pH Signaling in Human Fungal Pathogens: a New Target for Antifungal Strategies

Fungi are exposed to broadly fluctuating environmental conditions, to which adaptation is crucial for their survival. An ability to respond to a wide pH range, in particular, allows them to cope with rapid changes in their extracellular settings. PacC/Rim signaling elicits the primary pH response in both model and pathogenic fungi and has been studied in multiple fungal species. In the predominant human pathogenic fungi, namely, Candida albicans, Aspergillus fumigatus, and Cryptococcus neoformans, this pathway is required for many functions associated with pathogenesis and virulence. Aspects of this pathway are fungus specific and do not exist in mammalian cells. In this review, we highlight recent advances in our understanding of PacC/Rim-mediated functions and discuss the growing interest in this cascade and its factors as potential drug targets for antifungal strategies. We focus on both conserved and distinctive features in model and pathogenic fungi, highlighting the specificities of PacC/Rim signaling in C. albicans, A. fumigatus, and C. neoformans. We consider the role of this pathway in fungal virulence, including modulation of the host immune response. Finally, as now recognized for other signaling cascades, we highlight the role of pH in adaptation to antifungal drug pressure. By acting on the PacC/Rim pathway, it may therefore be possible (i) to ensure fungal specificity and to limit the side effects of drugs, (ii) to ensure broad-spectrum efficacy, (iii) to attenuate fungal virulence, (iv) to obtain additive or synergistic effects with existing antifungal drugs through tolerance inhibition, and (v) to slow the emergence of resistant mutants.     

A review of the volatile metabolites of fungi found on wood substrates

The holdings of eight collections of fungi have been examined for organisms isolated from wood and/or trees. Further selection of these fungi has been made according to their reported ability to produce volatile, biologically active metabolites. It is emphasized that the isolates in the collections do not necessarily produce such metabolites. The list of fungi fulfilling these conditions is slightly augmented by reports we have found in the literature, where the fungi concerned have not yet been deposited. The biochemistry of these compounds is considered with particular emphasis on their biosynthesis including that by Homo sapiens. The physiological and toxicological activity of these metabolites is reviewed especially with reference to their potential role in the complex symbioses existent in, for example, a tree. The review concludes with a discussion of areas of botany deserving increased attention in the hope that this will stimulate further work. The statements in the review are based on 173 references.     

Recent advances in fungal cellobiose oxidoreductases

When grown on cellulose, the white-rot fungus Phanerochaete chrysosporium (Sporotrichum pulverulentum), produces two cellobiose oxidoreductases, i.e., cellobiose:quinone oxidoreductase (CBQ) and cellobiose oxidase (CBO). Similar cellobiose-oxidizing enzymes, capable of utilizing a wide variety of electron acceptors, have been detected in many other fungi. However, the role of the cellobiose oxidoreductases in white-rot fungi, or in any fungi for that matter, is still not known. The original role ascribed to CBQ was as a link between cellulose and lignin degradation. CBQ has been shown to reduce quinones and phenoxyradicals released during lignin degradation concomitantly oxidizing cellobiose and other cellodextrins released during cellulose degradation. Thus, one function proposed for the cellobiose oxidoreductases is to prevent repolymerization of phenoxyradicals formed when phenoloxidases (peroxidases and laccases) attack lignin and lignin degradation products. However, evidence obtained so far indicates that the presence of CBO/CBQ with lignin peroxidases and laccases actually reduces the rate of oxidation of lignin degradation products. CBQ has a molecular mass of about 60 kD and contains an FAD cofactor. CBO contains both heme and FAD, and has a mass of about 90 kD. It has recently been demonstrated that CBO can be proteolytically cleaved into FAD and heme domains. The FAD domain of CBO seems to have all the properties of CBQ, suggesting that CBQ is a cleavage product of CBO. Whether CBO is a precursor of CBQ is not yet known. CBO and CBQ can be distinguished not only by the differences in their spectral properties, but also by the ability of CBO, but not CBQ, to reduce cytochrome c. Both CBO and CBQ have a cellulose-binding domain (CBD), as do a large number of endoglucanases and cellobiohydrolases. The induction-repression patterns regulating cellobiose oxidoreductase genes are not known in any detail. Most reports point to induction during cellulose degradation, but repression has not been studied. Induction has also been suggested to occur by addition of lignosulfonate to the medium.     

Functional analysis of the kinome of the wheat scab fungus Fusarium graminearum

As in other eukaryotes, protein kinases play major regulatory roles in filamentous fungi. Although the genomes of many plant pathogenic fungi have been sequenced, systematic characterization of their kinomes has not been reported. The wheat scab fungus Fusarium graminearum has 116 protein kinases (PK) genes. Although twenty of them appeared to be essential, we generated deletion mutants for the other 96 PK genes, including 12 orthologs of essential genes in yeast. All of the PK mutants were assayed for changes in 17 phenotypes, including growth, conidiation, pathogenesis, stress responses, and sexual reproduction. Overall, deletion of 64 PK genes resulted in at least one of the phenotypes examined, including three mutants blocked in conidiation and five mutants with increased tolerance to hyperosmotic stress. In total, 42 PK mutants were significantly reduced in virulence or non-pathogenic, including mutants deleted of key components of the cAMP signaling and three MAPK pathways. A number of these PK genes, including Fg03146 and Fg04770 that are unique to filamentous fungi, are dispensable for hyphal growth and likely encode novel fungal virulence factors. Ascospores play a critical role in the initiation of wheat scab. Twenty-six PK mutants were blocked in perithecia formation or aborted in ascosporogenesis. Additional 19 mutants were defective in ascospore release or morphology. Interestingly, F. graminearum contains two aurora kinase genes with distinct functions, which has not been reported in fungi. In addition, we used the interlog approach to predict the PK-PK and PK-protein interaction networks of F. graminearum. Several predicted interactions were verified with yeast two-hybrid or co-immunoprecipitation assays. To our knowledge, this is the first functional characterization of the kinome in plant pathogenic fungi. Protein kinase genes important for various aspects of growth, developmental, and infection processes in F. graminearum were identified in this study.     

Fungal toxins as a parasitic factor responsible for the establishment of fungal infections

Although the mechanism of fungal infections, particularly that of opportunistic fungus infections, has been studied extensively, much still remains to be clarified. As is the case for certain bacterial infections, it has long been assumed by numerous investigators that some toxins, enzymes and other metabolites produced in vitro as well as in vivo by pathogenic fungi or their cellular constituents might be responsible for the establishment of fungal infections. However, there are very few papers which deal with isolation and/or characterization of pathogenic fungus-derived toxins, particularly those of high molecular weight, to sufficiently meet various criteria for toxins including etiopathological ability. Likewise, it has been speculated that certain enzymes produced by pathogenic fungi are related to the pathogenesis of infections with the fungi implicated, but no direct evidence has been provided.It is commonly held by researchers concerned with medical mycology that the lowering of specific and/or nonspecific resistance of a host to pathogenic fungi is a prerequisite for the establishment of infections, particularly opportunistic infections. However, it is also accepted that if a given fungus possesses no parasite factors (e.g. toxigenicity, invasiveness and others), it would be unable to initiate infection even when the host is in a severe immunodeficient state. This is supported by our recent studies working with Saccharomyces cerevisiae and some other so-called nonpathogenic yeasts (unpublished data). Based on these considerations, the author and his co-workers have attempted to isolate several high and low molecular weight toxins in a pure state from virulent strains of Candida albicans and Aspergillus fumigatus as opportunist. Studies have also been made on the etiopathological roles of some successfully isolated toxins in infections with the fungi implicated (46).In addition to our experimental results, general concepts in fungal toxins, particularly those related to such toxins as isolated in our laboratory are outlined. Since opportunistic fungus infections have created a global problem because of their world-wide prevalence, a sharp demarcation between the so-called pathogenic and nonpathogenic fungi has become vague. Despite this situation, two terms are conventionally used throughout this paper.The author thanks Drs. H. Yamaguchi and K. Uchida, Y. Yamamoto, T. Hiratani, and Y. Nozu for their collaboration during these studies.     

Established and potential impacts of eukaryotic mycelial decomposers in marine/terrestrial ecotones

Marine mycelial decomposers (eumycotes, members of Kingdom Fungi, and oomycotes, zoosporic members of the Kingdom Protoctista) are highly adapted for capture of solid substrate by pervasion and digestion from within. Thus they exert their influence in areas of large input of litter of vascular plants, especially at some types of terrestrial/marine ecosystemic interfaces (ecotones). Unavailability of methods easily used by general microbial ecologists has hampered progress in the study of marine mycelial decomposers, and there are still pockets of difficulty in this regard (especially for oomycotes). Recently published or refined methods for measuring fungal mass and productivity have begun to allow us to realize the impacts of fungi in marine ecotones. For example, it is now clear that the older paradigm reflecting negligible contribution of microbial mass to litter nitrogen content is false for the standing-decay system of saltmarsh grasses — in these decay systems, fungal mass can account for virtually all of the nitrogen present at some point(s) in the standing-decay period. Another generally held belief about marine fungi has also been reversed — ascomycetes (Fungi) of a saltmarsh grass (smooth cordgrass) clearly do digest lignocellulose under natural-decay circumstances. Much more work is needed to clarify the situation, but at present it appears that major types of marine ecotones (e.g., saltmarshes and mangroves) differ sharply in the balance among major groups of decomposers (eumycotes, oomycotes, and bacteria) with regard to their utilization of vascular-plant litter. In saltmarshes, microbial production in standing grass litter is strongly dominated by fungi, and oomycotes do not show evidence of a substantial role in decomposition. In mangroves, submerged fallen leaves appear to support minor fungal occupancy, but ubiquitous and rapid occupancy by oomycotes (especially Halophytophthora vesicula). Many exciting areas of research are now more open than ever before to marine microbial ecologists interested in working with mycelial decomposers.     

Linking fungal morphogenesis with virulence

Pathogenic fungi have become an increasingly common cause of systemic disease in healthy people and those with impaired immune systems. Although a vast number of fungal species inhabit our planet, just a small number are pathogens, and one feature that links many of them is the ability to differentiate morphologically from mould to yeast, or yeast to mould. Morphological differentiation between yeast and mould forms has commanded attention for its putative impact on the pathogenesis of invasive fungal infections. This review explores the current body of evidence linking fungal morphogenesis and virulence. The topics addressed cover work on phase-locked fungal cells, expression of phase-specific virulence traits and modulation of host responses by fungal morphotypes. The effect of morphological differentiation on fungal interaction with host cells, immune modulation and the net consequence on pathogenesis of disease in animal model systems are considered. The evidence argues strongly that morphological differentiation plays a vital role in the pathogenesis of fungal infection, suggesting that factors associated with this conversion process represent promising therapeutic targets.     

Models for studying the role of fungal attachment in colonization and pathogenesis

Fungal adhesion and aggregation is considered an important event in human, animal and plant disease as well as in the ecology of fungi in nature (e.g., in mating reactions and the dispersion of fungal propagules). Because of this, numerous models have been developed to study fungal adhesion and aggregation mechanisms over the last decade. Unfortunately, however, nearly all of the work in this area has been carried out in simple in vitro models and has focused its attention on that of the attachment process alone, while realitively little effort has been made toward understanding the role adhesion and aggregation plays in colonization or pathogenesis. The emphasis on adhesion and aggregation mechanisms appears, therefore, to have somewhat obscured the study of the interaction of adhesion with other factors that may be of equal or greater importance in these processes and to the development of more complex adhesion models to explore the relationship between adhesion and colonization. Moreover, because it has not generally been appreciated that several methodologic pitfalls accompany the use of simple in vitro adhesion models, there is now emerging a confused literature base with regard to: (i) the nature of the cell wall component(s) of Candida albicans that mediates its attachment to, for example, epithelial cells; (ii) the mechanism(s) of invasion of mucosal and endothelial surfaces; and (iii) the role certain adhesive reactions observed in vitro play in colonization and pathogenesis by this fungus. Therefore, with an emphasis on C. albicans, this paper will attempt to put into perspective the uses and limitations of models for studying the role of fungal attachment in colonization and pathogenesis. In addition, factors that can modify fungal adhesion data will be discussed and the beginnings of a standardized assay to study the adhesion of C. albicans to buccal epithelial cells will be described.Presented as part of the Everett S. Beneke Symposium in Mycology, May 27, 1988.     

Development of the Antiviral State in Response to Interferon

The development of resistance in response to interferon depends on cellular RNA synthesis and probably also on cellular protein synthesis. The evidence for these requirements is reviewed, as well as the proposal that this evidence indicates the existence of a specific response of the cell to interferon, involving the induced synthesis of an antiviral protein. Direct evidence for such an interpretation has not been obtained, and alternative explanations are discussed which do not require quantitative or qualitative differences in the RNA and protein made in cells exposed to interferon. The possible role of the ribosome in the antiviral action of interferon is also discussed.     

Genetic Variability of Trypanosoma cruzi:Implications for the Pathogenesis of Chagas Disease

Chagas disease, caused by the protozoan Trypanosoma cruzi, has a variable clinical course, ranging from symptomless infection to severe chronic disease with cardiovascular or gastrointestinal involvement or even overwhelming acute episodes. The factors influencing this clinical variability have not been elucidated, but genetic variation of both the host and parasite is likely to be important. Here, Andréa M. Macedo and Sérgio D.J. Pena review the evidence showing a role for the genetic constitution of T. cruzi in determining the clinical characteristics of Chagas disease, and propose a ;clonal-histotropic model' for the pathogenesis of this disease.     

Regulation of low-molecular weight organic acid production in fungi

Organic acids produced by fungi have been proposed to have many roles in wood-decay processes, lignocellulose degradation or plant pathogenesis involving saprotrophic or pathogenic fungi, as well as in nutrient acquisition and metal detoxification involving mycorrhizal or rhizosphere-inhabiting fungi. In comparison with other fungi, a considerable body of work has been devoted to the comprehension of biosynthesis pathways in fungi involved in industrial production of organic acids, and also in those involved in wood-decay processes and pathogenicity. In this review we therefore focus on information available from these different types of low-molecular weight organic acid (LMWOA) producing fungi in order to better understand the environmental cues involved in regulating production of LMWOAs.     

Understanding fungal functional biodiversity during the mitigation of environmentally dispersed pentachlorophenol in cork oak forest soils

Pentachlorophenol (PCP) is globally dispersed and contamination of soil with this biocide adversely affects its functional biodiversity, particularly of fungi – key colonizers. Their functional role as a community is poorly understood, although a few pathways have been already elucidated in pure cultures. This constitutes here our main challenge – elucidate how fungi influence the pollutant mitigation processes in forest soils. Circumstantial evidence exists that cork oak forests in N. W. Tunisia – economically critical managed forests are likely to be contaminated with PCP, but the scientific evidence has previously been lacking. Our data illustrate significant forest contamination through the detection of undefined active sources of PCP. By solving the taxonomic diversity and the PCP‐derived metabolomes of both the cultivable fungi and the fungal community, we demonstrate here that most strains (predominantly penicillia) participate in the pollutant biotic degradation. They form an array of degradation intermediates and by‐products, including several hydroquinone, resorcinol and catechol derivatives, either chlorinated or not. The degradation pathway of the fungal community includes uncharacterized derivatives, e.g. tetrachloroguaiacol isomers. Our study highlights fungi key role in the mineralization and short lifetime of PCP in forest soils and provide novel tools to monitor its degradation in other fungi dominated food webs.     

The pathway of nitrogen assimilation in plants

The major route of nitrogen assimilation has been considered for many years to occur via the reductive amination of α-oxoglutarate, catalysed by glutamate dehydrogenase. However, recent work has shown that in most bacteria an alternative route via glutamine synthetase and glutamine: 2-oxoglutarate aminotransferase (glutamate synthase) operates under conditions of ammonia limitation. Subsequently the presence of a ferredoxin-dependent glutamate synthase in green leaves and green and blue-green algae, and a NAD(P)H and ferredoxin-dependent enzyme in roots and other non-green plant tissues, has suggested that this route may also function in most members of the plant kingdom. The only exceptions are probably the majority of the fungi, where so far most organisms studied do not appear to contain glutamate synthase. Besides the presence of the necessary enzymes there is other evidence to support the contention that the assimilation of ammonia into amino acids occurs via glutamine synthetase and glutamate synthase, and that it is unlikely that glutamate dehydrogenase plays a major role in nitrogen assimilation in bacteria or higher plants except in circumstances of ammonia excess.     

Hybridisation is associated with increased fecundity and size in invasive taxa: meta‐analytic support for the hybridisation‐invasion hypothesis

The hypothesis that interspecific hybridisation promotes invasiveness has received much recent attention, but tests of the hypothesis can suffer from important limitations. Here, we provide the first systematic review of studies experimentally testing the hybridisation‐invasion (H‐I) hypothesis in plants, animals and fungi. We identified 72 hybrid systems for which hybridisation has been putatively associated with invasiveness, weediness or range expansion. Within this group, 15 systems (comprising 34 studies) experimentally tested performance of hybrids vs. their parental species and met our other criteria. Both phylogenetic and non‐phylogenetic meta‐analyses demonstrated that wild hybrids were significantly more fecund and larger than their parental taxa, but did not differ in survival. Resynthesised hybrids (which typically represent earlier generations than do wild hybrids) did not consistently differ from parental species in fecundity, survival or size. Using meta‐regression, we found that fecundity increased (but survival decreased) with generation in resynthesised hybrids, suggesting that natural selection can play an important role in shaping hybrid performance – and thus invasiveness – over time. We conclude that the available evidence supports the H‐I hypothesis, with the caveat that our results are clearly driven by tests in plants, which are more numerous than tests in animals and fungi.     

Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1α of Ichthyophonus irregularis

Ichthyosporea is a recently recognized group of morphologically simple eukaryotes, many of which cause disease in aquatic organisms. Ribosomal RNA sequence analyses place Ichthyosporea near the divergence of the animal and fungal lineages, but do not allow resolution of its exact phylogenetic position. Some of the best evidence for a specific grouping of animals and fungi (Opisthokonta) has come from elongation factor 1α, not only phylogenetic analysis of sequences but also the presence or absence of short insertions and deletions. We sequenced the EF-1α gene from the ichthyosporean parasite Ichthyophonus irregularis and determined its phylogenetic position using neighbor-joining, parsimony and Bayesian methods. We also sequenced EF-1α genes from four chytrids to provide broader representation within fungi. Sequence analyses and the presence of a characteristic 12 amino acid insertion strongly indicate that I. irregularis is a member of Opisthokonta, but do not resolve whether I. irregularis is a specific relative of animals or of fungi. However, the EF-1α of I. irregularis exhibits a two amino acid deletion heretofore reported only among fungi.     

Rhizosphere and root surface fungi of some heath plants and the role of Dark Sterile forms

Many different species of fungi have been isolated from the root region of heath plants. In the absence of rapidly growing species,Dark Sterile forms predominated in culture plates. It is suggested that these have an important ecological role in the soil-root interface. AsDS forms do not appear in culture plates easily any floristic list of fungi from the root surface not mentioningDS forms must be accepted with caution. Attention is drawn to the fact that these are truly root-inhabiting fungi possessing some parasitic or mycorrhizal propensities.     

Are Ichthyosporea animals or fungi? Bayesian phylogenetic analysis of elongation factor 1alpha of Ichthyophonus irregularis

Ichthyosporea is a recently recognized group of morphologically simple eukaryotes, many of which cause disease in aquatic organisms. Ribosomal RNA sequence analyses place Ichthyosporea near the divergence of the animal and fungal lineages, but do not allow resolution of its exact phylogenetic position. Some of the best evidence for a specific grouping of animals and fungi (Opisthokonta) has come from elongation factor 1alpha, not only phylogenetic analysis of sequences but also the presence or absence of short insertions and deletions. We sequenced the EF-1alpha gene from the ichthyosporean parasite Ichthyophonus irregularis and determined its phylogenetic position using neighbor-joining, parsimony and Bayesian methods. We also sequenced EF-1alpha genes from four chytrids to provide broader representation within fungi. Sequence analyses and the presence of a characteristic 12 amino acid insertion strongly indicate that I. irregularis is a member of Opisthokonta, but do not resolve whether I. irregularis is a specific relative of animals or of fungi. However, the EF-1alpha of I. irregularis exhibits a two amino acid deletion heretofore reported only among fungi.     

Saprotrophic capabilities as functional traits to study functional diversity and resilience of ectomycorrhizal community

In an accompanying editorial Dr Petr Baldrian made a case casting doubt on our recent work addressing the saprophytic potential of ectomycorrhizal (EM) fungi. Dr Baldrian’s statements illustrate a very valid truth: the book is still very much open on this subject. The point he raised that the only logical reason for these fungi to be responding to high carbon demand or decreased host photosynthetic capacity by up-regulating enzymes is for the purpose of carbon acquisition is valid as well. Despite this, he makes the case that there is no compelling evidence that EM fungi exhibit saprophytic activity. The concept central to Dr Baldrian’s conclusion is that even though some EM fungi possess the genes necessary for saprophytic behaviour and may even express these genes, EM fungi do not inhabit a position in the soil column that provides access to usable substrate. In this paper we present both previously published and newly obtained data that demonstrate that this assumption is erroneous, and we present arguments that place the saprophytic potential of EM fungi within a broad ecological context.     

Allergenicity of airborne basidiospores and ascospores: need for further studies

Many known fungal species are grouped among basidiomycetes and ascomycetes. Active mechanisms of spore release into air currents are among the main features of these fungi. Aerobiological studies have described their presence in many regions worldwide. In some areas, fungi have been described as the predominant outdoor airborne biological particulate with much higher concentrations than pollen. Other studies have determined that among the fungal aerospora, the highest concentrations belong to basidiospores and ascospores. Nevertheless, the allergenic potential of spores from basidiomycetes and meiotic forms of ascomycetes has not been studied to the extent of mitosporic fungi and allergens from other sources. The need to further evaluate the role of basidiomycetes and meiotic ascomycetes in allergies is evidenced by the few genera with characterized allergens and limited studies that had demonstrated levels of sensitization similar or higher to that of mitosporic fungi and other allergens. In this review, based on the existing aerobiological, epidemiological, immunological, and molecular biology studies, we provide evidence that the role of basidiomycetes and ascomycetes deserves more attention with respect to their roles as potential aeroallergens.