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Regulatory sequences for expressing genes in oomycete fungi.

Promoter and terminator sequences from a range of species were tested for activity in the oomycetes, a group of lower fungi that bear an uncertain taxonomic affinity to other organisms and in which little is known of the sequences required for transcription. Transient assays, using the reporter gene beta-glucuronidase (GUS), were used to examine the function of these promoters and terminators in the plant pathogens Phytophthora infestans and P. megasperma f. sp. glycinea, and in the saprophytic water mold, Achlya ambisexualis. Oomycete promoters, isolated from the ham34 and hsp70 genes of Bremia lactucae and the actin gene of P. megasperma f. sp. glycinea, resulted in high levels of GUS accumulation in each of the three oomycetes. In contrast, little or no activity was detected when promoters from higher fungi (four ascomycetes and one basidiomycete), plants, and animals were tested. The terminator from the ham34 gene resulted in much higher levels of GUS accumulation than did others, although an oomycete terminator was not absolutely required for expression. Transcript mapping of RNA from stable transformants confirmed accurate initiation from the B. lactucae hsp70 promoter and termination within 3' ham34 sequences in P. infestans. Our results indicate that the transcriptional machinery of the oomycetes differs significantly from that of the higher fungi, but that enough conservation exists within the class to allow vectors developed from one oomycete species to be used for others.

Base Sequence

Outcrossing in the homothallic oomycete, Pythium ultimum, detected with molecular markers.

The oomycete Pythium ultimum is homothallic, thus a single isolate completes the sexual stage in pure culture. It has been generally assumed that homothallic oomycetes are predominantly inbreeding. In P. ultimum, antheridia occasionally develop from hyphae not directly connected to the oogonium and appear to participate in fertilization, suggesting a possible mechanism for outcrossing. We have used molecular markers to confirm that outcrossing can occur between isolates of P. ultimum. Genetic markers based on randomly amplified polymorphic DNA (RAPD) and restriction fragment length polymorphisms (RFLP) were used to distinguish isolates in a collection of P. ultimum. Two isolates displaying a high level of polymorphism were mixed and placed on media which allows the development of the sexual stage. RAPD markers were used to screen single oospore progeny to identify potential hybrids between the two parental isolates. Subsequent self-fertilization of one putative F1 yielded a F2 population which demonstrated segregation and independent assortment of RAPD and RFLP markers. A similar strategy was used to show that an isolate which is incapable of producing oospores in pure culture can outcross when mixed with a homothallic isolate. These results suggest that other homothallic oomycetes may be capable of outcrossing, and sexual reproduction may, therefore, play an important role in the generation of variation in homothallic oomycetes.

Crosses, Genetic

Microbody-like organelles as taxonomic markers among Oomycetes.

Zoospores of Oomycetes contain a variety of microbody-like organelles with highly structured matrices. Although in general their function is unknown, the appearance of similar organelles in related taxa suggests the ultrastructural differences could be used as taxonomic characters. This study surveys microbody-like organelles of oomycetous zoospores to determine if this is an additional criterion by which the phylogeny of these fungi can be evaluated. In zoospores of the order Saprolegniales, kinetosome-associated organelles (K-bodies) are found which typically consist of tubular and/or granular matrices. K-bodies are not found associated with kinetosomes in zoospores of the Peronosporales, but microbodies containing tubules, and in some genera marginal plates, are located near the kinetosomes, along the groove, and in other peripheral areas. K-bodies have been reported in only one member of the order Lagenidiales. These K-bodies lack a granular matrix, but contain a single curved plate from which tubules arise, forming a cone. In the one genus of the Leptomitales examined, a similar K-body contains a plate and scattered tubules. Organisms with similar microbody-like organelles are probably more closely related than those with different types of microbody-like organelles. The presence of an organelle resembling K-bodies in zoospores of an alga in the Tribophyceae supports the phylogenetic association between algae and Oomycetes. A complete survey of Oomycete genera may well reveal intermediates between the structurally different types of microbody-like organelles, allowing the reconstruction of the phylogenetic history of an organelle.

Biological Evolution

Application of Proteomic Methods in Oomycete Biology.

The biochemical makeup of any organism provides insight into key factors regarding its biological functions. These factors can be explored using proteomics, which allows us to obtain a snapshot of the protein content and abundance in an organism, cell type or sub-cellular compartment. Here, we describe proteomic methodologies that can be used to dissect the biochemical mechanism of phytopathogenicity in oomycetes. These methodologies include protein extraction, purification, subsequent processing, mass spectrometry analysis, and qualitative and quantitative data processing of oomycete proteomes for comparative studies. Additionally, the use of mass spectra to assist in gene validation and modelling in unfinished oomycete genomes is also described.

Oomycetes

Glycogen and other soluble glucans from chytridiomycete and oomycete species.

Dry weight, protein, lipid, and glycogen were determined at various times during cultivation of the Chytridiomycetes, Rhizophydium sphaerotheca and Monoblepharella elongata. M. elongata had relatively stable levels of glycogen, but, in R. sphaerotheca, glycogen levels showed significant changes, particularly in older cultures in which a depletion of glycogen was accompanied by a marked thickening of the cell walls. Glycogen was a significant cellular constituent in both chytridiomycete species. In R. sphaerotheca and M. elongata, respectively, glycogen accounted for as much as 6% and 8.1% of the dry weight. In purified glycogens of both species, only alpha-1,4- and alpha-1,6-linked glucosyl residues were detected and the absorbance spectra of I2-complexes were similar to those of other well characterized glycogens. Purified Rhizophydium glycogen had a beta-amylolysis limit of 43%, and a CL of approximately 12. For the Monoblepharella polysaccharide, the respective values were 45% and 11. In extracts of the Oomycetes, Pythium debaryanum, Mindeniella spinospora, and Apodachlya sp., only beta-1,3- and beta-1,6-linked glucosyl residues were detected. These glucans were not iodophilic nor were they sensitive to alpha-amylase and beta-amylase. The properties of the oomycete polysaccharides suggested that they were similar to the mycolaminarans of Phytophthora spp. Although both investigated chytridiomycete species produced glycogen with typical properties, glycogen was apparently absent in the investigated Oomycetes.

Fungal Proteins

Transformation of the oomycete pathogen, Phytophthora infestans.

A stable transformation procedure has been developed for Phytophthora infestans, an oomycete fungus that causes the late blight diseases of potato and tomato. This is the first description of reliable methods for transformation in an oomycete pathogen. Drug-resistant transformants were obtained by using vectors that contained bacterial genes for resistance to hygromycin B or G418 fused to promoters and terminators from the Hsp70 and Ham34 genes of the oomycete, Bremia lactucae. Using polyethylene glycol and CaCl2, vector DNA was introduced into protoplasts as a complex with cationic liposomes or with carrier DNA only. Transformants were obtained at similar frequencies with each combination of promoter and selectable marker and were confirmed by DNA and RNA hybridization and phosphotransferase assays. Transformation occurred through the integration of single or tandemly repeated copies of the plasmids into genomic DNA, conferring mitotically stable drug-resistant phenotypes. The sizes of the marker gene mRNAs in each transformant and the results of transcript mapping studies were consistent with the function of the B. lactucae regulatory sequences in P. infestans. A hygromycin-resistant transformant was tested and found to maintain pathogenicity, indicating that the gene transfer procedure will be useful for the molecular analysis of genes relevant to disease.

Base Sequence

Vacuolar reticulum in oomycete hyphal tips: An additional component of the Ca2+Regulatory system?

Cultures of Achlya sp., Phytophthora cinnamomi, Saprolegnia diclina, S. ferax, and S. parasitica, treated with 6-carboxyfluorescein diacetate solution, accumulate 6-carboxyfluorescein in a reticulate system of fine tubules. The network shows longitudinal polarity within the hyphae, tubules being finest toward the hyphal tips. In more mature subapical regions the network is connected with large vacuoles that also accumulate 6-carboxyfluorescein. A morphologically similar system has also been identified in freeze-substituted hyphae of S. ferax. The network is considered to be vacuolar, but differs from the tubular vacuole system of true fungi in that tubules are less motile, more frequently branched, and do not alternate with clusters of spherical vacuoles. The appearance of the network resembles patterns of calcium-sensitive dye staining and it is suggested that the vacuolar reticulum in the tip region of oomycete hyphae may act as a Ca2+ sink. The tubular reticulum in oomycetes is very fragile and can be shown with 6-carboxyfluorescein in only those hyphal tips with a motility and organelle distribution characteristic of growing hyphae with normal morphology. Diverse abnormal hyphae show a range of other fluorochrome localizations. These include large irregular compartments filled with fluorochrome, and fluorescent cytoplasm with organelles and vacuoles standing out in negative contrast. These localizations in abnormal hyphae are correlated with other structural changes indicative of damage. Special care is required in experiments with oomycetes to avoid such artefacts of localization. Copyright 1997 Academic Press. Copyright 1997 Academic Press

Journal Article

Structure of the large ribosomal subunit RNA of Phytophthora megasperma, and phylogeny of the oomycetes.

The 5.8S and 28S rRNA sequences of the oomycete Phytophthora megasperma were determined in order to study the secondary structure of these molecules and to assess the phylogenetic position of the oomycetes among the eukaryotes. Preliminary results point to an affiliation between the oomycetes, dinoflagellates and ciliates, a cluster which seems related to the fungi. In the course of this work, we developed a set of primers which allow sequencing and PCR amplification of eukaryotic large ribosomal subunit RNA genes of a wide range of phylogenetically distant organisms.

Base Sequence

Resistance to oomycetes: a general role for the hypersensitive response?

Oomycete plant pathogens, such as Phytophthora, downy mildews and Pythium, have devastating disease effects on numerous crop and ornamental plants. Various types of genetic resistance to oomycetes occur in plants, and can be determined at the subspecific or varietal level (race or cultivar-specific resistance), or at the species or genus level (nonhost resistance). In addition, resistance might be a quantitative phenotype (partial resistance). Resistance reactions are often associated with the hypersensitive response - a programed cell death pathway. Recent advances in the genetic, biochemical and cytological characterization of disease resistance suggests that the hypersensitive response is associated with all forms of resistance to Phytophthora and downy mildews. Identification of the resistance genes involved in nonhost and partial resistance to oomycetes remains an important challenge.

Journal Article

Nucleotide sequences of 5S ribosomal RNA from four oomycete and chytrid water molds.

The nucleotide sequences of the 5S rRNAs of the oomycete water molds Saprolegnia ferax and Pythium hydnosporum and of the chytrid water molds Blastocladiella simplex and Phlyctochytrium irregulare were determined by chemical and enzymatic partial degradation of 3' and 5' end-labelled molecules, followed by gel sequence analysis. The two oomycete sequences differed in 24 positions and the two chytrid sequences differed in 27 positions. These pairs differed in a mean of 44 positions. The chytrid sequences clearly most resemble the sequence from the zygomycete Phycomyces, while the oomycete sequences appear to be allied with those from protozoa and slime molds.

Base Sequence

Gene Editing and Protein Tagging in the Oomycete Phytophthora infestans Using CRISPR-Cas12a.

Molecular genetic tools such as CRISPR-Cas gene editing systems are invaluable for understanding gene and protein function and revealing the details of a pathogen's life and disease cycles. Here we present protocols for genome editing in Phytophthora infestans, an oomycete with global importance as a pathogen of potato and tomato. Using a vector system that expresses variants of Cas12a from Lachnospiraceae bacterium and its guide RNA from a unified transcript, we first present a method for editing genes through the non-homologous end-joining (NHEJ) pathway. We then describe an application of homology-directed repair (HDR), in which Cas12a is used to fuse a protein-coding gene with a fluorescent or epitope tag. Both methods should be adaptable to many oomycetes other than P. infestans.

Gene Editing

The 5S ribosomal RNA gene is linked to large and small subunit ribosomal RNA genes in the oomycetes, Phytophthora vignae, P. cinnamomi, P. megasperma f.sp. glycinea and Saprolegnia ferax.

Southern hybridization and polymerase chain reaction data indicate that the 5S ribosomal RNA gene is linked to the ribosomal RNA gene repeat unit in the oomycetes, Phytophthora vignae, P. cinnamomi, P. megasperma f.sp. glycinea and Saprolegnia ferax, and is apparently transcribed in the same direction as the large and small subunit ribosomal RNA genes. The polymerase chain reaction has been used to amplify all components of the entire ribosomal RNA gene repeat unit for each of these oomycetes. The total size of all amplified products is identical to the size of the ribosomal RNA gene repeat unit, as determined by Southern analysis.

Base Sequence

Crypticola clavulifera gen. et sp. nov. and Lagenidium giganteum: oomycetes pathogenic for dipterans infesting leaf axils in an Australian rain forest.

The isolation of two entomopathogenic fungi from Forcipomyia marksae larvae collected in leaf axils of Colocasia macrorrhiza in northeastern Queensland rain forests is reported. An oomycete, in which the zoospores complete their development wholly within the sporangium and are discharged through a short papillar extension, is described as a new genus and species, Crypticola clavulifera. A strain of the well-known oomycete, Lagenidium giganteum, was isolated from F. marksae--the first record of this fungus infecting a member of the Ceratopogonidae. The pathogenesis and zoosporogenesis of the two fungi in mosquito and ceratopogonid larvae are described.

Animals

Structure and expression of a gene encoding heat-shock protein Hsp70 from the Oomycete fungus Bremia lactucae.

A gene encoding a protein homologous to a 70-kDa heat-shock protein (Hsp70) was isolated from Bremia lactucae and its structure and pattern of expression were determined. This is the first report on the structure of a protein-coding gene from an Oomycete fungus. The cloned gene is a member of a small multigene family. The level of hsp70 mRNA in germlings increases from a low constitutive level in response to heat or cold treatment. A high level of the mRNA is also detected in spores. The hsp70 gene is expressed as a primary transcript of 2241 nucleotides (nt) and contains a continuous open reading frame of 2025 nt. Near the C terminus of the coding sequence is an unusual region that contains repeated enhancer-like sequences. This insert has not been described in other hsp70 genes and is not an intron. Upstream from the 5' terminus of the mRNA are multiple CCAAT motifs, a sequence similar to a consensus heat-shock regulatory element, and an A + T-rich putative 'TATA' box. A canonical polyadenylation recognition sequence is present downstream from the coding sequence. The deduced amino acid sequence is equally similar to yeast and maize Hsp70, providing further evidence of the dissimilarity between Oomycetes and true fungi. The cloning of this gene is part of our strategy to develop a transformation system for B. lactucae.

Amino Acid Sequence

Phylogenetic relationships between chlorophytes, chrysophytes, and oomycetes.

The phylogenetic relationships among the chlorophyte Chlamydomonas reinhardtii, the chrysophyte Ochromonas danica, and the oomycete Achyla bisexualis were explored by comparing the sequences of their small-subunit ribosomal RNA coding regions. Comparisons of similarity values or inspection of phylogenetic trees constructed by distance matrix methods reveal a very close relationship between oomycetes and chrysophytes. The separation of chrysophytes from chlorophytes is comparable to that of plants from animals, and both separations are far antedated by the divergence of a number of other protist groups.

Animals

CHS2, a chitin synthase gene from the oomycete Saprolegnia monoica.

PCR was used to amplify fragments corresponding to the chitin synthase (CHS) genes from the Oomycetes Saprolegnia monoica, Phytophthora capsici and Achlya ambisexualis, utilizing as primers, oligonucleotides designed from the conserved region of CHS genes of chitinous fungi. Chitin synthase homologues were found in the three cellulosic fungi. The chitin synthase 2 gene (CHS2) from S. monoica was cloned, sequenced and characterized. The amino acid sequence deduced from the CHS2 genomic DNA revealed several domains, corresponding to the catalytic domains and polypeptide signatures, of high identity with CHS genes from chitinous fungi. Existence of a CHS gene family in S. monoica was supported by the identification of two CHS sequences among the PCR products, the localization of CHS homologues on two chromosomes, and the detection of two transcripts in mycelia and protoplasts. Polyclonal anti-chitin synthase antibodies raised against the N-terminal and the neutral fragments of the CHS2 products revealed, respectively, two and four proteins in membrane fractions and a truncated active form in entrapped product. The overall comparison of the structure and organization of CHS genes indicates that in spite of their divergent evolution, Oomycetes and chitinous fungi have evolved with conserved chitin synthase systems.

Amino Acid Sequence

Transformation of the oomycete pathogen Phytophthora megasperma f. sp. glycinea occurs by DNA integration into single or multiple chromosomes.

A procedure for stable transformation was developed for Phytophthora megasperma f. sp. glycinea, an oomycete pathogen of soybean. Transformants were obtained using a bacterial hygromycin resistance gene fused to a promoter and terminator from the ham34 gene of another oomycete, Bremia lactucae. Vector DNA, alone or complexed to cationic liposomes, was introduced into protoplasts using polyethylene glycol and CaCl2. DNA and RNA hybridization, and phosphotransferase assays, confirmed the presence and expression of vector DNA in the transformants. Hybridization to electrophoretically separated chromosomes of P. m. glycinea showed that vector DNA had integrated into only one chromosome in four transformants, and into multiple chromosomes in one transformant.

Chromosome Mapping

Regulation of hsp90 and hsp70 genes during antheridiol-induced hyphal branching in the oomycete Achlya ambisexualis.

When mycelia of Achlya ambisexualis J. Raper strain E87 were undergoing antheridial branching, a marked increase was observed in the levels of transcript populations encoding the heat shock protein chaperone Hsp90 and transcript populations encoding three different Hsp70-family heat shock protein chaperones, respectively. Although up to 90% of hyphae in the hormone-treated thalli were undergoing antheridial branching, no similar increase in the level of transcripts encoding actin was observed. Nuclear run-on assays demonstrated that the observed antheridiol-induced increases in the levels of the chaperone RNAs resulted from increased transcription. Although not tested for function, the nucleotide sequence of the 5' flanking region of each of the two A. ambisexualis hsp90 genes revealed a diversity of sequences and motifs similar or identical to the sequences of known transcription factor response elements. Among these potential response element sequences observed in the A. ambisexualis genes were motifs observed also in animal steroid hormone response elements. Surrounding the primer-extension determined transcription start site of each A. ambisexualis hsp90 gene was a 16-nucleotide sequence that matched in 14 out of 16 nucleotides a sequence found in the transcription initiation region of many different oomycete genes.

Base Sequence