A polyketide synthase gene cluster associated with the sexual reproductive cycle of the banana pathogen, Pseudocercospora fijiensis

TRustDB: A comprehensive bioinformatics resource for understanding the complete Wheat-Stem rust host-pathogen interactome

The increasing infectious diseases in wheat immensely reduce crop yield and quality, thus affecting global wheat production. The evolution in phytopathogens hinders the understanding of the disease infection mechanisms. TRustDB is an open-access, comprehensive database that is specifically focused on the disease stem rust (also known as black rust) in Triticum aestivum, which is caused by the fungal pathogen Puccinia graminis (Pgt), strains 'Ug99' and '21-0'. The database aims at a broader focus of providing the researchers with comprehensive tools to predict the protein-protein interactions and avail the functional annotations of the proteins involved in the interactions that cause the disease. The network of the predicted interactome can also be visualized on the browser. Various modules for the functional annotations of the host and pathogen proteins such as subcellular localization, functional domains, gene ontology annotations, pathogen orthologs and effector proteins have been implemented. The host proteins that serve as transcription factors, along with the respective Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways are also available, which further enhance the understanding of the disease infection mechanisms and the defense responses of the host. The database is also linked with several other databases such as InterPro, KEGG pathways, Ensembl and National Center for Biotechnology Information (NCBI). TRustDB has a user-friendly web interface, which can be accessed through . Database URL http://bioinfo.usu.edu/trustdb/.

Genetic Characteristics and Metabolic Interactions between Pseudocercospora fijiensis and Banana: Progress toward Controlling Black Sigatoka

The international importance of banana and severity of black Sigatoka disease have led to extensive investigations into the genetic characteristics and metabolic interactions between the Dothideomycete Pseudocercospora fijiensis and its banana host. P. fijiensis was shown to have a greatly expanded genome compared to other Dothideomycetes, due to the proliferation of retrotransposons. Genome analysis suggests the presence of dispensable chromosomes that may aid in fungal adaptation as well as pathogenicity. Genomic research has led to the characterization of genes and metabolic pathways involved in pathogenicity, including: secondary metabolism genes such as PKS10-2, genes for mitogen-activated protein kinases such as Fus3 and Slt2, and genes for cell wall proteins such as glucosyl phosphatidylinositol (GPI) and glycophospholipid surface (Gas) proteins. Studies conducted on resistance mechanisms in banana have documented the role of jasmonic acid and ethylene pathways. With the development of banana transformation protocols, strategies for engineering resistance include transgenes expressing antimicrobial peptides or hydrolytic enzymes as well as host-induced gene silencing (HIGS) targeting pathogenicity genes. Pseudocercospora fijiensis has been identified as having high evolutionary potential, given its large genome size, ability to reproduce both sexually and asexually, and long-distance spore dispersal. Thus, multiple control measures are needed for the sustainable control of black Sigatoka disease.

Differential regulation and production of secondary metabolites among isolates of the fungal wheat pathogen Zymoseptoria tritici

The genome of the wheat pathogenic fungus, Zymoseptoria tritici, represents extensive presence-absence variation in gene content. Here, we addressed variation in biosynthetic gene clusters (BGCs) content and biochemical profiles among three isolates. We analysed secondary metabolite properties based on genome, transcriptome and metabolome data. The isolates represent highly distinct genome architecture, but harbor similar repertoire of BGCs. Expression profiles for most BGCs show comparable patterns of regulation among the isolates, suggesting a conserved "biochemical infection program". For all three isolates, we observed a strong up-regulation of a putative abscisic acid (ABA) gene cluster during biotrophic host colonization, indicating that Z. tritici potentially interfere with host defenses by the biosynthesis of this phytohormone. Further, during in vitro growth the isolates show similar metabolomes congruent with the predicted BGC content. We assessed if secondary metabolite production is regulated by histone methylation using a mutant impaired in formation of facultative heterochromatin (H3K27me3). In contrast to other ascomycete fungi, chromatin modifications play a less prominent role in regulation of secondary metabolites. In summary, we show that Z. tritici has a conserved program of secondary metabolite production contrasting the immense variation in effector expression, some of these metabolites might play a key role during host colonization. Importance Zymoseptoria tritici is one of the most devastating pathogens of wheat. So far the molecular determinants of virulence and their regulation are poorly understood. Previous studies have focused on proteinasous virulence factors and their extensive diversity. In this study, we focus on secondary metabolites produced by Z. tritici. Using a comparative framework, we here characterize core and non-core metabolites produced by Z. tritici by combining genome, transcriptome and metabolome datasets. Our findings indicate highly conserved biochemical profiles contrasting genetic and phenotypic diversity of the field isolates investigated here. This discovery has relevance for future crop protection strategies.

Deciphering the Crosstalk Mechanisms of Wheat-Stem Rust Pathosystem: Genome-Scale Prediction Unravels Novel Host Targets

Triticum aestivum (wheat), a major staple food grain, is affected by various biotic stresses. Among these, fungal diseases cause about 15-20% of yield loss, worldwide. In this study, we performed a comparative analysis of protein-protein interactions between two Puccinia graminis races (Pgt 21-0 and Pgt Ug99) that cause stem (black) rust in wheat. The available molecular techniques to study the host-pathogen interaction mechanisms are expensive and labor-intensive. We implemented two computational approaches (interolog and domain-based) for the prediction of PPIs and performed various functional analysis to determine the significant differences between the two pathogen races. The analysis revealed that T. aestivum-Pgt 21-0 and T. aestivum-Pgt Ug99 interactomes consisted of ∼90M and ∼56M putative PPIs, respectively. In the predicted PPIs, we identified 115 Pgt 21-0 and 34 Pgt Ug99 potential effectors that were highly involved in pathogen virulence and development. Functional enrichment analysis of the host proteins revealed significant GO terms and KEGG pathways such as O-methyltransferase activity (GO:0008171), regulation of signal transduction (GO:0009966), lignin metabolic process (GO:0009808), plastid envelope (GO:0009526), plant-pathogen interaction pathway (ko04626), and MAPK pathway (ko04016) that are actively involved in plant defense and immune signaling against the biotic stresses. Subcellular localization analysis anticipated the host plastid as a primary target for pathogen attack. The highly connected host hubs in the protein interaction network belonged to protein kinase domain including Ser/Thr protein kinase, MAPK, and cyclin-dependent kinase. We also identified 5,577 transcription factors in the interactions, associated with plant defense during biotic stress conditions. Additionally, novel host targets that are resistant to stem rust disease were also identified. The present study elucidates the functional differences between Pgt 21-0 and Pgt Ug99, thus providing the researchers with strain-specific information for further experimental validation of the interactions, and the development of durable, disease-resistant crop lines.

A polyketide synthase gene cluster required for pathogenicity of Pseudocercospora fijiensis on banana

Pseudocercospora fijiensis is the causal agent of the highly destructive black Sigatoka disease of banana. Previous research has focused on polyketide synthase gene clusters in the fungus, given the importance of polyketide pathways in related plant pathogenic fungi. A time course study of expression of the previously identified PKS7-1, PKS8-2, and PKS10-2 gene clusters showed high expression of all three PKS genes and the associated clustered genes in infected banana plants from 2 weeks post-inoculation through 9 weeks. Engineered transformants silenced for PKS8-2 and PKS10-2 were developed and tested for pathogenicity. Inoculation of banana plants with silencing transformants for PKS10-2 showed significant reduction in disease symptoms and severity that correlated with the degree of silencing in the conidia used for inoculation, supporting a critical role for PKS10-2 in disease development. Unlike PKS10-2, a clear role for PKS8-2 could not be determined. Two of four PKS8-2 silencing transformants showed reduced disease development, but disease did not correlate with the degree of PKS8-2 silencing in the transformants. Overall, the degree of silencing obtained for the PKS8-2 transformants was less than that obtained for the PKS10-2 transformants, which may have limited the utility of the silencing strategy to identify a role for PKS8-2 in disease. Orthologous PKS10-2 clusters had previously been identified in the related banana pathogens Pseudocercospora musae and Pseudocercospora eumusae. Genome analysis identified orthologous gene clusters to that of PKS10-2 in the newly sequenced genomes of Pseudocercospora fuligena and Pseudocercospora cruenta, pathogens of tomato and cowpea, respectively. Our results support an important role for the PKS10-2 polyketide pathway in pathogenicity of Pseudocercospora fijiensis, and suggest a possible role for this pathway in disease development by other Pseudocercospora species.

Deletion of a Rare Fungal PKS CgPKS11 Promotes Chaetoglobosin A Biosynthesis, Yet Defers the Growth and Development of Chaetomium globosum

We previously reported that chaetoglobosin A (ChA) exhibits a great potential in the biocontrol of nematodes and pathogenic fungi. To improve the production of ChA, a CRISPR-Cas9 system was created and applied for eliminating potential competitive polyketide products. One of the polyketide synthase encoding genes, Cgpks11, which is putatively involved in the biosynthesis of chaetoglocin A, was disrupted. Cgpks11 deletion led to the overexpression of the CgcheA gene cluster, which is responsible for ChA biosynthesis, and a 1.6-fold increase of ChA. Transcription of pks-1, a melanin PKS, was simultaneously upregulated. Conversely, the transcription of genes for chaetoglocin A biosynthesis, e.g., CHGG_10646 and CHGG_10649, were significantly downregulated. The deletion also led to growth retardation and seriously impaired ascospore development. This study found a novel regulatory means on the biosynthesis of ChA by CgPKS11. CgPKS11 affects chaetoglobosin A biosynthesis, growth, and development in Chaetomium globosum.

Size-exclusion chromatography allows the isolation of EVs from the filamentous fungal plant pathogen Fusarium oxysporum f. sp. vasinfectum (Fov)

Extracellular vesicles (EVs) are nano-sized compartments involved in cell communication and macromolecule transport that are well characterized in mammalian organisms. Fungal EVs transport virulence-related cargo and modulate the host immune response, but most work has been focused on human yeast pathogens. Additionally, the study of EVs from filamentous fungi has been hindered by the lack of protein markers and efficient isolation methods. In this study we performed the isolation and proteomic characterization of EVs from the filamentous cotton pathogen Fusarium oxysporum f. sp. vasinfectum (Fov). EVs were recovered from two different growth media, Czapek Dox and Saboraud's dextrose broth, and purified by size-exclusion chromatography. Our results show that the EV proteome changes depending on the growth medium but EV production remains constant. EVs contained proteins involved in polyketide synthesis, cell wall modifications, proteases and potential effectors. These results support a role in modulation of host-pathogen interactions for Fov EVs.