New (and used) approaches to the study of fungal pathogenicity

A polysaccharide deacetylase from Puccinia striiformis f. sp. tritici is an important pathogenicity gene that suppresses plant immunity

The cell wall of filamentous fungi, comprised of chitin, polysaccharide and glycoproteins, maintains the integrity of hyphae and protect them from defence responses by potential host plants. Here, we report that one polysaccharide deacetylase of Puccinia striiformis f. sp. tritici (Pst), Pst_13661, suppresses Bax-induced cell death in plants and Pst_13661 is highly induced during early stages of the interaction between wheat and Pst. Importantly, the transgenic wheat expressing the RNA interference (RNAi) construct of Pst_13661 exhibits high resistance to major Pst epidemic races CYR31, CYR32 and CYR33 by inhibiting growth and development of Pst, indicating that Pst_13661 is an available pathogenicity factor and is a potential target for generating broad-spectrum resistance breeding material of wheat. It forms a homo-polymer and has high affinity for chitin and germ tubes of Pst compared with the control. Besides, Pst_13661 suppresses chitin-induced plant defence in plants. Hence, we infer that Pst_13661 may modify the fungal cell wall to prevent recognition by apoplastic surveillance systems in plants. This study opens new approaches for developing durable disease-resistant germplasm by disturbing the growth and development of fungi and develops novel strategies to control crop diseases.

A systematic analysis of T-DNA insertion events in Magnaporthe oryzae

We describe here the analysis of random T-DNA insertions that were generated as part of a large-scale insertional mutagenesis project for Magnaporthe oryzae. Chromosomal regions flanking T-DNA insertions were rescued by inverse PCR, sequenced and used to search the M. oryzae genome assembly. Among the 175 insertions for which at least one flank was rescued, 137 had integrated in single-copy regions of the genome, 17 were in repeated sequences, one had no match to the genome, and the remainder were unassigned due to illegitimate T-DNA integration events. These included in order of abundance: head-to-tail tandem insertions, right border excision failures, left border excision failures and insertion of one T-DNA into another. The left borders of the T-DNA were frequently truncated and inserted in sequences with micro-homology to the left terminus. By contrast the right borders were less prone to degradation and appeared to have been integrated in a homology-independent manner. Gross genome rearrangements rarely occurred when the T-DNAs integrated in single-copy regions, although most insertions did cause small deletions at the target site. Significant insertion bias was detected, with promoters receiving two times more T-DNA hits than expected, and open reading frames receiving three times fewer. In addition, we found that the distribution of T-DNA inserts among the M. oryzae chromosomes was not random. The implications of these findings with regard to saturation mutagenesis of the M. oryzae genome are discussed.

Identification and comparative analysis of sixteen fungal peptidyl-prolyl cis/trans isomerase repertoires

BACKGROUND

The peptidyl-prolyl cis/trans isomerase (PPIase) class of proteins is present in all known eukaryotes, prokaryotes, and archaea, and it is comprised of three member families that share the ability to catalyze the cis/trans isomerisation of a prolyl bond. Some fungi have been used as model systems to investigate the role of PPIases within the cell, however how representative these repertoires are of other fungi or humans has not been fully investigated.

RESULTS

PPIase numbers within these fungal repertoires appears associated with genome size and orthology between repertoires was found to be low. Phylogenetic analysis showed the single-domain FKBPs to evolve prior to the multi-domain FKBPs, whereas the multi-domain cyclophilins appear to evolve throughout cyclophilin evolution. A comparison of their known functions has identified, besides a common role within protein folding, multiple roles for the cyclophilins within pre-mRNA splicing and cellular signalling, and within transcription and cell cycle regulation for the parvulins. However, no such commonality was found with the FKBPs. Twelve of the 17 human cyclophilins and both human parvulins, but only one of the 13 human FKBPs, identified orthologues within these fungi. hPar14 orthologues were restricted to the Pezizomycotina fungi, and R. oryzae is unique in the known fungi in possessing an hCyp33 orthologue and a TPR-containing FKBP. The repertoires of Cryptococcus neoformans, Aspergillus fumigatus, and Aspergillus nidulans were found to exhibit the highest orthology to the human repertoire, and Saccharomyces cerevisiae one of the lowest.

CONCLUSION

Given this data, we would hypothesize that: (i) the evolution of the fungal PPIases is driven, at least in part, by the size of the proteome, (ii) evolutionary pressures differ both between the different PPIase families and the different fungi, and (iii) whilst the cyclophilins and parvulins have evolved to perform conserved functions, the FKBPs have evolved to perform more variable roles. Also, the repertoire of Cryptococcus neoformans may represent a better model fungal system within which to study the functions of the PPIases as its genome size and genetic tractability are equal to those of Saccharomyces cerevisiae, whilst its repertoires exhibits greater orthology to that of humans. However, further experimental investigations are required to confirm this.

The dawn of fungal pathogen genomics

Recent advances in sequencing technologies have led to a remarkable increase in the number of sequenced fungal genomes. Several important plant pathogenic fungi are among those that have been sequenced or are being sequenced. Additional fungal pathogens are likely to be sequenced in the near future. Analysis of the available genomes has provided useful information about genes that may be important for plant infection and colonization. Genome features, such as repetitive sequences, telomeres, conserved syntenic blocks, and expansion of pathogenicity-related genes, are discussed in detail with Magnaporthe oryzae (M. grisea) and Fusarium graminearum as examples. Functional and comparative genomic studies in plant pathogenic fungi, although still in the early stages and limited to a few pathogens, have enormous potential to improve our understanding of the molecular mechanisms involved in host-pathogen interactions. Development of advanced genomics tools and infrastructure is critical for efficient utilization of the vast wealth of available genome sequence information and will form a solid foundation for systems biology studies of plant pathogenic fungi.

Comparative genomic analysis of phytopathogenic fungi using expressed sequence tag (EST) collections

SUMMARY We describe the analysis of 57 727 unique expressed sequence tags (ESTs) from 15 species of phytopathogenic and three species of saprophytic fungi. This resource is held within the COGEME phytopathogen EST database (http://cogeme.ex.ac.uk/). Comparative analysis was performed to investigate the differences between pathogenic and free-living fungi based on a substantial collection of expressed gene sequences and available, completed fungal genome sequences. We report that the expressed gene inventories of pathogenic fungi were not significantly more similar to each other than to those of free-living filamentous fungi. As expected, however, filamentous fungi as a group share more sequences in common than with the free-living yeast species Saccharomyces cerevisiae. Interestingly, ESTs of the obligate biotrophic fungus Blumeria graminis f. sp. hordei were more dissimilar to those of all other fungal species assessed, having a lower number of sequences in common with filamentous ascomycetes studied to date and also possessing a larger proportion of unisequences of unknown function. Our analysis of ESTs in the COGEME database enabled identification of a set of functional groups of genes that are more highly represented in the genomes of pathogenic fungi than non-pathogenic species.

Plant–pathogen interactions: will the understanding of common mechanisms lead to the unification of concepts?

Plant-pathogen interactions are still classically described using concepts that make a distinction between qualitative and quantitative aspects linked to these concepts. This article first describes these aspects, using the terminology associated with them. It then presents some recent experimental observations that demonstrate that such concepts share either common or closely related mechanisms at the cellular and molecular levels. The emergence of a more global vision and understanding of the interactions between plants and their parasites is discussed.

Random Insertional Mutagenesis Identifies Genes Associated with Virulence in the Wheat Scab Fungus Fusarium graminearum

ABSTRACT Fusarium graminearum is an important pathogen of small grains and maize in many areas of the world. To better understand the molecular mechanisms of F. graminearum pathogenesis, we used the restriction enzyme-mediated integration (REMI) approach to generate random insertional mutants. Eleven pathogenicity mutants were identified by screening 6,500 hygromycin-resistant transformants. Genetic analyses indicated that the defects in plant infection were tagged by the transforming vector in six of these mutants. In mutant M8, the transforming plasmid was integrated 110-bp upstream from the start codon of the cystathionine betalyase gene (CBL1). Gene replacement mutants deleted for CBL1 and the methionine synthase gene MSY1 were also obtained. Both the cbl1 and msy1 deletion mutants were methionine auxotrophic and significantly reduced in virulence on corn silks and wheat heads. We also identified genes disrupted by the transforming DNA in three other REMI mutants exhibiting reduced virulence. In mutants M68, the transforming vectors were inserted in the NADH: ubiquinone oxidoreductase. The putative b-ZIP transcription factor gene and the transducin beta-subunit-like gene disrupted in mutants M7 and M75, respectively, had no known homologs in filamentous fungi and were likely to be novel fungal virulence factors.

'PACLIMS': a component LIM system for high-throughput functional genomic analysis

BACKGROUND

Recent advances in sequencing techniques leading to cost reduction have resulted in the generation of a growing number of sequenced eukaryotic genomes. Computational tools greatly assist in defining open reading frames and assigning tentative annotations. However, gene functions cannot be asserted without biological support through, among other things, mutational analysis. In taking a genome-wide approach to functionally annotate an entire organism, in this application the approximately 11,000 predicted genes in the rice blast fungus (Magnaporthe grisea), an effective platform for tracking and storing both the biological materials created and the data produced across several participating institutions was required.

RESULTS

The platform designed, named PACLIMS, was built to support our high throughput pipeline for generating 50,000 random insertion mutants of Magnaporthe grisea. To be a useful tool for materials and data tracking and storage, PACLIMS was designed to be simple to use, modifiable to accommodate refinement of research protocols, and cost-efficient. Data entry into PACLIMS was simplified through the use of barcodes and scanners, thus reducing the potential human error, time constraints, and labor. This platform was designed in concert with our experimental protocol so that it leads the researchers through each step of the process from mutant generation through phenotypic assays, thus ensuring that every mutant produced is handled in an identical manner and all necessary data is captured.

CONCLUSION

Many sequenced eukaryotes have reached the point where computational analyses are no longer sufficient and require biological support for their predicted genes. Consequently, there is an increasing need for platforms that support high throughput genome-wide mutational analyses. While PACLIMS was designed specifically for this project, the source and ideas present in its implementation can be used as a model for other high throughput mutational endeavors.

Fusarium oxysporum as a multihost model for the genetic dissection of fungal virulence in plants and mammals

Fungal pathogens cause disease in plant and animal hosts. The extent to which infection mechanisms are conserved between both classes of hosts is unknown. We present a dual plant-animal infection system based on a single strain of Fusarium oxysporum, the causal agent of vascular wilt disease in plants and an emerging opportunistic human pathogen. Injection of microconidia of a well-characterized tomato pathogenic isolate (isolate 4287) into the lateral tail vein of immunodepressed mice resulted in disseminated infection of multiple organs and death of the animals. Knockout mutants in genes encoding a mitogen-activated protein kinase, a pH response transcription factor, or a class V chitin synthase previously shown to be implicated in virulence on tomato plants were tested in the mouse model. The results indicate that some of these virulence factors play functionally distinct roles during the infection of tomato plants and mice. Thus, a single F. oxysporum strain can be used to study fungal virulence mechanisms in plant and mammalian pathogenesis.

Isolation of a novel antimicrobial peptide gene (Sp-AMP) homologue fromPinus sylvestris(Scots pine) following infection with the root rot fungusHeterobasidion annosum

A new family of antimicrobial peptide homologues termed Sp-Amp has been discovered in Pinus sylvestris (Scots pine). This is the first report of such proteins to be characterized in a conifer species. Sp-AMP1 was identified in a substructured cDNA library of root tissue infected with the root rot fungus Heterobasidion annosum and encodes a mature peptide of 79 amino acid residues. Three additional members of the Sp-AMP family (Sp-AMPs 2-4) encode cysteine-rich proteins of 105 amino acids, each containing an N-terminal region with a probable cleavage signal sequence. Northern analysis confirmed that Sp-AMP expression is elevated in Scots pine roots upon infection with H. annosum. These peptides share 64% amino acid identity with a mature protein from Macadamia integrifolia (MiAMP1), which allowed us to build a homology model for preliminary analysis. Southern analyses further confirmed that several copies of the gene are present in the Scots pine genome. The potential significance of Sp-AMP in the H. annosum-conifer pathosystem is discussed.

Wanted: pathogenesis-related marker molecules for Fusarium oxysporum

Although Fusarium oxysporum pathogens cause severe wilts in about 80 botanical species, the mechanisms of pathogenicity and symptom induction are poorly understood. Knowledge about the genetic and biochemical pathways involved in the pathogenesis of F. oxysporum would be invaluable in getting targets for both fungicide development and search for biocontrol agents. In this respect, we described the main approaches that have been developed to identify some mechanisms underlying the pathogenesis of F. oxysporum. During the last decades, the potential functions triggering of F. oysporum pathogenicity have mainly been investigated by comparing soilborne pathogenic strains with nonpathogenic ones with regards to the analysis of the pre- and infection stages and of the resulting plant-fungus interactions. The relatively recent progress in the molecular biology of this fungus has allowed complementary approaches to be developed in order to identify key factors involved in F. oxysporum pathogenicity. Screening mutants of F. oxysporum for loss of virulence led to the successful identification of some pathogenesis-related factors, such as hydrophobicity or attachment of germlings. Taken together, the strategies described above support the idea that changes in fungal metabolism is also of importance in triggering of F. oxysporum pathogenesis.