Gene Replacement by a Selectable Marker in the Filamentous FungusMagnaporthe oryzae

Magnaporthe oryzaeis a filamentous fungus responsible for the detrimental rice blast disease afflicting rice crops worldwide. For years, M. oryzae has served as an excellent model organism to study plant pathogen interactions due to its sequenced genome, its amenability to functional genetics, and its capacity to be tracked in laboratory settings. As such, techniques to genetically manipulate M. oryzae for gene deletion range from genome editing via CRISPR-Cas9 to gene replacement through homologous recombination. This protocol focuses on detailing how to perform gene replacement in the model organism, M. oryzae, through a split marker method. This technique relies on replacing the open reading frame of a gene of interest with a gene conferring resistance to a specific selectable chemical, disrupting the transcription of the gene of interest and generating a knockout mutant M. oryzae strain. Key features Comprehensive overview of primer design, PEG-mediated protoplast transformation, and fungal DNA extraction for screening.

Efficient Agrobacterium tumefaciens-mediated transformation system of Diaporthe caulivora

This is the first report describing the genetic transformation of Diaporthe caulivora, the soybean stem canker fungus. A simple and 100% efficient protocol of Agrobacterium tumefaciens-mediated transformation used mycelium as starting material and the hygromycin B resistance and green fluorescent protein (GFP) as a selection and reporter agents, respectively. All transgenic isolates were mitotically stable in two independent experiments and polymerase chain reaction with hygromycin B resistance primers confirmed successful T-DNA integration into the fungal genome. Plant-fungus interaction studies, including pathogenicity, latency, and endophytism, as well as further studies of random and targeted mutagenesis will be possible with GFP-expressing isolates of D. caulivora and other species in the Diaporthe / Phomopsis complex.

Resistance Marker- and Gene Gun-Mediated Transformation of Trichoderma reesei

Transformation enables the transfer of DNA into fungal cells for subsequent integration into the genome. Due to its versatility in industrial application, transformation is of utmost importance in Trichoderma reesei and hence continuously optimized. As one of the most crucial obstacles in fungal transformation efforts, removal of the cell wall is required to efficiently target genome modification cassettes to the genome. Here we describe resistance marker-mediated gene gun (biolistic) transformation of fungal spores of T. reesei as an alternative to protoplast transformation.

Agrobacterium-mediated transformation of Ceratocystis albifundus

Functional association between genomic loci and specific biological traits remains lacking in many fungi, including the African tree pathogen Ceratocystis albifundus. This is mainly because of the absence of suitable transformation systems for allowing genetic manipulation of this and other fungi. Here, we present an optimized protocol for Agrobacterium tumefaciens-mediated transformation of C. albifundus. Strain AGL-1 of A. tumefaciens and four binary T-DNA vectors (conferring hygromycin B or geneticin resistance and/or expressing the green fluorescent protein [GFP]) were used for transforming germinated conidia of three isolates of C. albifundus. Stable expression of these T-DNA-encoded traits was confirmed through sequential sub-culturing of fungal transformants on selective and non-selective media and by using PCR and sequence analysis. Single-copy integration of the respective T-DNAs into the genomes of these fungi was confirmed using Southern hybridization analysis. The range of experimental parameters determined and optimised included: (i) concentrations of hygromycin B and geneticin required for inhibiting growth of the wild type fungus and (ii) the dependence of transformation on acetosyringone for inducing the bacterium's virulence genes, as well as (iii) the duration of fungus-bacterium co-cultivation periods and (iv) the concentrations of fungal conidia and bacterial cells used for the latter. The system developed in this study is stable with a high-efficiency, yielding up to 400 transformants per 10⁶ conidia. This is the first report of a transformation protocol for C. albifundus and its availability will be invaluable for functional studies in this important fungus.

Development of a yeast heterologous expression cassette based on the promoter and terminator elements of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene

A new expression cassette (EC0) consisting of the fused 5′ and 3′ intergenic regions (IGRs) of the Eremothecium cymbalariae translational elongation factor 1α (EcTEF1) gene was evaluated through expression of the bacterial hygromycin B phosphotransferase (hph) resistance gene in the common baker’s yeast Saccharomyces cerevisiae. Progressively shorter versions of the hph-containing EC cassette (hphEC1 though hphEC6) with trimmed 5′ and 3′ EcTEF1 IGRs were tested for their ability to confer resistance to hygromycin B in S. cerevisiae. Hygromycin B resistance was retained in all six generated hphEC variants up to a concentration of 400 mg/L. The hphEC6 cassette was the shortest cassette to be assayed in this study with 366 and 155 bp of the EcTEF1 5′ and 3′ IGRs, respectively. When tested for deletion of the S. cerevisiae proline oxidase gene PUT1, the hphEC6 cassette was shown to successfully act as a selection marker on hygromycin B-containing medium. The hphEC6 cassette could be placed immediately adjacent to a kanMX4 G418 disulfate resistance marker without any discernable effect on the ability of the yeast to grow in the presence of both hygromycin B and G418 disulfate. Co-cultivation experiments under non-selective conditions demonstrated that a PUT1 deletion strain carrying the hphEC6 cassette displayed equivalent fitness to an otherwise isogenic PUT1 deletion strain carrying the kanMX4 cassette.

Establishment of an efficient transformation system for Pleurotus ostreatus

Pleurotus ostreatus is widely cultivated worldwide, but the lack of an efficient transformation system regarding its use restricts its genetic research. The present study developed an improved and efficient Agrobacterium tumefaciens-mediated transformation method in P. ostreatus. Four parameters were optimized to obtain the most efficient transformation method. The strain LBA4404 was the most suitable for the transformation of P. ostreatus. A bacteria-to-protoplast ratio of 100:1, an acetosyringone (AS) concentration of 0.1 mM, and 18 h of co-culture showed the best transformation efficiency. The hygromycin B phosphotransferase gene (HPH) was used as the selective marker, and EGFP was used as the reporter gene in this study. Southern blot analysis combined with EGFP fluorescence assay showed positive results, and mitotic stability assay showed that more than 75% transformants were stable after five generations. These results showed that our transformation method is effective and stable and may facilitate future genetic studies in P. ostreatus.

Genetic transformation of the white-rot fungus Dichomitus squalens using a new commercial protoplasting cocktail

D. squalens, a white-rot fungus that efficiently degrades lignocellulose in nature, can be used in various biotechnological applications and has several strains with sequenced and annotated genomes. Here we present a method for the transformation of this basidiomycete fungus, using a recently introduced commercial ascomycete protoplasting enzyme cocktail, Protoplast F. In protoplasting of D. squalens mycelia, Protoplast F outperformed two other cocktails while releasing similar amounts of protoplasts to a third cocktail. The protoplasts released using Protoplast F had a regeneration rate of 12.5% (±6 SE). Using Protoplast F, the D. squalens monokaryon CBS464.89 was conferred with resistance to the antibiotics hygromycin and G418 via polyethylene glycol mediated protoplast transformation with resistance cassettes expressing the hygromycin phosphotransferase (hph) and neomycin phosphotransferase (nptII) genes, respectively. The hph gene was expressed in D. squalens using heterologous promoters from genes encoding β-tubulin or glyceraldehyde 3-phosphate dehydrogenase. A Southern blot confirmed integration of a resistance cassette into the D. squalens genome. An average of six transformants (±2 SE) were obtained when at least several million protoplasts were used (a transformation efficiency of 0.8 (±0.3 SE) transformants per μg DNA). Transformation of D. squalens demonstrates the suitability of the Protoplast F cocktail for basidiomycete transformation and furthermore can facilitate understanding of basidiomycete gene function and development of improved strains for biotechnological applications.

Highly efficient transformation system for Malassezia furfur and Malassezia pachydermatis using Agrobacterium tumefaciens-mediated transformation

Malassezia spp. are part of the normal human and animal mycobiota but are also associated with a variety of dermatological diseases. The absence of a transformation system hampered studies to reveal mechanisms underlying the switch from the non-pathogenic to pathogenic life style. Here we describe, a highly efficient Agrobacterium-mediated genetic transformation system for Malassezia furfur and M. pachydermatis. A binary T-DNA vector with the hygromycin B phosphotransferase (hpt) selection marker and the green fluorescent protein gene (gfp) was introduced in M. furfur and M. pachydermatis by combining the transformation protocols of Agaricus bisporus and Cryptococcus neoformans. Optimal temperature and co-cultivation time for transformation were 5 and 7days at 19°C and 24°C, respectively. Transformation efficiency was 0.75-1.5% for M. furfur and 0.6-7.5% for M. pachydermatis. Integration of the hpt resistance cassette and gfp was verified using PCR and fluorescence microscopy, respectively. The T-DNA was mitotically stable in approximately 80% of the transformants after 10 times sub-culturing in the absence of hygromycin. Improving transformation protocols contribute to study the biology and pathophysiology of Malassezia.

Yeast recombination-based cloning as an efficient way of constructing vectors for Zymoseptoria tritici

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Yeast recombination-based cloning (YRBC) is a reliable and inexpensive way of generating plasmids.

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We provide 4 vectors for YRBC that a cover different resistance genes.

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Using this technique promises rapid generation of molecular tools to study Z. tritici.

Many pathogenic fungi are genetically tractable. Analysis of their cellular organization and invasion mechanisms underpinning virulence determinants profits from exploiting such molecular tools as fluorescent fusion proteins or conditional mutant protein alleles. Generation of these tools requires efficient cloning methods, as vector construction is often a rate-limiting step. Here, we introduce an efficient yeast recombination-based cloning (YRBC) method to construct vectors for the fungus Zymoseptoria tritici. This method is of low cost and avoids dependency on the availability of restriction enzyme sites in the DNA sequence, as needed in more conventional restriction/ligation-based cloning procedures. Furthermore, YRBC avoids modification of the DNA of interest, indeed this potential risk limits the use of site-specific recombination systems, such as Gateway cloning. Instead, in YRBC, multiple DNA fragments, with 30 bp overlap sequences, are transformed into Saccharomyces cerevisiae, whereupon homologous recombination generates the vector in a single step. Here, we provide a detailed experimental protocol and four vectors, each encoding a different dominant selectable marker cassette, that enable YRBC of constructs to be used in the wheat pathogen Z. tritici.

Production of transgenic local rice cultivars (Oryza sativa L.) for improved drought tolerance using Agrobacterium mediated transformation

Rice being the staple food of middle and south India, there is an extensive research undertaken in protecting the species and improving the quality and yield. Several recombinations have been made to the rice genome to impart various qualities which lack in the pure breed. Oryza faces various natural stress, like temperature variance, high salinity, etc., drought is one of the major parameters affecting the growth and yield of the plant. Transgenic rice cultivars can be generated for drought tolerance using the Agrobacterium mediated transformations. The current work aims to impart the gene for drought tolerance in Oryza sativa L. using Agrobacterium mediated transformation. The gene targeted in this context is dehydration response element binding factors (DREB). DREB plays a major role in response to drought mediated stress. Sambha mahsuri (Indica type) and Cotton dora sannalu (Indica type) the two local cultivars have been transformed for the gene AtDREB1A under 35s CaMV promoters (pBIH binary vector) for which the vector used was Agrobacterium. The target plant tissue being used was calli. Optimization of the parameters was performed for a lethal dose of hygromycin, cefotaxime level, and acetosyringone level. PCR amplification was used for the confirmation of the transgenic (T ₀) species in which 23% and 18% for Sambha mahsuri and Cotton dora sannalu, respectively. Southern blotting was performed for the genomic DNA. Normal growth was shown by the T ₁ transgenic plants whose expression was confirmed by RT-PCR. The T ₁ transgenic plants showed good tolerance to drought mediated stress for a total period of one and a half week under greenhouse condition. The study can be concluded by producing a potentially successful drought resistance T ₁ species produced using Agrobacterium mediated transformation.

An efficient particle bombardment system for the genetic transformation of asparagus (Asparagus officinalis L.)

The microprojectile bombardment method was used to transfer DNA into embryogenic callus of asparagus (Asparagus officcinalis L.) and to produce stably transformed asparagus plants. Embryogenic callus, derived from UC 157 and UC72 asparagus cultivars, was bombarded with tungsten particles coated with plasmid DNA that contained genes encoding hygromycin phosphotransferase, phosphinothricin acetyl transferase and β-glucuronidase. Putatively transformed calli were identified from the bombarded tissue after 4 months selection on 25 mg/L hygromycin B plus 4 mg/L phosphinothricin (PPT). By selecting embryogenic callus on hygromycin plus PPT the overall transformation and selection efficiencies were substantially improved over selection with hygromycin or PPT alone, where no transgenic clones were recovered. The transgenic nature of the selected material was demonstrated by GUS histochemical assays and Southern blot hybridization analysis. Transgenic asparagus plants were found to withstand the prescribed levels of the PPT-based herbicide BASTATM for weed control.