Friend or foe? Evolutionary history of glycoside hydrolase family 32 genes encoding for sucrolytic activity in fungi and its implications for plant-fungal symbioses

Background  

Many fungi are obligate biotrophs of plants, growing in live plant tissues, gaining direct access to recently photosynthesized carbon. Photosynthate within plants is transported from source to sink tissues as sucrose, which is hydrolyzed by plant glycosyl hydrolase family 32 enzymes (GH32) into its constituent monosaccharides to meet plant cellular demands. A number of plant pathogenic fungi also use GH32 enzymes to access plant-derived sucrose, but less is known about the sucrose utilization ability of mutualistic and commensal plant biotrophic fungi, such as mycorrhizal and endophytic fungi. The aim of this study was to explore the distribution and abundance of GH32 genes in fungi to understand how sucrose utilization is structured within and among major ecological guilds and evolutionary lineages. Using bioinformatic and PCR-based analyses, we tested for GH32 gene presence in all available fungal genomes and an additional 149 species representing a broad phylogenetic and ecological range of biotrophic fungi.     

Mechanisms of survival of necrotrophic fungal plant pathogens in hosts expressing the hypersensitive response

The hypersensitive response (HR), elicited when resistant hosts are infected by incompatible races of biotrophic fungi, has been researched extensively. New studies on host responses to necrotrophic fungi are beginning to show that when the HR occurs in hosts colonized by necrotrophs, fungal growth is accelerated rather than retarded. We review current knowledge about how necrotrophs survive in host plants in which the HR is expressed. We discuss how necrotrophs cope with the environmental factors formed as a result of the HR. Necrotrophs contain an array of enzymes, which can help in exploiting the hostile environment in order to colonize the host and to remove or inactivate active oxygen species (AOS). Among this array of enzymes are superoxide dismutase (SOD), peroxidases, catalase, and perhaps laccases and polyphenol oxidases. Of these, only SOD and catalase have been studied in any detail. The precise significance of SOD and catalase in host invasion and fungal resistance is still not adequately known. The importance of different peroxidases is also still far from clear. We speculate that AOS species may trigger the response of necrotrophs to the host environment.     

Phylogenomic Relationships between Amylolytic Enzymes from 85 Strains of Fungi

Fungal amylolytic enzymes, including α-amylase, gluocoamylase and α-glucosidase, have been extensively exploited in diverse industrial applications such as high fructose syrup production, paper making, food processing and ethanol production. In this paper, amylolytic genes of 85 strains of fungi from the phyla Ascomycota, Basidiomycota, Chytridiomycota and Zygomycota were annotated on the genomic scale according to the classification of glycoside hydrolase (GH) from the Carbohydrate-Active enZymes (CAZy) Database. Comparisons of gene abundance in the fungi suggested that the repertoire of amylolytic genes adapted to their respective lifestyles. Amylolytic enzymes in family GH13 were divided into four distinct clades identified as heterologous α- amylases, eukaryotic α-amylases, bacterial and fungal α-amylases and GH13 α-glucosidases. Family GH15 had two branches, one for gluocoamylases, and the other with currently unknown function. GH31 α-glucosidases showed diverse branches consisting of neutral α-glucosidases, lysosomal acid α-glucosidases and a new clade phylogenetically related to the bacterial counterparts. Distribution of starch-binding domains in above fungal amylolytic enzymes was related to the enzyme source and phylogeny. Finally, likely scenarios for the evolution of amylolytic enzymes in fungi based on phylogenetic analyses were proposed. Our results provide new insights into evolutionary relationships among subgroups of fungal amylolytic enzymes and fungal evolutionary adaptation to ecological conditions.     

Specificity in host-fungus associations: Do mutualists differ from antagonists?

Summary Physically intimate interactions between organisms are assumed to be highly specific, yet intimate mutualisms exhibiting little specificity are common and important in many communities. We compare host records for ectomycorrhizal fungi (mutualists) to those for biotrophic shoot fungi and necrotrophic root fungi (both antagonists) in order to test two alternative predictions: (1) intimate physical associations (biotrophy) are more specific than less intimate ones (necrotrophy); (2) antagonisms are more specific than mutualisms. Specificity of fungi for hosts supports prediction (1): ectomycorrhizal fungi and shoot biotrophs are more host specific than root necrotrophs. Fungal symbiont ranges of hosts supports prediction (2): woody hosts are associated with a greater number of mutualistic fungi than antagonistic fungi. The numbers of fungi in the three groups infecting hosts are all significantly positively correlated. This result suggests that some hosts are resistant to fungal invasion and others are quite susceptible. Thus, plants may not be able to erect selective barriers to only antagonistic fungi. The marked asymmetry of specificity from the perspectives of hosts vs fungi suggests that evolutionary and ecological processes act differently on partners in symbioses.     

Insights into the role of jasmonic acid-mediated defenses against necrotrophic and biotrophic fungal pathogens

Jasmonic acid (JA) is a natural hormone regulator involved in development,responses against wounding and pathogen attack.Upon perception of pathogens,JA is synthesized and mediates a signaling cascade ...     

Characterization of a Heterobasidion irregulare endo‐rhamnogalacturonase that mediate growth on pectin

Heterobasidion irregulare is one of five Heterobasidion annosum sensu lato (s.l.) species, which are destructive pathogens in boreal and temperate forests of the northern hemisphere that causes root and butt rot in conifer. A gene encoding endo‐rhamnogalacturonase (HIRHG), which belongs to the glycoside hydrolase family 28 (GH28), was found in a quantitative trait loci (QTL) region for virulence in Heterobasidion. In this study, we showed that HIRHG is highly upregulated during necrotrophic infection of Norway spruce compared with growth in liquid culture and that the HIRHG encoded protein is produced during fungal growth on complex carbon sources. Phylogenetic analysis of endo‐rhamnogalacturonases revealed that rhamnogalacturonase genes have been lost in most of the biotrophic and hemibiotrophic plant pathogens investigated but were common in necrotrophic pathogens and saprophytic fungi. Heterologous expression of the HIRHG gene in the hemibiotrophic fungus Magnaporthe oryzae increased its capacity to grow on pectin; however, the transformed M. oryzae isolates showed significant less infection of rice leaves compared to the wild type.     

Genomic analysis of the necrotrophic fungal pathogens Sclerotinia sclerotiorum and Botrytis cinerea

Sclerotinia sclerotiorum and Botrytis cinerea are closely related necrotrophic plant pathogenic fungi notable for their wide host ranges and environmental persistence. These attributes have made these species models for understanding the complexity of necrotrophic, broad host-range pathogenicity. Despite their similarities, the two species differ in mating behaviour and the ability to produce asexual spores. We have sequenced the genomes of one strain of S. sclerotiorum and two strains of B. cinerea. The comparative analysis of these genomes relative to one another and to other sequenced fungal genomes is provided here. Their 38-39 Mb genomes include 11,860-14,270 predicted genes, which share 83% amino acid identity on average between the two species. We have mapped the S. sclerotiorum assembly to 16 chromosomes and found large-scale co-linearity with the B. cinerea genomes. Seven percent of the S. sclerotiorum genome comprises transposable elements compared to <1% of B. cinerea. The arsenal of genes associated with necrotrophic processes is similar between the species, including genes involved in plant cell wall degradation and oxalic acid production. Analysis of secondary metabolism gene clusters revealed an expansion in number and diversity of B. cinerea-specific secondary metabolites relative to S. sclerotiorum. The potential diversity in secondary metabolism might be involved in adaptation to specific ecological niches. Comparative genome analysis revealed the basis of differing sexual mating compatibility systems between S. sclerotiorum and B. cinerea. The organization of the mating-type loci differs, and their structures provide evidence for the evolution of heterothallism from homothallism. These data shed light on the evolutionary and mechanistic bases of the genetically complex traits of necrotrophic pathogenicity and sexual mating. This resource should facilitate the functional studies designed to better understand what makes these fungi such successful and persistent pathogens of agronomic crops.     

Genome‐based estimates of fungal rDNA copy number variation across phylogenetic scales and ecological lifestyles

Ribosomal DNA (rDNA) copy number variation (CNV) has major physiological implications for all organisms, but how it varies for fungi, an ecologically ubiquitous and important group of microorganisms, has yet to be systemically investigated. Here, we examine rDNA CNV using an in silico read depth approach for 91 fungal taxa with sequenced genomes and assess copy number conservation across phylogenetic scales and ecological lifestyles. rDNA copy number varied considerably across fungi, ranging from an estimated 14 to 1,442 copies (mean = 113, median = 82), and copy number similarity was inversely correlated with phylogenetic distance. No correlations were found between rDNA CNV and fungal trophic mode, ecological guild or genome size. Taken together, these results show that like other microorganisms, fungi exhibit substantial variation in rDNA copy number, which is linked to their phylogeny in a scale‐dependent manner.     

Mutualistic interactions on a knife-edge between saprotrophy and pathogenesis

Saprophytic, ectomycorrhizal (ECM) and pathogenic fungi play a key role in carbon and nutrient cycling in forest ecosystems. Whereas more than 50 genomes of saprotrophic and pathogenic fungi have been published, only two genomes of ECM fungi, Laccaria bicolor and Tuber melanosporum, have been released. Comparative analysis of the genomes of biotrophic species highlighted convergent evolution. Mutualistic and pathogenic biotrophic fungi share expansion of genome size through transposon proliferation and common strategies to avoid plant detection. Differences mainly rely on nutritional strategies. Such analyses also pinpointed how blurred the molecular boundaries are between saprotrophism, symbiosis and pathogenesis. Sequencing of additional ECM species, as well as soil saprotrophic fungi, will facilitate the identification of conserved traits for ECM symbiosis and those leading to the transition from white-rotting and brown-rotting to the ECM lifestyle.     

A new promising phylogenetic marker to study the diversity of fungal communities: The Glycoside Hydrolase 63 gene

In molecular ecology, the development of efficient molecular markers for fungi remains an important research domain. Nuclear ribosomal internal transcribed spacer (ITS) region was proposed as universal DNA barcode marker for fungi, but this marker was criticized for Indel‐induced alignment problems and its potential lack of phylogenetic resolution. Our main aim was to develop a new phylogenetic gene and a putative functional marker, from single‐copy gene, to describe fungal diversity. Thus, we developed a series of primers to amplify a polymorphic region of the Glycoside Hydrolase GH63 gene, encoding exo‐acting α‐glucosidases, in basidiomycetes. These primers were validated on 125 different fungal genomic DNAs, and GH63 amplification yield was compared with that of already published functional markers targeting genes coding for laccases, N‐acetylhexosaminidases, cellobiohydrolases and class II peroxidases. Specific amplicons were recovered for 95% of the fungal species tested, and GH63 amplification success was strikingly higher than rates obtained with other functional genes. We downloaded the GH63 sequences from 483 fungal genomes publicly available at the JGI mycocosm database. GH63 was present in 461 fungal genomes belonging to all phyla, except Microsporidia and Neocallimastigomycota divisions. Moreover, the phylogenetic trees built with both GH63 and Rpb1 protein sequences revealed that GH63 is also a promising phylogenetic marker. Finally, a very high proportion of GH63 proteins was predicted to be secreted. This molecular tool could be a new phylogenetic marker of fungal species as well as potential indicator of functional diversity of basidiomycetes fungal communities in term of secretory capacities.     

Tryptophan‐derived secondary metabolites in Arabidopsis thaliana confer non‐host resistance to necrotrophic Plectosphaerella cucumerina fungi

A defence pathway contributing to non‐host resistance to biotrophic fungi in Arabidopsis involves the synthesis and targeted delivery of the tryptophan (trp)‐derived metabolites indol glucosinolates (IGs) and camalexin at pathogen contact sites. We have examined whether these metabolites are also rate‐limiting for colonization by necrotrophic fungi. Inoculation of Arabidopsis with adapted or non‐adapted isolates of the ascomycete Plectosphaerella cucumerina triggers the accumulation of trp‐derived metabolites. We found that their depletion in cyp79B2 cyp79B3 mutants renders Arabidopsis fully susceptible to each of three tested non‐adapted P. cucumerina isolates, and super‐susceptible to an adapted P. cucumerina isolate. This assigns a key role to trp‐derived secondary metabolites in limiting the growth of both non‐adapted and adapted necrotrophic fungi. However, 4‐methoxy‐indol‐3‐ylmethylglucosinolate, which is generated by the P450 monooxygenase CYP81F2, and hydrolyzed by PEN2 myrosinase, together with the antimicrobial camalexin play a minor role in restricting the growth of the non‐adapted necrotrophs. This contrasts with a major role of these two trp‐derived phytochemicals in limiting invasive growth of non‐adapted biotrophic powdery mildew fungi, thereby implying the existence of other unknown trp‐derived metabolites in resistance responses to non‐adapted necrotrophic P. cucumerina. Impaired defence to non‐adapted P. cucumerina, but not to the non‐adapted biotrophic fungus Erysiphe pisi, on cyp79B2 cyp79B3 plants is largely restored in the irx1 background, which shows a constitutive accumulation of antimicrobial peptides. Our findings imply differential contributions of antimicrobials in non‐host resistance to necrotrophic and biotrophic pathogens.     

CONCEPTS IN FUNGAL NUTRITION AND THE ORIGIN OF BIOTROPHY

1. Since use of the terms, symbiosis and obligate parasitism, is ambiguous, an attempt is made to re-impose precision by a re-evaluation of basic concepts. 2. For symbiosis, there should be a return to a concept closer to that of de Bary's original, embracing those parasitic and mutualistic associations which involve permanent, intimate contact. 3. Culturability should be abandoned as a criterion for classifying fungal behaviour. 4. Instead of culturability, emphasis should be placed on the ecological and nutritional behaviour of fungi, permitting the recognition of five groups: obligate saprotrophs, facultative necrotrophs, obligate necrotrophs, facultative biotrophs and obligate biotrophs. 5. Since environmental conditions can determine whether the nutrition of a fungus is biotrophic or necrotrophic, a scheme, speculative but amenable to experimental test, for the origin of biotrophy is proposed. This involves the interplay of alterations to patterns of translocation produced by fungally-induced changes in hormonal balance in infected plants and catabolite repression of degradative enzymes of the fungus. 6. The dependence of mutualistic symbiosis on the maintenance of biotrophy is stressed. 7. Based on the nutrition of the diverse kinds of fungi involved in mycorrhizas, a re-alignment of groupings of mycorrhizal associations is proposed. This directs research towards seeking generalizations within, and differences between, four clearly defined groups (sheathing, vesicular-arbuscular, orchidaceous and ericaceous) instead of, as at present, within and between two (variously termed ectotrophic and endotrophic or ectomycorrhiza and endomycorrhiza), the second of which is highly artificial. Earlier drafts of the paper were read by Professors J. L. Harley, L. B. Thrower and S. D. Garrett, and Drs M. J. Carlile, B. C. Clifford, G. Hadley, P. M. Holligan, D. M. Losel and D. C. Smith. I am most grateful for their advice on specific points. Many, but not all, of their comments have been incorporated and I must stress that some views expressed, particularly with regard to the classification of mycorrhizas, are at variance with those of some of these colleagues.     

Phylogenetic comparison and classification of laccase and related multicopper oxidase protein sequences

A phylogenetic analysis of more than 350 multicopper oxidases (MCOs) from fungi, insects, plants, and bacteria provided the basis for a refined classification of this enzyme family into laccases sensu stricto (basidiomycetous and ascomycetous), insect laccases, fungal pigment MCOs, fungal ferroxidases, ascorbate oxidases, plant laccase-like MCOs, and bilirubin oxidases. Within the largest group of enzymes, formed by the 125 basidiomycetous laccases, the gene phylogeny does not strictly follow the species phylogeny. The enzymes seem to group at least partially according to the lifestyle of the corresponding species. Analyses of the completely sequenced fungal genomes showed that the composition of MCOs in the different species can be very variable. Some species seem to encode only ferroxidases, whereas others have proteins which are distributed over up to four different functional clusters in the phylogenetic tree.     

Genome-Wide Annotation and Comparative Analysis of Cytochrome P450 Monooxygenases in Basidiomycete Biotrophic Plant Pathogens

Fungi are an exceptional source of diverse and novel cytochrome P450 monooxygenases (P450s), heme-thiolate proteins, with catalytic versatility. Agaricomycotina saprophytes have yielded most of the available information on basidiomycete P450s. This resulted in observing similar P450 family types in basidiomycetes with few differences in P450 families among Agaricomycotina saprophytes. The present study demonstrated the presence of unique P450 family patterns in basidiomycete biotrophic plant pathogens that could possibly have originated from the adaptation of these species to different ecological niches (host influence). Systematic analysis of P450s in basidiomycete biotrophic plant pathogens belonging to three different orders, Agaricomycotina (Armillaria mellea), Pucciniomycotina (Melampsora laricis-populina, M. lini, Mixia osmundae and Puccinia graminis) and Ustilaginomycotina (Ustilago maydis, Sporisorium reilianum and Tilletiaria anomala), revealed the presence of numerous putative P450s ranging from 267 (A. mellea) to 14 (M. osmundae). Analysis of P450 families revealed the presence of 41 new P450 families and 27 new P450 subfamilies in these biotrophic plant pathogens. Order-level comparison of P450 families between biotrophic plant pathogens revealed the presence of unique P450 family patterns in these organisms, possibly reflecting the characteristics of their order. Further comparison of P450 families with basidiomycete non-pathogens confirmed that biotrophic plant pathogens harbour the unique P450 families in their genomes. The CYP63, CYP5037, CYP5136, CYP5137 and CYP5341 P450 families were expanded in A. mellea when compared to other Agaricomycotina saprophytes and the CYP5221 and CYP5233 P450 families in P. graminis and M. laricis-populina. The present study revealed that expansion of these P450 families is due to paralogous evolution of member P450s. The presence of unique P450 families in these organisms serves as evidence of how a host/ecological niche can influence shaping the P450 content of an organism. The present study initiates our understanding of P450 family patterns in basidiomycete biotrophic plant pathogens.     

Genomic Patterns of Positive Selection at the Origin of Rust Fungi

Understanding the origin and evolution of pathogenicity and biotrophic life-style of rust fungi has remained a conundrum for decades. Research on the molecular mechanisms responsible for rust fungi evolution has been hampered by their biotrophic life-style until the sequencing of some rust fungi genomes. With the availability of multiple whole genomes and EST data for this group, it is now possible to employ genome-wide surveys and investigate how natural selection shaped their evolution. In this work, we employed a phylogenomics approach to search for positive selection and genes undergoing accelerated evolution at the origin of rust fungi on an assembly of single copy genes conserved across a broad range of basidiomycetes. Up to 985 genes were screened for positive selection on the phylogenetic branch leading to rusts, revealing a pervasive signal of positive selection throughout the data set with the proportion of positively selected genes ranging between 19.6–33.3%. Additionally, 30 genes were found to be under accelerated evolution at the origin of rust fungi, probably due to a mixture of positive selection and relaxation of purifying selection. Functional annotation of the positively selected genes revealed an enrichment in genes involved in the biosynthesis of secondary metabolites and several metabolism and transporter classes.     

An evolutionary analysis of the helix-hairpin-helix superfamily of DNA repair glycosylases

The helix-hairpin-helix (HhH) superfamily of base excision repair DNA glycosylases is composed of multiple phylogenetically diverse enzymes that are capable of excising varying spectra of oxidatively and methyl-damaged bases. Although these DNA repair glycosylases have been widely studied through genetic, biochemical, and biophysical approaches, the evolutionary relationships of different HhH homologs and the extent to which they are conserved across phylogeny remain enigmatic. We provide an evolutionary framework for this pervasive and versatile superfamily of DNA glycosylases. Six HhH gene families (named AlkA: alkyladenine glycosylase; MpgII: N-methylpurine glycosylase II; MutY/Mig: A/G-specific adenine glycosylase/mismatch glycosylase; Nth: endonuclease III; OggI: 8-oxoguanine glycosylase I; and OggII: 8-oxoguanine glycosylase II) are identified through phylogenetic analysis of 234 homologs found in 94 genomes (16 archaea, 64 bacteria, and 14 eukaryotes). The number of homologs in each gene family varies from 117 in the Nth family (nearly every genome surveyed harbors at least one Nth homolog) to only five in the divergent OggII family (all from archaeal genomes). Sequences from all three domains of life are included in four of the six gene families, suggesting that the HhH superfamily diversified very early in evolution. The phylogeny provides evidence for multiple lineage-specific gene duplication events, most of which involve eukaryotic homologs in the Nth and AlkA gene families. We observe extensive variation in the number of HhH superfamily glycosylase genes present in different genomes, possibly reflecting major differences among species in the mechanisms and pathways by which damaged bases are repaired and/or disparities in the basic rates and spectra of mutation experienced by different genomes.     

New evidence for broad trophic status of leaf endophytic fungi of Quercus gambelii

Endophytic fungi inhabit the living tissues of every terrestrial plant species thus far examined. In at least some cases they significantly improve stress tolerance of their hosts. We asked whether endophytic fungi play other ecological roles, specifically whether the leaf endophytes of Quercus gambelii persist during the course of leaf decomposition, requiring a transition from a biotrophic to a saprotrophic mode of nutrition. Using automated ribosomal intergenic spacer analysis (ARISA), we found that endophyte fungal OTU diversity declined as decomposition commenced, but some endophytes persisted for months during which leaves were decomposing. In contrast, saprotroph fungi OTU diversity increased as decomposition progressed. These results are consistent with the hypothesis that some biotrophic endophytes persist in leaves during decomposition by becoming saprotrophic, and that the niche occupied by them is broader than expected.