis. Nevertheless, we far from understand which N form is preferentially transferred and what are the key molecular determinants required for this transfer. Exhaustive in silico analysis of N-compound transporter families were performed within the genome of the ectomycorrhizal model fungus Laccaria bicolor. A broad phylogenetic approach was undertaken for all families and gene regulation was investigated using whole-genome expression arrays. A repertoire of proteins involved in the transport of N compounds in L. bicolor was established that revealed the presence of at least 128 gene models in the genome of L. bicolor. Phylogenetic comparisons with other basidiomycete genomes highlighted the remarkable expansion of some families. Whole-genome expression arrays indicate that 92% of these gene models showed detectable transcript levels. This work represents a major advance in the establishment of a transportome blueprint at a symbiotic interface, which will guide future experiments.

Impact of ammonium permeases mepA, mepB, and mepC on nitrogen-regulated secondary metabolism in Fusarium fujikuroi

In Fusarium fujikuroi, the production of gibberellins and bikaverin is repressed by nitrogen sources such as glutamine or ammonium. Sensing and uptake of ammonium by specific permeases play key roles in nitrogen metabolism. Here, we describe the cloning of three ammonium permease genes, mepA, mepB, and mepC, and their participation in ammonium uptake and signal transduction in F. fujikuroi. The expression of all three genes is strictly regulated by the nitrogen regulator AreA. Severe growth defects of DeltamepB mutants on low-ammonium medium and methylamine uptake studies suggest that MepB functions as the main ammonium permease in F. fujikuroi. In DeltamepB mutants, nitrogen-regulated genes such as the gibberellin and bikaverin biosynthetic genes are derepressed in spite of high extracellular ammonium concentrations. mepA mepB and mepC mepB double mutants show a similar phenotype as DeltamepB mutants. All three F. fujikuroi mep genes fully complemented the Saccharomyces cerevisiae mep1 mep2 mep3 triple mutant to restore growth on low-ammonium medium, whereas only MepA and MepC restored pseudohyphal growth in the mep2/mep2 mutant. Overexpression of mepC in the DeltamepB mutants partially suppressed the growth defect but did not prevent derepression of AreA-regulated genes. These studies provide evidence that MepB functions as a regulatory element in a nitrogen sensing system in F. fujikuroi yet does not provide the sensor activity of Mep2 in yeast, indicating differences in the mechanisms by which nitrogen is sensed in S. cerevisiae and F. fujikuroi.

Amt2 permease is required to induce ammonium-responsive invasive growth and mating in Cryptococcus neoformans

The conserved AmtB/Mep/Rh family of proteins mediate the transport of ammonium across cellular membranes in a wide range of organisms. Certain fungal members of this group are required to initiate filamentous growth. We have investigated the functions of two members of the AmtB/Mep/Rh family from the pathogenic basidiomycete Cryptococcus neoformans. Amt1 and Amt2 are low- and high-affinity ammonium permeases, respectively, and a mutant lacking both permeases is unable to grow under ammonium-limiting conditions. AMT2 is transcriptionally induced in response to nitrogen limitation, whereas AMT1 is constitutively expressed. Single and double amt mutants exhibit wild-type virulence in two models of cryptococcosis. Consistent with this, the formation of two C. neoformans virulence factors, cell wall melanin and the extracellular polysaccharide capsule, is not impaired in cells lacking either or both of the Amt1 and Amt2 permeases. Amt2 is, however, required for the initiation of invasive growth of haploid cells under low-nitrogen conditions and for the mating of wild-type cells under the same conditions. We propose that Amt2 may be a new fungal ammonium sensor and an element of the signaling cascades that govern the mating of C. neoformans in response to environmental nutritional cues.