Reduced virulence caused by meiotic instability of the TOX2 chromosome of the maize pathogen Cochliobolus carbonum

Recent Advances in Alternaria Phytotoxins: A Review of Their Occurrence, Structure, Bioactivity and Biosynthesis

Alternaria is a ubiquitous fungal genus in many ecosystems, consisting of species and strains that can be saprophytic, endophytic, or pathogenic to plants or animals, including humans. Alternaria species can produce a variety of secondary metabolites (SMs), especially low molecular weight toxins. Based on the characteristics of host plant susceptibility or resistance to the toxin, Alternaria phytotoxins are classified into host-selective toxins (HSTs) and non-host-selective toxins (NHSTs). These Alternaria toxins exhibit a variety of biological activities such as phytotoxic, cytotoxic, and antimicrobial properties. Generally, HSTs are toxic to host plants and can cause severe economic losses. Some NHSTs such as alternariol, altenariol methyl-ether, and altertoxins also show high cytotoxic and mutagenic activities in the exposed human or other vertebrate species. Thus, Alternaria toxins are meaningful for drug and pesticide development. For example, AAL-toxin, maculosin, tentoxin, and tenuazonic acid have potential to be developed as bioherbicides due to their excellent herbicidal activity. Like altersolanol A, bostrycin, and brefeldin A, they exhibit anticancer activity, and ATX V shows high activity to inhibit the HIV-1 virus. This review focuses on the classification, chemical structure, occurrence, bioactivity, and biosynthesis of the major Alternaria phytotoxins, including 30 HSTs and 50 NHSTs discovered to date.

Detecting and prioritizing biosynthetic gene clusters for bioactive compounds in bacteria and fungi

Secondary metabolites (SM) produced by fungi and bacteria have long been of exceptional interest owing to their unique biomedical ramifications. The traditional discovery of new natural products that was mainly driven by bioactivity screening has now experienced a fresh new approach in the form of genome mining. Several bioinformatics tools have been continuously developed to detect potential biosynthetic gene clusters (BGCs) that are responsible for the production of SM. Although the principles underlying the computation of these tools have been discussed, the biological background is left underrated and ambiguous. In this review, we emphasize the biological hypotheses in BGC formation driven from the observations across genomes in bacteria and fungi, and provide a comprehensive list of updated algorithms/tools exclusively for BGC detection. Our review points to a direction that the biological hypotheses should be systematically incorporated into the BGC prediction and assist the prioritization of candidate BGC.

Phenotypic instability in fungi

Fungi are prone to phenotypic instability, that is, the vegetative phase of these organisms, be they yeasts or molds, undergoes frequent switching between two or more behaviors, often with different morphologies, but also sometime having different physiologies without any obvious morphological outcome. In the context of industrial utilization of fungi, this can have a negative impact on the maintenance of strains and/or on their productivity. Instabilities have been shown to result from various mechanisms, either genetic or epigenetic. This chapter will review different types of instabilities and discuss some lesser-known ones, mostly in filamentous fungi, while it will direct readers to additional literature in the case of well-known phenomena such as the amyloid prions or fungal senescence. It will present in depth the "white/opaque" switch of Candida albicans and the "crippled growth" degeneration of the model fungus Podospora anserina. These are two of the most thoroughly studied epigenetic phenotypic switches. I will also discuss the "sectors" presented by many filamentous ascomycetes, for which a prion-based model exists but is not demonstrated. Finally, I will also describe intriguing examples of phenotypic instability for which an explanation has yet to be provided.

Accessories Make the Outfit: Accessory Chromosomes and Other Dispensable DNA Regions in Plant-Pathogenic Fungi

Fungal pathogen genomes can often be divided into core and accessory regions. Accessory regions ARs) may be comprised of either ARs (within core chromosomes (CCs) or wholly dispensable (accessory) chromosomes (ACs). Fungal ACs and ARs typically accumulate mutations and structural rearrangements more rapidly over time than CCs and many harbor genes relevant to host-pathogen interactions. These regions are of particular interest in plant pathology and include host-specific virulence factors and secondary metabolite synthesis gene clusters. This review outlines known ACs and ARs in fungal genomes, methods used for their detection, their common properties that differentiate them from the core genome, and what is currently known of their various roles in pathogenicity. Reports on the evolutionary processes generating and shaping AC and AR compartments are discussed, including repeat induced point mutation and breakage fusion bridge cycles. Previously ACs have been studied extensively within key genera, including Fusarium, Zymoseptoria, and Alternaria, but are growing in frequency of observation and perceived importance across a wider range of fungal species. Recent advances in sequencing technologies permit affordable genome assembly and resequencing of populations that will facilitate further discovery and routine screening of ACs.

Conservation of the genes for HC-toxin biosynthesis in Alternaria jesenskae

Background

HC-toxin, a cyclic tetrapeptide, is a virulence determinant for the plant pathogenic fungus Cochliobolus carbonum. It was recently discovered that another fungus, Alternaria jesenskae, also produces HC-toxin.

Results

The major genes (collectively known as AjTOX2) involved in the biosynthesis of HC-toxin were identified from A. jesenskae by genomic sequencing. The encoded orthologous proteins share 75-85% amino acid identity, and the genes for HC-toxin biosynthesis are duplicated in both fungi. The genomic organization of the genes in the two fungi show a similar but not identical partial clustering arrangement. A set of representative housekeeping proteins show a similar high level of amino acid identity between C. carbonum and A. jesenskae, which is consistent with the close relatedness of these two genera within the family Pleosporaceae (Dothideomycetes).

Conclusions

This is the first report that the plant virulence factor HC-toxin is made by an organism other than C. carbonum. The genes may have moved by horizontal transfer between the two species, but it cannot be excluded that they were present in a common ancestor and lost from other species of Alternaria and Cochliobolus.

Recent fungal diseases of crop plants: is lateral gene transfer a common theme?

A cursory glance at old textbooks of plant pathology reveals that the diseases which are the current scourge of agriculture in many parts of the world are a different set from those that were prominent 50 or 100 years ago. Why have these new diseases arisen? The traditional explanations subscribe to the "nature abhors a vacuum" principle-that control of one disease creates the condition for the emergence of a replacement-but does little to explain why the new pathogen succeeds. The emergence of a new disease requires a series of conditions and steps, including the enhanced fecundity of the new pathogen, enhanced survival from season to season, and spread around the world. Recently, evidence was obtained that wheat tan spot emerged through a lateral gene transfer event some time prior to 1941. Although there have been sporadic and persistent reports of lateral gene transfer between and into fungal plant pathogens, most examples have been dismissed through incomplete evidence. The completion of whole genome sequences of an increasing number of fungal pathogens no longer allows such proposed cases of lateral gene transfer to be dismissed so easily. How frequent are lateral gene transfers involving fungal plant pathogens, and can this process explain the emergence of many of the new diseases of the recent past? Many of the apparently new diseases are dependant on the expression of host-specific toxins. These are enigmatic molecules whose action requires the presence of plant genes with products that specifically encode sensitivity to the toxin and susceptibility to the disease. It is also notable that many new diseases belong to the fungal taxon dothideomycetes. This review explores the coincidence of new diseases, interspecific gene transfer, host-specific toxins, and the dothideomycete class.

Virulence genes and the evolution of host specificity in plant-pathogenic fungi

In the fungal kingdom, the ability to cause disease in plants appears to have arisen multiple times during evolution. In many cases, the ability to infect particular plant species depends on specific genes that distinguish virulent fungi from their sometimes closely related nonvirulent relatives. These genes encode host-determining "virulence factors," including small, secreted proteins and enzymes involved in the synthesis of toxins. These virulence factors typically are involved in evolutionary arms races between plants and pathogens. We briefly summarize current knowledge of these virulence factors from several fungal species in terms of function, phylogenetic distribution, sequence variation, and genomic location. Second, we address some issues that are relevant to the evolution of virulence in fungi toward plants; in particular, horizontal gene transfer and the genomic organization of virulence genes.

HC-toxin

HC-toxin is a cyclic tetrapeptide of structure cyclo(D-Pro-L-Ala-D-Ala-L-Aeo), where Aeo stands for 2-amino-9,10-epoxi-8-oxodecanoic acid. It is a determinant of specificity and virulence in the interaction between the producing fungus, Cochliobolus carbonum, and its host, maize. HC-toxin qualifies as one of the few microbial secondary metabolites whose ecological function in nature is understood. Reaction to C. carbonum and to HC-toxin is controlled in maize by the Hm1 and Hm2 loci. These loci encode HC-toxin reductase, which detoxifies HC-toxin by reducing the 8-carbonyl group of Aeo. HC-toxin is an inhibitor of histone deacetylases (HDACs) in many organisms, including plants, insects, and mammals, but why inhibition of HDACs during infection by C. carbonum leads to disease is not understood. The genes for HC-toxin biosynthesis (collectively known as the TOX2 locus) are loosely clustered over >500 kb in C. carbonum. All of the known TOX2 genes are present in multiple, functional copies and are absent from natural toxin non-producing isolates. The central enzyme in HC-toxin biosynthesis is a 570-kDa non-ribosomal synthetase encoded by a 15.7-kb open reading frame. Other genes known to be required for HC-toxin encode alpha and beta subunits of fatty acid synthase, which are presumed to contribute to the synthesis of Aeo; a pathway-specific transcription factor; an efflux carrier; a predicted branched-chain amino acid aminotransferase; and an alanine racemase.

Concurrence of losing a chromosome and the ability to produce destruxins in a mutant ofMetarhizium anisopliae

In a previous study, a spontaneous subtilisin pr1A and pr1B gene-deficient mutant of the entomopathogenic fungus Metarhizium anisopliae strain V275 has been identified [Wang, C.-S. et al. (2002) FEMS Microbiol. Lett. 213, 251-255]. The insecticidal metabolites of this mutant were studied further. High-performance liquid chromatography (HPLC) analysis indicated that the mutant isolate lost the ability to produce cyclic peptide toxins, destruxins, both in vitro and in vivo. Pulsed-field gel electrophoresis revealed that the mutant concurrently lost a 1.05 Mb (approximately) chromosome, demonstrating for the first time that a conditionally dispensable (CD) chromosome exists in the insect pathogenic fungus, M. anisopliae. Concurrence of losing the ability to produce destruxins and a CD chromosome in the mutant suggests that the toxin synthetase genes of M. anisopliae are located on this CD chromosome, as similarly described for plant pathogenic fungi. Semi-quantitative api ZYM analysis showed more biochemical disparities between the mutant and the wild-type strain.

Identification of new pisatin demethylase genes (PDA5 and PDA7) in Nectria haematococca and non-Mendelian segregation of pisatin demethylating ability and virulence on pea due to loss of chromosomal elements

Previous studies have shown that high virulence on pea in Nectria haematococca Mating Population VI is linked to the ability to detoxify the pea phytoalexin, pisatin, via demethylation (Pda). To test this linkage further, a highly virulent Pda(+) isolate (34-18) was used as the recurrent parent in backcrosses to Pda(-) isolates, but most of the progeny were low in virulence on pea, and tetrad analysis gave conflicting ratios for the genetic control of Pda. Southern analysis of 34-18 and progeny showed that 34-18 carries a gene similar to PDA1 (PDA1-2), two new PDA genes, PDA5 and PDA7, and that all three genes can be lost during meiosis. Southern analysis of electrophoretic karyotypes showed that PDA1-2 is on a 1.5-Mb dispensable chromosome in 34-18 and that PDA5 and PDA7 are on a 4.9-Mb chromosome in 34-18 but are found on variably sized chromosomes in progeny. Loss of PDA5 or PDA7 in progeny was not generally associated with morphological phenotypes, except in progeny from some crosses between PDA5 parents. Loss of PDA5 was associated with growth abnormalities in these crosses, suggesting that in some genetic backgrounds at least a portion of the PDA5/PDA7 chromosome is essential for normal growth. All highly virulent progeny had PDA1-2 or a combination of PDA5 and PDA7 while isolates that lacked the three genes were low in virulence, supporting the hypothesis that Pda, or genes linked to PDA genes, are necessary for virulence on pea. However, low virulence isolates with PDA genes were also identified, suggesting that there are pathogenicity genes that can segregate independently of PDA genes.

Detection and characterisation of pr1 virulent gene deficiencies in the insect pathogenic fungus Metarhizium anisopliae

In an initial attempt to characterise single-spore isolates from Metarhizium anisopliae wild-type strain V275, three genetically identical spontaneous pr1A- and pr1B-deficient mutants were detected. These mutants were identified by Nested-PCR amplification and verified by Southern hybridisation. Sequencing and comparison of the highly conserved sequences of 28S rDNA domains 9-11 confirmed that the mutant isolates were Metarhizium anisopliae, but each had both morphological and genetic differences from the wild-type parent. RAPD analyses indicated that the overall genetic similarity between wild-type strain and the mutant was less than 70%. Enzyme assays proved that the mutant isolates had significantly lower Pr1 and elastase activities. Bioassays showed reduced lethal activity of the mutants (20%) on Tenebrio molitor, but lethal activities were similar to those of the wild-type parent on the larvae of Galleria mellonella. This paper shows for the first time that a stable mutant strain lacking the most important pr1 genes is still able to infect its respective hosts. Our observations suggest that it is not uncommon for Metarhizium anisopliae to lose its virulence genes during maintenance on artificial medium.

An extended physical map of the TOX2 locus of Cochliobolus carbonum required for biosynthesis of HC-toxin

In genetic crosses, HC-toxin production in the filamentous fungus Cochliobolus carbonum appears to be controlled by a single locus, TOX2. At the molecular level, TOX2 is composed of at least seven duplicated and coregulated genes involved in HC-toxin biosynthesis, export, and regulation. All copies of four of the TOX2 genes were previously mapped within a 540-kb stretch of DNA in strain SB111. Subsequently, an additional three TOX2 genes, TOXE, TOXF, and TOXG, have been discovered. In this paper we have mapped all copies of the new genes, a total of seven, and show that except for one of the two copies of TOXE, which was previously shown to be on a chromosome of 0.7 Mb in strain SB111, they are all linked to the previously known TOX2 genes within approximately 600 kb of each other on a chromosome of 3.5 Mb. We show here that this chromosome also contains at least one non-TOX2 gene, EXG2, which encodes an exo-beta1,3-glucanase. EXG2 is still present in strains that have undergone spontaneous deletion of up to approximately 1.4 Mb of the 3.5-Mb chromosome. The results contribute to our understanding of the complex organization of the genes involved in HC-toxin biosynthesis and are consistent with the hypothesis that a reciprocal chromosomal translocation accounts for the pattern of distribution of the TOX2 genes in different C. carbonum isolates.

Meiotic deletion at the BUF1 locus of the fungus Magnaporthe grisea is controlled by interaction with the homologous chromosome

The Magnaporthe grisea BUF1 gene suffers high-frequency mutation in certain genetic crosses, resulting in buff-colored progeny. Analysis of 16 buf1 mutants arising from a cross with a mutation frequency of 25% revealed that, in every case, the BUF1 gene was deleted. The deletions occurred in only one of the parental chromosomes and were due to intrachromosomal recombination. Tetrad analysis revealed that deletions occurred in 44% of meioses and usually affected both chromatids of the mutable chromosome. This suggests that they happen before the premeiotic round of DNA synthesis. However, they were also almost entirely restricted to heteroallelic crosses. This, together with the discovery of numerous repetitive elements that were present only in the mutable BUF1 locus, suggests that the deletion process is sensitive to pairing interactions between homologous chromosomes, such that only unpaired loci are subject to deletion. Given that karyogamy is not supposed to occur until after premeiotic DNA replication in Pyrenomycetous fungi such as M. grisea, this latter observation would place the time of deletion during, or after, DNA synthesis. These conflicting results suggest that karyogamy might actually precede DNA replication in Pyrenomycetous fungi or that parts of the genome remain unreplicated until after karyogamy and subsequent chromosome pairing have taken place.

Host-selective toxins as agents of cell death in plant-fungus interactions

Summary Host-selective toxins are known determinants of compatibility in plant-fungus interactions and provide a powerful model for understanding the specificity of these associations. The identification of genes required for toxin biosynthesis has shown that the genes are unique to the toxin producing species and are clustered in complex loci. These loci may have been acquired by horizontal gene transfer. Many, if not all, host-selective toxins act by disrupting biochemical processes and in several cases the resulting cell death has the characteristics of programmed cell death. This ability to make dead tissue from living has enabled these facultative saprophytic fungi to become plant pathogens.

Role of Horizontal Gene Transfer in the Evolution of Fungi

Although evidence for horizontal gene transfer (HGT) in eukaryotes remains largely anecdotal, literature on HGT in fungi suggests that it may have been more important in the evolution of fungi than in other eukaryotes. Still, HGT in fungi has not been widely accepted because the mechanisms by which it may occur are unknown, because it is usually not directly observed but rather implied as an outcome, and because there are often equally plausible alternative explanations. Despite these reservations, HGT has been justifiably invoked for a variety of sequences including plasmids, introns, transposons, genes, gene clusters, and even whole chromosomes. In some instances HGT has also been confirmed under experimental conditions. It is this ability to address the phenomenon in an experimental setting that makes fungi well suited as model systems in which to study the mechanisms and consequences of HGT in eukaryotic organisms.