Heterologous transposition in Ustilago maydis

What is the role of the nitrate reductase (euknr) gene in fungi that live in nitrate-free environments? A targeted gene knock-out study in Ampelomyces mycoparasites

Mycoparasitic fungi can be utilized as biocontrol agents (BCAs) of many plant pathogens. Deciphering the molecular mechanisms of mycoparasitism may improve biocontrol efficiency. This work reports the first functional genetic studies in Ampelomyces, widespread mycoparasites and BCAs of powdery mildew fungi, and a molecular genetic toolbox for future works. The nitrate reductase (euknr) gene was targeted to reveal the biological function of nitrate assimilation in Ampelomyces. These mycoparasites live in an apparently nitrate-free environment, i.e. inside the hyphae of powdery mildew fungi that lack any nitrate uptake and assimilation system. Homologous recombination-based gene knock-out (KO) was applied to eliminate the euknr gene using Agrobacterium tumefaciens-mediated transformation. Efficient KO of euknr was confirmed by PCR, and visible phenotype caused by loss of euknr was detected on media with different nitrogen sources. Mycoparasitic ability was not affected by knocking out euknr as a tested transformant readily parasitized Blumeria graminis and Podosphaera xanthii colonies on barley and cucumber, respectively, and the rate of mycoparasitism did not differ from the wild type. These results indicate that euknr is not involved in mycoparasitism. Dissimilatory processes, involvement in nitric oxide metabolism, or other, yet undiscovered processes may explain why a functional euknr is maintained in Ampelomyces.

Biology, dynamics, and applications of transposable elements in basidiomycete fungi

The phylum Basidiomycota includes filamentous fungi and yeast species with different ecological and genomic characteristics. Transposable elements (TEs) are abundant components of most eukaryotic genomes, and their transition from being genomic parasites to key drivers of genomic architecture, functionality, and evolution is a subject receiving much attention. In light of the abundant genomic information released during the last decade, the aims of this mini-review are to discuss the dynamics and impact of TEs in basidiomycete fungi. To do this, we surveyed and explored data from 75 genomes, which encompass the phylogenetic diversity of the phylum Basidiomycota. We describe annotation approaches and analyze TE distribution in the context of species phylogeny and genome size. Further, we review the most relevant literature about the role of TEs in species lifestyle, their impact on genome architecture and functionality, and the defense mechanisms evolved to control their proliferation. Finally, we discuss potential applications of TEs that can drive future innovations in fungal research.

Genome editing in Ustilago maydis using the CRISPR-Cas system

This communication describes the establishment of the type II bacterial CRISPR-Cas9 system to efficiently disrupt target genes in the fungal maize pathogen Ustilago maydis. A single step transformation of a self-replicating plasmid constitutively expressing the U. maydis codon-optimized cas9 gene and a suitable sgRNA under control of the U. maydis U6 snRNA promoter was sufficient to induce genome editing. On average 70% of the progeny of a single transformant were disrupted within the respective b gene. Without selection the self-replicating plasmid was lost rapidly allowing transient expression of the CRISPR-Cas9 system to minimize potential long-term negative effects of Cas9. This technology will be an important advance for the simultaneous disruption of functionally redundant genes and gene families to investigate their contribution to virulence of U. maydis.

Identification of virulence genes in Fusarium oxysporum f. sp. lycopersici by large-scale transposon tagging

Forward genetic screens are efficient tools for the dissection of complex biological processes, such as fungal pathogenicity. A transposon tagging system was developed in the vascular wilt fungus Fusarium oxysporum f. sp. lycopersici by inserting the novel modified impala element imp160::gfp upstream of the Aspergillus nidulans niaD gene, followed by transactivation with a constitutively expressed transposase. A collection of 2072 Nia(+) revertants was obtained from reporter strain T12 and screened for alterations in virulence, using a rapid assay for invasive growth on apple slices. Seven strains exhibited reduced virulence on both apple slices and intact tomato plants. Five of these were true revertants showing the re-insertion of imp160::gfp within or upstream of predicted coding regions, whereas the other two showed either excision without re-insertion or no excision. Linkage between imp160::gfp insertion and virulence phenotype was determined in four transposon-tagged loci using targeted deletion in the wild-type strain. Knockout mutants in one of the genes, FOXG_00016, displayed significantly reduced virulence, and complementation of the original revertant with the wild-type FOXG_00016 allele fully restored virulence. FOXG_00016 has homology to the velvet gene family of A. nidulans. The high rate of untagged virulence mutations in the T12 reporter strain appears to be associated with increased genetic instability, possibly as a result of the transactivation of endogenous transposable elements by the constitutively expressed transposase.

Hallmarks of RNA silencing are found in the smut fungus Ustilago hordei but not in its close relative Ustilago maydis

RNA interference (RNAi) acts through transcriptional and post-transcriptional gene silencing of homologous sequences. With the goal of using RNAi as a tool for studying gene function in the related basidiomycete cereal pathogens Ustilago hordei and Ustilago maydis, we developed a general purpose RNAi expression vector. Tandem, inverted fragments of the GUS gene were inserted into this vector flanking an intron and used to transform engineered GUS-expressing haploid cells. Down-regulation of the GUS gene and production of siRNAs were seen only in U. hordei, even though corresponding GUS double-stranded RNA was detected in both species. Similarly, when the endogenous bW mating-type gene was targeted by RNAi, mating was reduced only in U. hordei. Our work demonstrates the feasibility of using RNAi in U. hordei and provides experimental support for the observed lack of RNAi components in the U. maydis genome. We hypothesize that the sharply limited transposon complement in U. maydis is a biological consequence of this absence.

Agrobacterium-mediated transformation as a tool for functional genomics in fungi

In the era of functional genomics, the need for tools to perform large-scale targeted and random mutagenesis is increasing. A potential tool is Agrobacterium-mediated fungal transformation. A. tumefaciens is able to transfer a part of its DNA (transferred DNA; T-DNA) to a wide variety of fungi and the number of fungi that can be transformed by Agrobacterium-mediated transformation (AMT) is still increasing. AMT has especially opened the field of molecular genetics for fungi that were difficult to transform with traditional methods or for which the traditional protocols failed to yield stable DNA integration. Because of the simplicity and efficiency of transformation via A. tumefaciens, it is relatively easy to generate a large number of stable transformants. In combination with the finding that the T-DNA integrates randomly and predominantly as a single copy, AMT is well suited to perform insertional mutagenesis in fungi. In addition, in various gene-targeting experiments, high homologous recombination frequencies were obtained, indicating that the T-DNA is also a useful substrate for targeted mutagenesis. In this review, we discuss the potential of the Agrobacterium DNA transfer system to be used as a tool for targeted and random mutagenesis in fungi.

Ustilago maydis: how its biology relates to pathogenic development

The smut fungus Ustilago maydis is a ubiquitous pathogen of corn. Although of minor economical importance, U. maydis has become the most attractive model among the plant pathogenic basidiomycetes under study. This fungus undergoes a number of morphological transitions throughout its life-cycle, the most prominent being the dimorphic switch from budding to filamentous growth that is prerequisite for entry into the biotrophic phase. The morphological transition is controlled by the tetrapolar mating system. Understanding the mating system has allowed connections to signalling cascades operating during pathogenic development. Here, we will review the status and recent insights into understanding pathogenic development of U. maydis and emphasize areas and directions of future research. Contents Summary 31 I. Introduction 31 II. Important tools for exprimentation with Ustilago myadis 32 III. Cell fusion requres a complex signalling network 33 IV. Development of the dikaryon: the bE/bW complex at work 34 V. A connection between cell cycle, morphogenesis and virulence 36 VI. The early infection stages 38 VII. Proliferation and differentiaton in the plant host 38 VIII. The Ustilago maydis genome 39 IX. Conclusions 40 Acknowledgements 40 References 40.

Ustilago maydis, model system for analysis of the molecular basis of fungal pathogenicity

SUMMARY Ustilago maydis, a facultative biotrophic basidiomycete fungus, causes smut disease in maize. A hallmark of this disease is the induction of large plant tumours that are filled with masses of black-pigmented teliospores. During the last 15 years U. maydis has become an important model system to unravel molecular mechanisms of fungal phytopathogenicity. This review highlights recent insights into molecular mechanisms of complex signalling pathways that are involved in the transition from budding to filamentous growth and operate during the pathogenic growth phase. In addition, we describe recent progress in understanding the structural basis of morphogenesis and polar growth in different stages of U. maydis development. Finally, we present an overview of recently identified genes related to pathogenic development and summarize novel molecular and genomic approaches that are powerful tools to explore the genetic base of pathogenicity.

TAXONOMY

Ustilago maydis (DC) Corda (synonymous with Ustilago zeae Ung.)-Kingdom Eukaryota, Phylum Fungi, Order Basidiomycota, Family Ustilaginomycetes, Genus Ustilago.

HOST RANGE

Infects aerial parts of corn plants (Zea mays) and its progenitor teosinte (Zea mays ssp. parviglumis). Maize smut is distributed throughout the world. Disease symptoms: U. maydis causes chlorotic lesions in infected areas, the formation of anthocyanin pigments, necrosis, hyperplasia and hypertrophy of infected organs. Infection by U. maydis can inhibit development and lead to stunting of infected plants. A few days after infection plant tumours develop in which massive fungal proliferation and the formation of the black-pigmented, diploid teliospores occurs. Under natural conditions tumours predominantly develop on sexual organs (tassels and ears), stems and nodal shoots. Tumours may vary in size from minute pustules to several centimetres in diameter and contain up to 200 billion spores. Useful web site: http://www-genome.wi.mit.edu/annotation/fungi/ustilago_maydis/