Cloning of the PYR3 gene of Ustilago maydis and its use in DNA transformation

A secreted lipase of Fusarium graminearum is a virulence factor required for infection of cereals

Fusarium graminearum is the causal agent of the Fusarium head blight (FHB) and a destructive pathogen of cereals accounting for high grain yield losses especially on wheat and maize. Like other fungal pathogens, F. graminearum secretes various extracellular enzymes, which are hypothesized to be involved in host infection. Extracellular lipolytic activity of F. graminearum was strongly induced in culture by wheat germ oil; this allowed us to isolate, clone, and characterize a gene (FGL1) encoding a secreted lipase. Expression analysis indicated that FGL1 is induced by lipid-containing substrates and repressed by glucose. In planta, FGL1 transcription was detected 1 day post-infection of wheat spikes. The function of the FGL1 gene product was verified by specifically demonstrating lipase activity after expression in a heterologous host. Ebelactone B, a known lipase inhibitor, repressed the lipolytic activity of the enzyme. Disease severity was strongly reduced when wild-type conidia were supplemented with ebelactone B. Transformation-mediated disruption of FGL1 led to reduced extracellular lipolytic activity in culture and to reduced virulence to both wheat and maize.

A PCR-based system for highly efficient generation of gene replacement mutants in Ustilago maydis

Ustilago maydis, the causative agent of corn smut disease, is one of the most versatile model systems for the study of plant pathogenic fungi. With the availability of the complete genomic sequence there is an increasing need to improve techniques for the generation of deletion mutants in order to elucidate the functions of unknown genes. Here a method is presented which allows one to generate constructs for gene replacement without the need for cloning. The 5' and 3'-regions of the target gene are first amplified by PCR, and subsequently ligated directionally to a marker cassette via two distinct SfiI sites, providing the flanking homologies needed for homologous recombination in U. maydis. Then the ligation product is used as a template for the amplification of the deletion construct, which can be used directly for transformation of U. maydis. The use of the fragments generated by PCR drastically increases the frequency of homologous recombination when compared to the linearized plasmids routinely used for gene replacement in U. maydis.

Lack of evidence for antisense suppression in the fungal plant pathogen Ustilago maydis

Modulation of the expression of the Ustilago maydis Pyr3 gene, encoding dihydroorotase (DHOase), through antisense RNA regulation has been explored. This was done by placing the gene in sense and antisense orientations under the control of an hsp70-like gene promoter in a high-copy number autonomously replicating expression vector. Cells transformed with the antisense vector contained similar levels of DHOase activity to those found in cells harboring the expression vector alone. Transformants containing the antisense vector did not exhibit uridine-dependent growth, which would be expected for a Pyr3-deficient phenocopy. This was despite detection of high levels of antisense RNA transcripts in cells transformed with the Pyr3 antisense vector.

Characterization of the ugatA gene of Ustilago maydis, isolated by homology to the gatA gene of Aspergillus nidulans

A gene encoding a putative GABA aminotransferase (ugatA) was isolated from the basidiomycete Ustilago maydis via heterologous hybridization to the GABA aminotransferase gene (gatA) of Aspergillus nidulans . The derived amino-acid sequence of ugatA shows strong identity throughout the protein to the GABA aminotransferase enzymes from A. nidulans and Saccharomyces cerevisiae. Northern analysis in U. maydis indicated that the ugatA transcript is inducible by the omega-amino acids GABA and beta-alanine, and is not subject to nitrogen catabolite repression. With the use of ugatA promoter-lacZ fusion constructs, it was demonstrated that the removal of sequences located approximately 250 bp 5' to the translational start site of ugatA (including multiple copies of a 7-bp direct repeat) resulted in the loss of induction by omega-amino acids. While the ugatA gene under the control of the A. nidulans gatA promoter was able to fully complement a gatA- phenotype in A. nidulans, the full-length ugatA gene was not, suggesting a lack of expression from the U. maydis promoter in A. nidulans. A U. maydis strain with a gene disruption at the ugatA locus showed decreased growth on beta-alanine as a sole nitrogen source, but was able to grow on GABA as a sole nitrogen source, indicating an alternative pathway for the utilization of GABA in U. maydis.

Cloning, sequencing, and characterizing the Lactobacillus leichmannii pyrC gene encoding dihydroorotase

The gene encoding dihydroorotase (DHOase) of Lactobacillus leichmannii, the third enzyme of the pyrimidine biosynthetic pathway (Genbank (EMBL) accession no X78999), was cloned by phenotypic complementation of an E coli pyrC deficient mutant after transformation with Lactobacillus leichmannii genomic library DNA. The open reading frame of the L leichmannii pyrC gene spans 1281 bp and codes for a 427 amino cid polypeptide with a calculated M(r) of 46,316 Da. Primer extension showed that the initiation site for transcription is 37 bp upstream of the putative start codon ATG and Northern blot analysis confirmed its independent transcription from the adjacent pyrB gene. Comparison of the deduced amino acid sequence of L leichmannii DHOase with sequences established for other organisms yielded 46.6% identity with the corresponding Bacillus subtilis enzyme. Highly conserved protein domains suggest importance for the enzyme's function.

The Ustilago maydis nar1 gene encoding nitrate reductase activity: sequence and transcriptional regulation

The nar1 gene was cloned from Ustilago maydis and the 908-amino-acid (aa) sequence of the encoded protein found to have strong identities with other nitrate reductases from fungi and plants. This was especially so in three domains which define enzyme cofactor-binding sites. The gene was isolated alone and in association with the nir1 gene, suggesting that the two genes are closely linked on the chromosome. The phenotype of a strain in which nar1 had been disrupted was consistent with the only role of nar1 being in nitrate reduction. Nitrate ions induced a 90-fold increase in nar1 transcript levels, while ammonium ions repressed transcript levels.

The influence of the Ustilago maydis REC1 gene on plasmid-chromosome recombination

The REC1 gene of U. maydis has an important but ill-defined role in DNA recombination and repair. We have examined its role in plasmid-chromosome recombination. Plasmid DNA was linearized at various locations with respect to the cloned U. maydis PYR3 gene and introduced into cells by transformation. Chromosomal integration and repair by an homologous cross-over with plasmid containing a double-strand break or gap in the PYR3 gene was markedly reduced in the absence of the REC1 gene product. Homologous replacement of the chromosomal pyr3-1 allele by a single copy of wild-type sequences from plasmid cut outside PYR3 was not found in the absence of the REC1 product. Instead, novel transformants generated in its absence suggests that ligation plays a role in their generation.

The Ustilago maydis pyr3 gene: sequence and transcriptional analysis

The pyr3 gene of Ustilago maydis encodes a 391-amino acid (aa) polypeptide. The sequence has identifies with dihydro-orotases (DHOases) from other organisms, but is most related to sequences of other monofunctional enzymes. The polypeptide contains the three domains conserved in other DHOases. The polypeptide encoded by the pyr3-1 allele has an aa change seven residues away from the C-terminal conserved domain. Transcription start point (tsp) is 58 nucleotides upstream from the start codon, and is in a region characterised by CTTT and CATC motifs. In the absence of TATA and CAAT boxes, these motifs might be important in transcriptional regulation. Gene disruption experiments suggest that the pyr3 gene product might have another function in addition to that in pyrimidine biosynthesis.

Cloning the REC1 gene of Ustilago maydis

The REC1 gene of Ustilago maydis plays a key role in homologous recombination and the repair of damaged DNA. In order to understand the nature and functions of the gene product, the gene has been cloned by functional complementation. A 3.8 kb cloned fragment complements the pleiotropic mitotic phenotype of different rec1 alleles. It does not complement the UV sensitivity of two other sensitive mutants. Disruption of the chromosomal copy of the 1.566 kb open reading frame within this fragment reproduces the rec1 pleiotropic phenotype. Furthermore, in diploids this disrupted reading frame is unable to complement previously characterised rec1 alleles.

Isolation, characterization and sequence of a gene conferring resistance to the systemic fungicide carboxin from the maize smut pathogen, Ustilago maydis

A gene which confers resistance to the systemic fungicide carboxin (Cbx) has been isolated from the maize pathogen, Ustilago maydis, by transferring a plasmid gene library from a Cbx-resistant mutant strain into a sensitive strain and selecting for expression of the resistance gene. Five plasmids, rescued from transformants which exhibited enhanced resistance to Cbx, were shown to have DNA inserts with common restriction enzyme fragments. All the plasmids transformed a sensitive U. maydis strain to Cbx resistance. The gene (Cbxr), sub-cloned on a 3.2 kb EcoR1-HindIII fragment, transformed U. maydis to Cbx resistance at frequencies similar to those obtained with the bacterial Hygromycin B resistance (HygBr) gene. The sequence of the Cbxr gene showed a high degree of homology to succinate dehydrogenase (EC 1.3.99.1) iron-sulphur subunit genes from other organisms.

Pathways of transformation in Ustilago maydis determined by DNA conformation

Ustilago maydis was transformed by plasmids bearing a cloned, selectable gene but lacking an autonomously replicating sequence. Transformation was primarily through integration at nonhomologous loci when the plasmid DNA was circular. When the DNA was made linear by cleavage within the cloned gene, the spectrum of integration events shifted from random to targeted recombination at the resident chromosomal allele. In a large fraction of the transformants obtained using linear DNA, the plasmid DNA was not integrated but was maintained in an extrachromosomal state composed of a concatameric array of plasmid units joined end-to-end. The results suggest the operation of several pathways for transformation in U. maydis, and that DNA conformation at the time of transformation governs choice of pathways.

Isolation of metabolic genes and demonstration of gene disruption in the phytopathogenic fungus Ustilago maydis

A cDNA library was constructed in the yeast expression vector pYcDE8 using mRNA from the phytopathogenic fungus Ustilago maydis and cDNAs capable of complementing mutations in three yeast genes, URA3, LEU2 and TPI1, were identified. Nucleotide sequence analysis indicated that the cDNA clone, which complemented the yeast ura3 mutation, carries the pyr6 gene encoding orotidine-5'-phosphate decarboxylase. The genomic copy of the pyr6 gene was isolated by hybridization with the cDNA and used to complement a pyr- mutant of U. maydis. One-step gene disruption was demonstrated by transforming U. maydis with a copy of the pyr6 gene interrupted in the coding region by a selectable marker for resistance to hygromycin B.