Turning the Table: Plants Consume Microbes as a Source of Nutrients

Interactions between plants and microbes in soil, the final frontier of ecology, determine the availability of nutrients to plants and thereby primary production of terrestrial ecosystems. Nutrient cycling in soils is considered a battle between autotrophs and heterotrophs in which the latter usually outcompete the former, although recent studies have questioned the unconditional reign of microbes on nutrient cycles and the plants' dependence on microbes for breakdown of organic matter. Here we present evidence indicative of a more active role of plants in nutrient cycling than currently considered. Using fluorescent-labeled non-pathogenic and non-symbiotic strains of a bacterium and a fungus (Escherichia coli and Saccharomyces cerevisiae, respectively), we demonstrate that microbes enter root cells and are subsequently digested to release nitrogen that is used in shoots. Extensive modifications of root cell walls, as substantiated by cell wall outgrowth and induction of genes encoding cell wall synthesizing, loosening and degrading enzymes, may facilitate the uptake of microbes into root cells. Our study provides further evidence that the autotrophy of plants has a heterotrophic constituent which could explain the presence of root-inhabiting microbes of unknown ecological function. Our discovery has implications for soil ecology and applications including future sustainable agriculture with efficient nutrient cycles

A Novel High-Affinity Sucrose Transporter Is Required for Virulence of the Plant Pathogen Ustilago maydis

A novel, high-affinity sucrose transporter identified in the plasma membrane of the plant pathogen Ustilago maydis is essential for fungal virulence and successful infection of maize

The Impact of Small Molecule Binding on the Energy Landscape of the Intrinsically Disordered Protein C-Myc

Intrinsically disordered proteins are attractive therapeutic targets owing to their prevalence in several diseases. Yet their lack of well-defined structure renders ligand discovery a challenging task. An intriguing example is provided by the oncoprotein c-Myc, a transcription factor that is over expressed in a broad range of cancers. Transcriptional activity of c-Myc is dependent on heterodimerization with partner protein Max. This protein-protein interaction is disrupted by the small molecule 10058-F4 (1), that binds to monomeric and disordered c-Myc. To rationalize the mechanism of inhibition, structural ensembles for the segment of the c-Myc domain that binds to 1 were computed in the absence and presence of the ligand using classical force fields and explicit solvent metadynamics molecular simulations. The accuracy of the computed structural ensembles was assessed by comparison of predicted and measured NMR chemical shifts. The small molecule 1 was found to perturb the composition of the apo equilibrium ensemble and to bind weakly to multiple distinct c-Myc conformations. Comparison of the apo and holo equilibrium ensembles reveals that the c-Myc conformations binding 1 are already partially formed in the apo ensemble, suggesting that 1 binds to c-Myc through an extended conformational selection mechanism. The present results have important implications for rational ligand design efforts targeting intrinsically disordered proteins

RNA-seq analysis in plant–fungus interactions

Many fungi are pathogens that infect important food and plantation crops, reducing both yield and quality of food products. Understanding plant–fungus interactions is crucial as knowledge in this area is required to formulate sustainable strategies to improve plant health and crop productivity. High-throughput RNA-sequencing (RNA-seq) enables researchers to gain insights of the mixed and multispecies transcriptomes in plant–fungus interactions. Interpretation of huge data generated by RNA-seq has led to new insights in this area, facilitating a system approach in unraveling interactions between plant hosts and fungal pathogens. In this review, the application and challenges of RNA-seq analysis in plant–fungus interactions will be discussed

Impact of genomics on fungal biology

Fungi represent an extremely diverse and complex class of organisms, and their categorization as lower eukaryotes should by no means be mistaken as meaning low-end. At present, fungi serve as model systems for various aspects of molecular and cellular biology, for example cell cycle regulation, intracellular signaling, metabolic pathway analysis and transcriptional regulation (Feldbrügge et al., 2004; Jiang, 2006; Oliver, 2006). They are also increasingly used on an industrial scale in the production of chemical compounds or in bioremediation (Grimm et al., 2005; Tortella et al., 2005). Some of the most recent and exciting advances within the field of fungal biology have been linked with genomic studies. To explore these, the IXth International Fungal Biology Conference & 16th New Phytologist Symposium entitled Impact of Genomics in Fungal Biology was held in Nancy, France (http://www.newphytologist. org/fungal-genomics/default.htm). The meeting brought together nearly 100 scientists, from all areas of fungal research, and highlighted a wide range of impacts that genome sequencing has and will have on our understanding of fungal biology

Rust haustoria : nutrient uptake and beyond

Haustoria are morphological features of an extremely successful class of plant parasites, the obligate biotrophs. The broad phylogenetic spectrum of organisms producing haustoria suggests that these structures have arisen many times in the course of evolution and represent specific adaptations of these organisms to the close interaction with their respective host plants. This close interaction and the fact that these structures cannot be produced in vitro have hampered an analysis of the roles of haustoria in biotrophy for many decades. Only recently has it become possible to analyse haustorial function at a molecular level. A picture is beginning to emerge indicating that haustoria do not only serve in nutrient uptake a task postulated for these elements ever since their discovery. Moreover, they seem to perform enormous biosynthetic duties. They also seem to be engaged in the suppression of host defense responses and in redirecting or reprogramming the host s metabolic flow. This review intends to summarize current knowledge about the structure and function especially of rust haustoria

The Uredinales : Cytology, Biochemistry, and Molecular Biology

Fungi belonging to the order Uredinales are commonly referred to as rust fungi. All members of the Uredinales are parasitic on plants, often causing dramatic losses in various important crop plants (Alexopoulos et al. 1996). Together with the powdery mildew fungi and the downy mildew-causing oomycetes, rust fungi form an extremely successful group of parasites, the obligate biotrophs. The term obligate biotrophic characterizes a specific lifestyle in which the pathogen is absolutely dependent on a living host to complete its life cycle. In turn, the host plant as a whole usually suffers only limited damage over an extended period of time (Staples 2000). By contrast, necrotrophic parasites kill their hosts quickly after infection and subsequently thrive on the dead plant material (Staples 2001). Hemibiotrophic fungi, such as Colletotrichum spp., are characterized by a more or less extended biotrophic phase before switching to necrotrophic growth and killing their host (Perfect and Green 2001). In order to separate the true obligate biotrophic pathogens from hemibiotrophs and necrotrophs we suggest the following six criteria:1. Obligate biotrophs are not culturable in vitro (at least not to a point representing the parasitic phase)2. They form highly differentiated infection structures (variations of the normally tubular cell shape, which are necessary for pathogenesis)3. They have limited secretory activity4. They establish a narrow contact zone separating fungal and plant plasma membranes5. They engage in a long-term suppression of host defense responses6. They form haustoria (specialized hyphae that penetrate host cells).The peculiarities of the lifestyle of obligate biotrophs, paired with their huge economic impact, make rust fungi a versatile field of study at both the fundamental and the applied level. This chapter on Uredinales can by no means cover the complete literature on rust fungi. It is intended to summarize key references, review articles, and books to provide the interested reader witha gateway to more specialized literature on most aspects of research involving rust fungi. Readers new to the field are encouraged to consult the excellent textbooks by Alexopoulos et al. (1996) and Webster and Weber (2007) to gain easier access into the exciting field of mycology in general and obligate biotrophic plant parasites like the rust fungi in particular

High Level Activation of Vitamin B1 Biosynthesis Genes in Haustoria of the Rust Fungus Uromyces fabae

In the rust fungus Uromyces fabae, the transition from the early stages of host plant invasion toward parasitic growth is accompanied by the activation of many genes (PIGs = in planta induced genes). Two of them, PIG1 (= THI1) and PIG4 (= THI2), were found to be highly transcribed in haustoria, and are homologous to genes involved in thiamine (vitamin B1) biosynthesis in yeast. Their functional identity was confirmed by complementation of Schizosaccharomyces pombe thiamine auxotrophic thi3 (nmt1) and thi2 (nmt2) mutants, respectively. In contrast to thiamine biosynthesis genes of other fungi that are completely suppressed by thiamine, THI1 and THI2 expression was not affected by the addition of thiamine to rust hyphae grown either in vitro or in planta. Immunoblot analysis revealed decreasing amounts of THI1p in extracts from spores, germlings, and in vitro-grown infection structures with increasing time after inoculation. Immunofluorescence microscopy of rust-infected leaves detected high concentrations of THI1p in haustoria, and only low amounts in intercellular hyphae. In the sporulating mycelium, THI1p was found in the basal hyphae of the uredia, but not in the pedicels and only at very low levels in uredospores. These data indicate that the haustorium is an essential structure of the biotrophic rust mycelium not only for nutrient uptake but also for the biosynthesis of metabolites such as thiamine

Differential Regulation of Gene Expression in the Obligate Biotrophic Interaction of Uromyces fabae with Its Host Vicia faba

Classical analysis of obligate biotrophic fungi revealed changes of enzyme activities or the concentration of metabolites in infected areas. However, due to the intricate integration of host and parasite metabolism, it was not possible to delineate the individual contributions of the two organisms. Here, we used reverse-transcription polymerase chain reaction to monitor expression of genes from the rust fungus Uromyces fabae and its host Vicia faba. We focused on genes relevant for amino acid and sugar uptake and metabolism in both organisms. In the fungus, mRNA for plasma membrane ATPase was detected in spores and all infection structures. Two genes for fungal amino acid transporters showed dissimilar regulation. Transcripts for one were detected during all developmental stages, whereas those of the other appeared to be under developmental control. The latter result was also obtained for the so far only hexose transporter known from U. fabae and for one gene of the thiamine biosynthesis pathway. In the host plant, transcripts for two ATPases analyzed generally declined upon infection. Sucrose synthase expression increased in leaves, but decreased in roots. Transcript levels of glucose and sucrose transporter genes appeared unchanged. Markers for amino acid metabolism did not show a uniform trend: transcripts for asparagine synthetase increased, whereas those for two amino acid transporters either decreased or increased. Our analyses revealed that not only expression of genes in the immediate vicinity of the primary infection site is altered, but infection also influences transcription of certain genes in remote organs, like stems and roots. This demonstrates alterations in the source-sink relationships