Gene expression profiling in the human pathogenic dermatophyte Trichophyton rubrum during growth on proteins

Diagnostic ability of Peptidase S8 gene in the Arthrodermataceae causing dermatophytoses: A metadata analysis

An unambiguous identification of dermatophytes causing dermatophytoses is necessary for accurate clinical diagnosis and epidemiological implications. In the current taxonomy of the Arthrodermataceae, the etiological agents of dermatophytoses consist of seven genera and members of the genera Trichophyton are the most prevalent etiological agents at present. The genera Trichophyton consists of 16 species that are grouped as clades, but the species borderlines are not clearly delimited. The aim of the present study was to determine the discriminative power of subtilisin gene variants (SUB1-SUB12) in family Arthrodermataceae, particularly in Trichophyton. Partial and complete reads from 288 subtilisin gene sequences of 12 species were retrieved and a stringent filtering following two different approaches for analysis (probability of correct identification (PCI) and gene gap analysis) conducted to determine the uniqueness of the subtilisin gene subtypes. SUB1 with mean PCI value of 60% was the most suitable subtilisin subtype for specific detection of T.rubrum complex, however this subtype is not reported in members of T. mentagrophytes complex which is one of the most prevalent etiological agent at present. Hence, SUB7 with 40% PCI value was selected for testing its discriminative power in Trichophyton species. SUB7 specific PCR based detection of dermatophytes was tested for sensitivity and specificity. Sequences of SUB7 from 42 isolates and comparison with the ITS region showed that differences within the subtilisin gene can further be used to differentiate members of the T. mentagrophytes complex. Further, subtilisin cannot be used for the differentiation of T. benhamiae complex since all SUB subtypes show low PCI scores. Studies on the efficiency and limitations of the subtilisin gene as a diagnostic tool are currently limited. Our study provides information that will guide researchers in considering this gene for identifying dermatophytes causing dermatophytoses in human and animals.

Subtilisin 3 production from Microsporum canis is independent of keratin substrate availability

Dermatophytes are highly infectious fungi that cause superficial infections in keratinized tissues in humans and animals. This group of fungi is defined by their ability to digest keratin and encompasses a wide range of species. We investigated a critical adhesion protein, subtilisin 3, utilized by Microsporum canis during initial stages of infection, analyzing its production and expression under varying growth conditions. Additionally, as this protein must be expressed and produced for dermatophyte infections to occur, we developed and optimized a diagnostic antibody assay targeting this protein. Subtilisin 3 levels were increased in culture when grown in baffled flasks and supplemented with either l-cysteine or cat hair. As subtilisin 3 was also produced in cultures not supplemented with keratin or cysteine, this study demonstrated that subtilisin 3 production is not reliant on the presence of keratin or its derivatives. These findings could help direct future metabolic studies of dermatophytes, particularly during the adherence phase of infections.

Review on host-pathogen interaction in dermatophyte infections

Dermatophytosis is a common superficial fungal infection of the skin and its appendages caused by dermatophytes. Recent times have witnessed a dynamic evolution of dermatophytes driven by their ecology, reproduction, pathogenicity and host immune response, influenced by population migration and socioeconomic status. Dermatophytes establish infection following successful adherence of arthroconidia to the surface of keratinized tissues. The proteolytic enzymes released during adherence and invasion not only ascertain their survival but also allow the persistence of infection in the host. While the cutaneous immune surveillance mechanism, after antigen exposure and presentation, leads to activation of T lymphocytes and subsequent clonal expansion generating effector T cells that differentially polarize to a predominant Th17 response, the response fails to eliminate the pathogen despite the presence of high levels of IFN-γ. In chronic dermatophytosis, antigens are a constant source of stimulus promoting a dysregulated Th17 response causing inflammation. The host-derived iTreg response fails to counterbalance the inflammation and instead polarizes to Th17 lineage, aggravating the chronicity of the infection. Increasing antifungal resistance and recalcitrant dermatophytosis has impeded the overall clinical remission. Human genetic research has the potential to generate knowledge to explore new therapeutic targets. The review focuses on understanding specific virulence factors involved in pathogenesis and defining the role of dysregulated host immune response against chronic dermatophytic infections for future management strategies.

Comprehensive Assessment of the Virulence Factors sub 3, sub 6 and mcpA in the Zoonotic Dermatophyte Trichophyton benhamiae Using FISH and qPCR

Skin infections by keratinophilic fungi are commonly referred to as dermatophytosis and represent a major health burden worldwide. Although patient numbers are on the rise, data on virulence factors, their function and kinetics are scarce. We employed an ex vivo infection model based on guinea pig skin explants (GPSE) for the zoonotic dermatophyte Trichophyton (T.) benhamiae to investigate kinetics of the virulence factors subtilisin (sub) 3, sub 6, metallocarboxypeptidase A (mcpA) and isocitrate lyase (isol) at gene level for ten days. Fluorescence in situ hybridization (FISH) and quantitative polymerase chain reaction (qPCR) were used to detect and quantify the transcripts, respectively. Kingdom-spanning, species-specific and virulence factor-specific probes were successfully applied to isolated fungal elements showing inhomogeneous fluorescence signals along hyphae. Staining results for inoculated GPSE remained inconsistent despite thorough optimization. qPCR revealed a significant increase of sub 3- and mcpA-transcripts toward the end of culture, sub 6 and isol remained at a low level throughout the entire culture period. Sub 3 is tightly connected to the de novo formation of conidia during culture. Since sub 6 is considered an in vivo disease marker. However, the presented findings urgently call for further research on the role of certain virulence factors during infection and disease.

Photodynamic antifungal activity of a superparamagnetic and fluorescent drug carrier system against antibiotic-resistant fungal strains

Increased antimicrobial resistance demands the development of new antimicrobial agents with high potency. A wide variety of microbial systems are continuously subjected to mutations which ultimately results in antimicrobial resistance. The present study aimed at the fabrication of a nano drug delivery system which simultaneously is superparamagnetic, fluorescent, non-cytotoxic and antifungal. The developed system is an easily targetable and detectable tool owing to its superparamagnetic and fluorescent characteristics respectively. Superparamagnetic iron oxide nanoparticles stabilized by macromolecular starch have been incorporated into a fluorescently modified carrier system to get the final drug delivery system. The finally developed drug carrier system is found to be non-cytotoxic from the in vitro cytotoxicity studies performed against normal rat spleen cells. The photodynamic antifungal capability of the system was the premier concern of investigation of the present study. The antifungal studies were conducted against Histoplasma capsulatum and Trichophyton rubrum by well diffusion method and the results were compared with the activity of the antibiotic, griseofulvin. The minimum inhibitory concentration against each fungal strain was determined using broth dilution method.

SUPPLEMENTARY INFORMATION

The online version contains supplementary material available at 10.1007/s10570-021-04107-y.

Comprehensive genome and transcriptome analysis of the dermatophyte Trichophyton schoenleinii reveals the candidate pathogenic genes

BACKGROUND

Trichophyton schoenleinii is an anthropophilic dermatophyte that causes tinea favosa. Nowadays, it remains an important pathogen in some regions of the world, mainly epidemic in Africa and West Asia. Despite the medical importance of T. schoenleinii infections, a high-quality reference genome for T. schoenleinii is still unavailable, neither its transcriptomic profile.

OBJECTIVES

The aim of the current study was to improve understanding of the underlying pathogenic mechanism of T. schoenleinii, and to define the candidate pathogenic genes of T. schoenleinii.

METHODS

Comprehensive genomic analysis of T. schoenleinii was carried out by Illumina and PacBio sequencing platforms. Transcriptome profiles of T. schoenleinii cultured in vitro in two media containing either keratin or soy protein were determined using RNA sequencing (RNA-seq) technology.

RESULTS

Here, we present the first draft genome sequence of T. schoenleinii strain T2s, which consists of 11 scaffolds containing 7474 predicted genes. Transcriptome analysis showed that genes involved in keratin hydrolysis have higher expression in T. schoenleinii grown in keratin medium, including genes encoding proteases, cysteine dioxygenase and acetamidase. Other genes with higher expression include genes encoding the components of the pH-responsive signal transduction pathways and transcription factors, many of which may play a role in pathogenicity.

CONCLUSION

In summary, this study provides new insights into the pathogenic mechanism of T. schoenleinii and highlights candidate genes for further development of novel targets in disease diagnosis and treatment of tinea favosa.

Gene expression profiling of protease and non-protease genes in Trichophyton mentagrophytes isolates from dermatophytosis patients by qRT-PCR analysis

Trichophyton mentagrophytes secretes Metallocarboxypeptidase A and B of the M14 family as endoproteases and exoprotease. T. mentagrophytes produce Metalloprotease 3 and 4 which degrades the protein into the short peptides and amino acids. To understand the host fungal relationship and identification of such genes expressed during infection is utmost important. T. mentagrophytes encodes some proteins which are associated with the glyoxylate cycle. The glyoxylate cycle enzymes have been involving in virulence of dermatophytes and their up-regulation during dermatophytes growth on keratin. On comparing the expression level of virulence protease and non-protease genes, we observed, among exoprotease protease genes, Metallocarboxypeptidase B was strongly up regulated (134.6 fold high) followed by Metallocarboxypeptidase A (115.6 fold high) and Di-peptidyl-peptidases V (10.1 fold high), in dermatophytic patients as compared to ATCC strain. Furthermore, among endoprotease, Metalloprotease 4 was strongly up regulated (131.6 fold high) followed by Metalloprotease 3 (16.7 fold high), in clinical strains as compared to T. mentagrophytes ATCC strain. While among non-protease genes, Citrate Synthase was highly expressed (118 fold high), followed by Isocitrate Lyase (101.6 fold high) and Malate Synthase (52.9 fold high). All the studied virulence genes were considered the best suitable ones by geNorm, Best keeper, Norm Finder and Ref finder.

Microbial enzymes catalyzing keratin degradation: Classification, structure, function

Keratin is an insoluble and protein-rich epidermal material found in e.g. feather, wool, hair. It is produced in substantial amounts as co-product from poultry processing plants and pig slaughterhouses. Keratin is packed by disulfide bonds and hydrogen bonds. Based on the secondary structure, keratin can be classified into α-keratin and β-keratin. Keratinases (EC 3.4.-.- peptide hydrolases) have major potential to degrade keratin for sustainable recycling of the protein and amino acids. Currently, the known keratinolytic enzymes belong to at least 14 different protease families: S1, S8, S9, S10, S16, M3, M4, M14, M16, M28, M32, M36, M38, M55 (MEROPS database). The various keratinolytic enzymes act via endo-attack (proteases in families S1, S8, S16, M4, M16, M36), exo-attack (proteases in families S9, S10, M14, M28, M38, M55) or by action only on oligopeptides (proteases in families M3, M32), respectively. Other enzymes, particularly disulfide reductases, also play a key role in keratin degradation as they catalyze the breakage of disulfide bonds for better keratinase catalysis. This review aims to contribute an overview of keratin biomass as an enzyme substrate and a systematic analysis of currently sequenced keratinolytic enzymes and their classification and reaction mechanisms. We also summarize and discuss keratinase assays, available keratinase structures and finally examine the available data on uses of keratinases in practical biorefinery protein upcycling applications.

Comprehensive analysis of the dermatophyte Trichophyton rubrum transcriptional profile reveals dynamic metabolic modulation

The environmental challenges imposed onto fungal pathogens require a dynamic metabolic modulation, which relies on activation or repression of critical factors and is essential for the establishment and perpetuation of host infection. Wherefore, to overcome the different host microenvironments, pathogens not only depend on virulence factors but also on metabolic flexibility, which ensures their dynamic response to stress conditions in the host. Here, we evaluate Trichophyton rubrum interaction with keratin from a metabolic perspective. We present information about gene modulation of the dermatophyte during early infection stage after shifting from glucose- to keratin-containing culture media, in relation to its use of glucose as the carbon source. Analyzing T. rubrum transcriptome using high-throughput RNA-sequencing technology, we identified the modulation of essential genes related to nitrogen, fatty acid, ergosterol, and carbohydrate metabolisms, among a myriad of other genes necessary for the growth of T. rubrum in keratinized tissues. Our results provide reliable and critical strategies for adaptation to keratin and confirm that the urea-degrading activity associated with the reduction in disulfide bonds and proteolytic activity facilitated keratin degradation. The global modulation orchestrates the responses that support virulence and the proper adaptation to keratin compared with glucose as the carbon source. The gene expression profiling of the host-pathogen interaction highlights candidate genes involved in fungal adaptation and survival and elucidates the machinery required for the establishment of the initial stages of infection.

Familial Dermatophytosis in India: A Study of the Possible Contributing Risk Factors

Background: Dermatophytes are keratinophilic fungi responsible for skin, nail, and scalp infections. Chronic dermatophytosis, defined as persistent infection for six months or more, was very rare in the 1980s and mostly limited to patients with nail involvement, but this is no longer true. Currently, patients with chronic dermatophytosis are increasing, and about 50 percent of patients with dermatophytosis have at least one other member of their family infected at the same time, sometimes with entire families being affected at once. Objective: We sought to study the possible risk factors associated with familial dermatophytosis. Methods: The present questionnaire-based study was conducted from May 2017 to July 2017. Patients with a clinical diagnosis of dermatophytosis and at least one other family member affected were included. A proforma was filled and history was taken, including number of family members affected, site of infection in the index case, site(s) of infection of all other subsequent family members affected, and use of over-the-counter drugs. Results: Out of the 113 families surveyed, which included 673 subjects, a little over half (55.4%) were affected by dermatophytosis. In 103 families, the initial site of infection in the subsequent family member affected was the same site as that affected in the first member. All families reported a history of using an irritant soap and over-the-counter drugs. Washing all the family's clothing together was a common factor. All families had a single bathroom and used the same soap and stool for bathing. Conclusion: Through our survey, we identified possible risk factors that might be responsible for the increasing epidemic of familial dermatophytosis in India, including sharing of soaps and towels, washing clothes in the same vessel, sharing of lavatories, abuse of topical steroids and over the counter topicals, and use of antiseptic soaps that kill normal flora.

Alternative Splicing in Heat Shock Protein Transcripts as a Mechanism of Cell Adaptation in Trichophyton rubrum

Heat shock proteins (HSPs) are involved in critical processes like host tissue invasion, resistance, and pathogenicity in dermatophytes. RNA-Seq analysis of Trichophyton rubrum exposed to undecanoic acid (UDA) revealed intron retention events in HSP transcripts. Because HSPs are modulated in response to various stimuli and as alternative splicing (AS) can result in a broad diversity in the proteome of eukaryotic cells, our objective was to confirm the aforementioned retention events, investigating their consequences and extent. Furthermore, we aimed to determine: (1) the expression profile of HSP genes in an infection-like scenario and (2) the importance of Hsp90 for the keratinolytic potential of T. rubrum. RT and qPCR analyses comparing the exposure to UDA and terbinafine (TRB) confirmed the presence of two mRNA isoforms of the hsp7-like gene, with distinct expression patterns in response to UDA and TRB. The HSP expression profile revealed two upregulated, three downregulated, and four unmodulated transcripts; Hsp90 inhibition by 17-AAG resulted in a significant decrease in keratinolytic potential at 37 °C. Altogether, these results broaden the current knowledge on the importance of HSP-mediated pathways for cell adaptation and other aspects of dermatophyte biology, indicating that HSP network proteins can be potential targets for antifungal therapy.

Keratin hydrolysis by dermatophytes

Dermatophytes are the most common cause of superficial fungal infections (tinea infections) and are a specialized group of filamentous fungi capable of infecting and degrading keratinised tissues, including skin, hair, and nail. Essential to their pathogenicity and virulence is the production of a broad spectrum of proteolytic enzymes and other key proteins involved in keratin biodegradation and utilization of its breakdown products. The initial stage of biodegradation of native keratin is considered to be sulfitolysis, in which the extensive disulfide bridges present in keratin are hydrolyzed, although some secreted subtilisins can degrade dye-impregnated keratin azure without prior reduction (Sub3 and Sub4). Sulfitolysis facilitates the extracellular biodegradation of keratin by the dermatophytes' extensive array of endo- and exoproteases. The importance of dermatophyte proteases in infection is widely recognized, and these enzymes have also been identified as important virulence determinants and allergens. Finally, the short peptide and amino acid breakdown products are taken up by the dermatophytes, using as yet poorly characterised transporters, and utilized for metabolism. In this review, we describe the process of keratin biodegradation by dermatophytes, with an especial focus on recent developments in cutting edge molecular biology and '-omic' studies that are helping to dissect the complex process of keratin breakdown and utilization.

An ex vivo Human Skin Model to Study Superficial Fungal Infections

Human skin fungal infections (SFIs) affect 25% of the world's population. Most of these infections are superficial. The main limitation of current animal models of human superficial SFIs is that clinical presentation is different between the different species and animal models do not accurately reflect the human skin environment. An ex vivo human skin model was therefore developed and standardised to accurately model SFIs. In this manuscript, we report our protocol for setting up ex vivo human skin infections and report results from a primary superficial skin infection with Trichophyton rubrum, an anthropophilic fungus. The protocol includes a detailed description of the methodology to prepare the skin explants, establish infection, avoid contamination, and obtain high quality samples for further downstream analyses. Scanning electronic microscopy (SEM), histology and fluorescent microscopy were applied to evaluate skin cell viability and fungal morphology. Furthermore, we describe a broad range of assays, such as RNA extraction and qRT-PCR for human gene expression, and protein extraction from tissue and supernatants for proteomic analysis by liquid chromatography-mass spectrometry (LC-MS/MS). Non-infected skin was viable after 14 days of incubation, expressed genes and contained proteins associated with proliferative, immune and differentiation functions. The macroscopic damage caused by T. rubrum had a similar appearance to the one expected in clinical settings. Finally, using this model, the host response to T. rubrum infection can be evaluated at different levels.

A combination of photodynamic therapy and antimicrobial compounds to treat skin and mucosal infections: a systematic review

BACKGROUND

Antimicrobial photodynamic therapy (aPDT) is a growing approach to treat skin and mucosal infections. Despite its effectiveness, investigators have explored whether aPDT can be further combined with antibiotics and antifungal drugs.

OBJECTIVE

To systematically assess the in vivo studies on the effectiveness of combinations of aPTD plus antimicrobials in the treatment of cutaneous and mucosal infections.

MATERIALS AND METHODS

Searches were performed in four databases (PubMed, EMBASE, Cochrane library databases, ClinicaTrials.gov) until July 2018. The pooled information was evaluated according to the PRISMA guidelines.

RESULTS

11 full-text articles were finally evaluated and included. The best aPDT combinations involved 5-aminolevulinic acid or phenothiazinium dye-based aPDT. In general, the combination shows benefits such as reducing treatment times, lowering drug dosages, decreasing drug toxicity, improving patient compliance and diminishing the risk of developing resistance. The mechanism of action may be that first aPDT damages the microbial cell wall or membrane, which allows better penetration of the antimicrobial drug.

LIMITATIONS

The number of studies was low, the protocols used were heterogeneous, and there was a lack of clinical trials.

CONCLUSIONS

The additive or synergistic effect of aPDT combined with antimicrobials could be promising to manage skin and mucosal infections, helping to overcome the microbial drug resistance.

Majocchi's granuloma: current perspectives

Majocchi’s granuloma (MG) is a rare fungal infection of the dermis that is mainly caused by dermatophytes (in ≥95% of cases); the most frequently identified cause is anthropophilic Trichophyton rubrum. In the rest of the cases, the causes are non-dermatophytic fungi such as Aspergillus species. This review aimed to provide information about the current perspectives on MG regarding its clinical characteristics, predisposing factors, laboratory diagnosis, and treatment strategies. Although the lower extremities were reported to be the most common site of infection, facial involvement has been predominant in the past 5 years. Our literature research showed that the most common predisposing factor (55%) is the use of topical steroid creams without potassium hydroxide examination during treatment of erythematous squamous dermatoses. A reliable diagnosis of MG is based on histopathological examination, including fungal culture and molecular analyses. MG should be treated not only with topical agents but also with systemic antifungal agents that are continued until the lesions are completely resolved. In systemic treatment, the most preferred drug is terbinafine, because of its efficacy, side effects, and safety.

Skin Fungi from Colonization to Infection

Humans are exceptional among vertebrates in that their living tissue is directly exposed to the outside world. In the absence of protective scales, feathers, or fur, the skin has to be highly effective in defending the organism against the gamut of opportunistic fungi surrounding us. Most (sub)cutaneous infections enter the body by implantation through the skin barrier. On intact skin, two types of fungal expansion are noted: (A) colonization by commensals, i.e., growth enabled by conditions prevailing on the skin surface without degradation of tissue, and (B) infection by superficial pathogens that assimilate epidermal keratin and interact with the cellular immune system. In a response-damage framework, all fungi are potentially able to cause disease, as a balance between their natural predilection and the immune status of the host. For this reason, we will not attribute a fixed ecological term to each species, but rather describe them as growing in a commensal state (A) or in a pathogenic state (B).

Transcriptome-wide survey of gene expression changes and alternative splicing in Trichophyton rubrum in response to undecanoic acid

While fatty acids are known to be toxic to dermatophytes, key physiological aspects of the Trichophyton rubrum response to undecanoic acid (UDA), a medium chain saturated fatty acid (C_11:0), are not well understood. Thus, we analysed RNA-seq data from T. rubrum exposed to sub-lethal doses of UDA for 3 and 12 h. Three putative pathways were primarily involved in UDA detoxification: lipid metabolism and cellular membrane composition, oxidative stress, and pathogenesis. Biochemical assays showed cell membrane impairment, reductions in ergosterol content, and an increase in keratinolytic activity following UDA exposure. Moreover, we assessed differential exon usage and intron retention following UDA exposure. A key enzyme supplying guanine nucleotides to cells, inosine monophosphate dehydrogenase (IMPDH), showed high levels of intron 2 retention. Additionally, phosphoglucomutase (PGM), which is involved in the glycogen synthesis and degradation as well as cell wall biosynthesis, exhibited a significant difference in exon 4 usage following UDA exposure. Owing to the roles of these enzymes in fungal cells, both have emerged as promising antifungal targets. We showed that intron 2 retention in impdh and exon 4 skipping in pgm might be related to an adaptive strategy to combat fatty acid toxicity. Thus, the general effect of UDA fungal toxicity involves changes to fungal metabolism and mechanisms for regulating pre-mRNA processing events.

Immunoresponses in dermatomycoses

Contact with fungal pathogens initiates a series of host responses beginning with innate immunity, which leads to fungal recognition and microbial killing. The innate immune system also modulates the adaptive immune responses, leading to the establishment of immunological memory and protection against pathogens. In the case of dimorphic fungi such as Candida albicans and Malassezia, the immune system plays an important role in tolerance and resistance when managing the organisms either as commensal microbiota or invading pathogens, and disruption of this balance can result in pathological consequences for the host. In addition, Malassezia and dermatophytes have immunomodulatory capabilities that allow them to adapt to their environments and they may exert different effects in healthy and diseased skin. Here, we discuss the host immune responses to dermatomycoses caused by dimorphic fungi such as C. albicans and Malassezia as well as dermatophytes such as Trichophyton spp. and Arthroderma benhamiae to gain a better understanding of the mechanisms of the host-dermatomycosis interaction.

Genetic Manipulations in Dermatophytes

Dermatophytes are a group of closely related fungi that nourish on keratinized materials for their survival. They infect stratum corneum, nails, and hair of human and animals, accounting the largest portion of fungi causing superficial mycoses. Huge populations are suffering from dermatophytoses, though the biology of these fungi is largely unknown yet. Reasons are partially attributed to the poor amenability of dermatophytes to genetic manipulation. However, advancements in this field over the last decade made it possible to conduct genetic studies to satisfying extents. These included genetic transformation methods, indispensable molecular tools, i.e., dominant selectable markers, inducible promoter, and marker recycling system, along with improving homologous recombination frequency and gene silencing. Furthermore, annotated genome sequences of several dermatophytic species have recently been available, ensuring an optimal recruitment of the molecular tools to expand our knowledge on these fungi. In conclusion, the establishment of basic molecular tools and the availability of genomic data will open a new era that might change our understanding on the biology and pathogenicity of this fungal group.

In Vitro Antifungal Activity of Kampo Medicine Water Extracts against Trichophyton Rubrum

Kampo medicines consist of a variety of crude animal, plant, and mineral extracts that have long been used to relieve different symptoms, and are relatively safe. However, their mechanisms of actions have not been well investigated. We screened 61 commercially available Kampo medicines to determine if they contain constituents with antifungal activity against Trichophyton rubrum. The antifungal effect of the Kampo medicines was determined by measuring the mean absorbance of treated fungal culture media. Lower absorbance values suggested a higher inhibition of the growth rate of T. rubrum by the Kampo medicines. We found that seven of the evaluated formulations exhibited a comparable antifungal activity to that of fluconazole at 14 mg/mL. The seven active Kampo medicines were Saiko-keishi-kankyou-to, Saiko-ka-ryukotsu-borei-to, Saiko-keishi-to, Keishi-ka-ryukotsu-borei-to, Dai-saiko-to, Bohu-tsu-sho-san, and Otsu-ji-to. The seven Kampo medicines with antifungal activity contain 30 different crude extracts, and Ou-gon (Scutellaria root) is a supplement contained in six of the seven formulations. Therefore, Ou-gon was considered to play a major role in their antifungal effect. The antifungal assay of the Ou-gon water extract showed that it significantly inhibited the growth of T. rubrum at a concentration of 20 mg/mL. Future studies will focus on the isolation and identification of the antifungal components of the crude extracts of Ou-gon, which may be potentially useful, new, and safe antifungal drugs.

Heat Shock Proteins in Dermatophytes: Current Advances and Perspectives

Heat shock proteins (HSPs) are proteins whose transcription responds rapidly to temperature shifts. They constitute a family of molecular chaperones, involved in the proper folding and stabilisation of proteins under physiological and adverse conditions. HSPs also assist in the protection and recovery of cells exposed to a variety of stressful conditions, including heat. The role of HSPs extends beyond chaperoning proteins, as they also participate in diverse cellular functions, such as the assembly of macromolecular complexes, protein transport and sorting, dissociation of denatured protein aggregates, cell cycle control, and programmed cell death. They are also important antigens from a variety of pathogens, are able to stimulate innate immune cells, and are implicated in acquired immunity. In fungi, HSPs have been implicated in virulence, dimorphic transition, and drug resistance. Some HSPs are potential targets for therapeutic strategies. In this review, we discuss the current understanding of HSPs in dermatophytes, which are a group of keratinophilic fungi responsible for superficial mycoses in humans and animals. Computational analyses were performed to characterise the group of proteins in these dermatophytes, as well as to assess their conservation and to identify DNA-binding domains (5′-nGAAn-3′) in the promoter regions of the hsp genes. In addition, the quantification of the transcript levels of few genes in a pacC background helped in the development of an extended model for the regulation of the expression of the hsp genes, which supports the participation of the pH-responsive transcriptional regulator PacC in this process.

The transcriptional regulators SteA and StuA contribute to keratin degradation and sexual reproduction of the dermatophyte Arthroderma benhamiae

Most superficial fungal infections are caused by dermatophytes, a specialized group of filamentous fungi which exclusively infect keratinized host structures such as hair, skin and nails. Since little is known about the molecular basis of pathogenicity and sexual reproduction in dermatophytes, here we functionally addressed two central transcriptional regulators, SteA and StuA. In the zoophilic species Arthroderma benhamiae a strategy for targeted genetic manipulation was recently established, and moreover, the species is teleomorphic and thus allows performing assays based on mating. By comparative genome analysis homologs of the developmental regulators SteA and StuA were identified in A. benhamiae. Knock-out mutants of the corresponding genes as well as complemented strains were generated and phenotypically characterized. In contrast to A. benhamiae wild type and complemented strains, both mutants failed to produce sexual reproductive structures in mating experiments. Analysis of growth on keratin substrates indicated that loss of steA resulted in the inability of ΔsteA mutants to produce hair perforation organs, but did not affect mycelia formation during growth on hair and nails. By contrast, ΔstuA mutants displayed a severe growth defect on these substrates, but were still able to produce hair perforations. Hence, formation of hair perforation organs and fungal growth on hair per se are differentially regulated processes. Our findings on the major role of SteA and StuA during sexual development and keratin degradation in A. benhamiae provide insights into their role in dermatophytes and further enhance our knowledge of basic biology and pathogenicity of these fungi.

Use of systems biology to decipher host-pathogen interaction networks and predict biomarkers

In systems biology, researchers aim to understand complex biological systems as a whole, which is often achieved by mathematical modelling and the analyses of high-throughput data. In this review, we give an overview of medical applications of systems biology approaches with special focus on host-pathogen interactions. After introducing general ideas of systems biology, we focus on (1) the detection of putative biomarkers for improved diagnosis and support of therapeutic decisions, (2) network modelling for the identification of regulatory interactions between cellular molecules to reveal putative drug targets and (3) module discovery for the detection of phenotype-specific modules in molecular interaction networks. Biomarker detection applies supervised machine learning methods utilizing high-throughput data (e.g. single nucleotide polymorphism (SNP) detection, RNA-seq, proteomics) and clinical data. We demonstrate structural analysis of molecular networks, especially by identification of disease modules as a novel strategy, and discuss possible applications to host-pathogen interactions. Pioneering work was done to predict molecular host-pathogen interactions networks based on dual RNA-seq data. However, currently this network modelling is restricted to a small number of genes. With increasing number and quality of databases and data repositories, the prediction of large-scale networks will also be feasible that can used for multidimensional diagnosis and decision support for prevention and therapy of diseases. Finally, we outline further perspective issues such as support of personalized medicine with high-throughput data and generation of multiscale host-pathogen interaction models.

Transcription profile of Trichophyton rubrum conidia grown on keratin reveals the induction of an adhesin-like protein gene with a tandem repeat pattern

Background

Trichophyton rubrum is a cosmopolitan filamentous fungus that can infect human keratinized tissue (skin, nails and, rarely, hair) and is the major agent of all chronic and recurrent dermatophytoses. The dermatophyte infection process is initiated through the release of arthroconidial adhesin, which binds to the host stratum corneum. The conidia then germinate, and fungal hyphae invade keratinized skin structures through the secretion of proteases. Although arthroconidia play a central role in pathogenesis, little is known about the dormancy and germination of T. rubrum conidia and the initiation of infection. The objective of this study was to evaluate the transcriptional gene expression profile of T. rubrum conidia during growth on keratin- or elastin-containing medium, mimicking superficial and deep dermatophytosis, respectively.

Results

A transcriptional profiling analysis was conducted using a custom oligonucleotide-based microarray by comparing T. rubrum conidia grown on elastin and keratin substrates. This comparison shows differences according to protein source used, but consisted of a very small set of genes, which could be attributed to the quiescent status of conidia. The modulated genes were related to the dormancy, survival and germination of conidia, including genes involved in the respiratory chain, signal transduction and lipid metabolism. However, an induction of a great number of proteases occurred when T. rubrum was grown in the presence of keratin such as the subtilisin family of proteases (Sub 1 and Sub 3) and leucine aminopeptidase (Lap 1 and Lap 2). Interestingly, keratin also promoted the up-regulation of a gene encoding an adhesin-like protein with a tandem repeat sequence. In silico analysis showed that the protein contains a domain related to adhesin that may play a role in host-pathogen interactions. The expression of this adhesin-like gene was also induced during the co-culture of T. rubrum with a human keratinocyte cell line, confirming its role in fungal-host interactions.

Conclusion

These results contribute to the discovery of new targets involved in the adhesion of conidia and the maintenance of conidial dormancy, which are essential for triggering the process of infection and the chronicity of dermatophytosis.

HapX Mediates Iron Homeostasis in the Pathogenic Dermatophyte Arthroderma benhamiae but Is Dispensable for Virulence

For many pathogenic fungi, siderophore-mediated iron acquisition is essential for virulence. The process of siderophore production and further mechanisms to adapt to iron limitation are strictly controlled in fungi to maintain iron homeostasis. Here we demonstrate that the human pathogenic dermatophyte Arthroderma benhamiae produces the hydroxamate siderophores ferricrocin and ferrichrome C. Additionally, we show that the iron regulator HapX is crucial for the adaptation to iron starvation and iron excess, but is dispensable for virulence of A. benhamiae. Deletion of hapX caused downregulation of siderophore biosynthesis genes leading to a decreased production of siderophores during iron starvation. Furthermore, HapX was required for transcriptional repression of genes involved in iron-dependent pathways during iron-depleted conditions. Additionally, the ΔhapX mutant of A. benhamiae was sensitive to high-iron concentrations indicating that HapX also contributes to iron detoxification. In contrast to other pathogenic fungi, HapX of A. benhamiae was redundant for virulence and a ΔhapX mutant was still able to infect keratinized host tissues in vitro. Our findings underline the highly conserved role of the transcription factor HapX for maintaining iron homeostasis in ascomycetous fungi but, unlike in many other human and plant pathogenic fungi, HapX of A. benhamiae is not a virulence determinant.

Microbial decomposition of keratin in nature-a new hypothesis of industrial relevance

Discovery of keratin-degrading enzymes from fungi and bacteria has primarily focused on finding one protease with efficient keratinase activity. Recently, an investigation was conducted of all keratinases secreted from a fungus known to grow on keratinaceous materials, such as feather, horn, and hooves. The study demonstrated that a minimum of three keratinases is needed to break down keratin, an endo-acting, an exo-acting, and an oligopeptide-acting keratinase. Further, several studies have documented that disruption of sulfur bridges of the keratin structure acts synergistically with the keratinases to loosen the molecular structure, thus giving the enzymes access to their substrate, the protein structure. With such complexity, it is relevant to compare microbial keratin decomposition with the microbial decomposition of well-studied polymers such as cellulose and chitin. Interestingly, it was recently shown that the specialized enzymes, lytic polysaccharide monoxygenases (LPMOs), shown to be important for breaking the recalcitrance of cellulose and chitin, are also found in keratin-degrading fungi. A holistic view of the complex molecular self-assembling structure of keratin and knowledge about enzymatic and boosting factors needed for keratin breakdown have been used to formulate a hypothesis for mode of action of the LPMOs in keratin decomposition and for a model for degradation of keratin in nature. Testing such hypotheses and models still needs to be done. Even now, the hypothesis can serve as an inspiration for designing industrial processes for keratin decomposition for conversion of unexploited waste streams, chicken feather, and pig bristles into bioaccessible animal feed.

Classification of fungal and bacterial lytic polysaccharide monooxygenases

Background

Lytic polysaccharide monooxygenases are important enzymes for the decomposition of recalcitrant biological macromolecules such as plant cell wall and chitin polymers. These enzymes were originally designated glycoside hydrolase family 61 and carbohydrate-binding module family 33 but are now classified as auxiliary activities 9, 10 and 11 in the CAZy database. To obtain a systematic analysis of the divergent families of lytic polysaccharide monooxygenases we used Peptide Pattern Recognition to divide 5396 protein sequences resembling enzymes from families AA9 (1828 proteins), AA10 (2799 proteins) and AA11 (769 proteins) into subfamilies.

Results

The results showed that the lytic polysaccharide monooxygenases have two conserved regions identified by conserved peptides specific for each AA family. The peptides were used for in silico PCR discovery of the lytic polysaccharide monooxygenases in 79 fungal and 95 bacterial genomes. The bacterial genomes encoded 0 – 7 AA10s (average 0.6). No AA9 or AA11 were found in the bacteria. The fungal genomes encoded 0 – 40 AA9s (average 7) and 0 – 15 AA11s (average 2) and two of the fungi possessed a gene encoding a putative AA10. The AA9s were mainly found in plant cell wall-degrading asco- and basidiomycetes in agreement with the described role of AA9 enzymes. In contrast, the AA11 proteins were found in 36 of the 39 ascomycetes and in only two of the 32 basidiomycetes and their abundance did not correlate to the degradation of cellulose and hemicellulose.

Conclusions

These results provides an overview of the sequence characteristics and occurrence of the divergent AA9, AA10 and AA11 families and pave the way for systematic investigations of the of lytic polysaccharide monooxygenases and for structure-function studies of these enzymes.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1601-6) contains supplementary material, which is available to authorized users.

RNA-sequencing analysis of Trichophyton rubrum transcriptome in response to sublethal doses of acriflavine

BACKGROUND

The dermatophyte Trichophyton rubrum is an anthropophilic filamentous fungus that infects keratinized tissues and is the most common etiologic agent isolated in human dermatophytoses. The clinical treatment of these infections is challenging because only few antifungal drugs are commercially available. To understand the mode of action of cytotoxic drugs against fungi, we evaluated the time-dependent effects of acriflavine on T. rubrum transcriptome using high-throughput RNA-sequencing (RNA-seq) technology.

RESULTS

RNA-seq analysis generated approximately 200 million short reads that were mapped to the Broad Institute's Dermatophyte Comparative Database before differential gene expression analysis was performed. By employing a stringent cut-off threshold of -1.5 and 1.5 log₂-fold changes in gene expression, a subset of 490 unique genes were found to be modulated in T. rubrum in response to acriflavine exposure. Among the selected genes, 69 genes were modulated at all exposure time points. Functional categorization indicated the putative involvement of these genes in various cellular processes such as oxidation-reduction reaction, transmembrane transport, and metal ion binding. Interestingly, genes putatively involved in the pathogenicity of dermatophytoses were down-regulated suggesting that this drug interferes with the virulence of T. rubrum. Moreover, we identified 159 novel putative transcripts in intergenic regions and two transcripts in intron regions of T. rubrum genome.

CONCLUSION

The results provide insights into the molecular events underlying the stress responses of T. rubrum to acriflavine, revealing that this drug interfered with important molecular events involved in the establishment and maintenance of fungal infection in the host. In addition, the identification of novel transcripts will further enable the improvement of gene annotation and open reading frame prediction of T. rubrum and other dermatophyte genomes.

Metabolism in fungal pathogenesis

Fungal pathogens must assimilate local nutrients to establish an infection in their mammalian host. We focus on carbon, nitrogen, and micronutrient assimilation mechanisms, discussing how these influence host-fungus interactions during infection. We highlight several emerging trends based on the available data. First, the perturbation of carbon, nitrogen, or micronutrient assimilation attenuates fungal pathogenicity. Second, the contrasting evolutionary pressures exerted on facultative versus obligatory pathogens have led to contemporary pathogenic fungal species that display differing degrees of metabolic flexibility. The evolutionarily ancient metabolic pathways are conserved in most fungal pathogen, but interesting gaps exist in some species (e.g., Candida glabrata). Third, metabolic flexibility is generally essential for fungal pathogenicity, and in particular, for the adaptation to contrasting host microenvironments such as the gastrointestinal tract, mucosal surfaces, bloodstream, and internal organs. Fourth, this metabolic flexibility relies on complex regulatory networks, some of which are conserved across lineages, whereas others have undergone significant evolutionary rewiring. Fifth, metabolic adaptation affects fungal susceptibility to antifungal drugs and also presents exciting opportunities for the development of novel therapies.

Flippase (FLP) recombinase-mediated marker recycling in the dermatophyte Arthroderma vanbreuseghemii

Biological processes can be elucidated by investigating complex networks of relevant factors and genes. However, this is not possible in species for which dominant selectable markers for genetic studies are unavailable. To overcome the limitation in selectable markers for the dermatophyte Arthroderma vanbreuseghemii (anamorph: Trichophyton mentagrophytes), we adapted the flippase (FLP) recombinase-recombination target (FRT) site-specific recombination system from the yeast Saccharomyces cerevisiae as a selectable marker recycling system for this fungus. Taking into account practical applicability, we designed FLP/FRT modules carrying two FRT sequences as well as the flp gene adapted to the pathogenic yeast Candida albicans (caflp) or a synthetic codon-optimized flp (avflp) gene with neomycin resistance (nptII) cassette for one-step marker excision. Both flp genes were under control of the Trichophyton rubrum copper-repressible promoter (PCTR4). Molecular analyses of resultant transformants showed that only the avflp-harbouring module was functional in A. vanbreuseghemii. Applying this system, we successfully produced the Ku80 recessive mutant strain devoid of any selectable markers. This strain was subsequently used as the recipient for sequential multiple disruptions of secreted metalloprotease (fungalysin) (MEP) or serine protease (SUB) genes, producing mutant strains with double MEP or triple SUB gene deletions. These results confirmed the feasibility of this system for broad-scale genetic manipulation of dermatophytes, advancing our understanding of functions and networks of individual genes in these fungi.

Analysis of gene expression changes in Trichophyton rubrum after skin interaction

Trichophyton rubrum, an anthropophilic and cosmopolitan fungus, is the most common agent of superficial mycoses. In this study, T. rubrum infection was modelled by adding human skin sections to a limited medium containing glucose and cDNA microarrays were used to monitor T. rubrum gene expression patterns on a global level. We observed that exposure to human skin resulted in upregulation of the expression levels of T. rubrum genes related to many cellular and biological processes, including transcription and translation, metabolism and secondary transport, the stress response, and signalling pathways. These results provide a reference set of T. rubrum genes whose expression patterns change upon infection and reveal previously unknown genes that most likely correspond to proteins that should be considered as virulence factor candidates and potential new drug targets for T. rubrum infection.

Comparative genome analysis of Trichophyton rubrum and related dermatophytes reveals candidate genes involved in infection

The major cause of athlete's foot is Trichophyton rubrum, a dermatophyte or fungal pathogen of human skin. To facilitate molecular analyses of the dermatophytes, we sequenced T. rubrum and four related species, Trichophyton tonsurans, Trichophyton equinum, Microsporum canis, and Microsporum gypseum. These species differ in host range, mating, and disease progression. The dermatophyte genomes are highly colinear yet contain gene family expansions not found in other human-associated fungi. Dermatophyte genomes are enriched for gene families containing the LysM domain, which binds chitin and potentially related carbohydrates. These LysM domains differ in sequence from those in other species in regions of the peptide that could affect substrate binding. The dermatophytes also encode novel sets of fungus-specific kinases with unknown specificity, including nonfunctional pseudokinases, which may inhibit phosphorylation by competing for kinase sites within substrates, acting as allosteric effectors, or acting as scaffolds for signaling. The dermatophytes are also enriched for a large number of enzymes that synthesize secondary metabolites, including dermatophyte-specific genes that could synthesize novel compounds. Finally, dermatophytes are enriched in several classes of proteases that are necessary for fungal growth and nutrient acquisition on keratinized tissues. Despite differences in mating ability, genes involved in mating and meiosis are conserved across species, suggesting the possibility of cryptic mating in species where it has not been previously detected. These genome analyses identify gene families that are important to our understanding of how dermatophytes cause chronic infections, how they interact with epithelial cells, and how they respond to the host immune response.

Antimicrobial effects of allicin and ketoconazole on trichophyton rubrum under in vitro condition

Dermatophytosis is caused by a group of pathogenic fungi namely, dermatophytes, is among the most prevalent infectious diseases worldwide. Azole drugs are widely used in the treatment of dermatomycosis, but can cause various side effects and drug resistance to the patients. Hence, for solving this problem can be used from the plant extract as alternative for chemical drugs. Allicin is a pure bioactive compound isolated from garlic was tested for its potential as a treatment of dermatomycosis in this study. This study evaluated the in vitro efficacy of pure allicin against ten isolates of Trichophyton rubrum and the MIC₅₀ and MIC₉₀ ranged from 0.78-12.5 μg/ml for allicin. The results revealed that the order of efficacy based on the MICs values, all isolates showed almost comparable response to allicin and ketoconazole except for some isolates, at 28 °C for both 7 and 10 days incubation. Mann-Whitney test indicate that MICs at 7 days incubation was not observed a significant difference between the effects of allicin and ketoconazole (p > 0.05), but MICs at 10 days incubation, a significant difference was observed (p ≤ 0.05). On the other side, time kill studies revealed that allicin used its fungicidal activity within 12-24 h of management in vitro as well as ketoconazole. In conclusion, allicin showed very good potential as an antifungal compound against mycoses-causing dermatophytes, almost the same as the synthetic drug ketoconazole. Therefore, this antifungal agent appears to be effective, safe and suitable alternative for the treatment of dermatomycosis.

Dermatophytes: host-pathogen interaction and antifungal resistance

Cutaneous mycoses are among the most common infections in humans and have become an important public health issue because they cause invasive infections in immunocompromised patients. During the infectious process, dermatophyte-host interactions trigger specific metabolic adaptations that allow the pathogen to adhere to and penetrate the host tissue, scavenge nutrients, and overcome the host defense mechanisms. This metabolic shift and the interplay between metabolism, morphogenesis and stress response are important factors that have been extensively studied in several pathogens. Host cells also respond to the pathogen stimuli by activating intracellular signaling pathways that trigger the immune response against the infectious agent. The comprehension of the molecular aspects of these responses may help to establish new therapeutical strategies. In this review, different aspects of the biology of dermatophytes are addressed, with emphasis on the dermatophyte-host interaction and the mechanisms of antifungal resistance.

Identification of novel secreted proteases during extracellular proteolysis by dermatophytes at acidic pH

The dermatophytes are a group of closely related fungi which are responsible for the great majority of superficial mycoses in humans and animals. Among various potential virulence factors, their secreted proteolytic activity attracts a lot of attention. Most dermatophyte-secreted proteases which have so far been isolated in vitro are neutral or alkaline enzymes. However, inspection of the recently decoded dermatophyte genomes revealed many other hypothetical secreted proteases, in particular acidic proteases similar to those characterized in Aspergillus spp. The validation of such genome predictions instigated the present study on two dermatophyte species, Microsporum canis and Arthroderma benhamiae. Both fungi were found to grow well in a protein medium at acidic pH, accompanied by extracellular proteolysis. Shotgun MS analysis of secreted protein revealed fundamentally different protease profiles during fungal growth in acidic versus neutral pH conditions. Most notably, novel dermatophyte-secreted proteases were identified at acidic pH such as pepsins, sedolisins and acidic carboxypeptidases. Therefore, our results not only support genome predictions, but demonstrate for the first time the secretion of acidic proteases by dermatophytes. Our findings also suggest the existence of different pathways of protein degradation into amino acids and short peptides in these highly specialized pathogenic fungi.

Dermatophyte virulence factors: identifying and analyzing genes that may contribute to chronic or acute skin infections

Dermatophytes are prevalent causes of cutaneous mycoses and, unlike many other fungal pathogens, are able to cause disease in immunocompetent individuals. They infect keratinized tissue such as skin, hair, and nails, resulting in tinea infections, including ringworm. Little is known about the molecular mechanisms that underlie the ability of these organisms to establish and maintain infection. The recent availability of genome sequence information and improved genetic manipulation have enabled researchers to begin to identify and study the role of virulence factors of dermatophytes. This paper will summarize our current understanding of dermatophyte virulence factors and discuss future directions for identifying and testing virulence factors.

Nutrient acquisition by pathogenic fungi: nutrient availability, pathway regulation, and differences in substrate utilization

All pathogenic microorganisms have in common that they need to feed on nutrients available from their host. Therefore, the specific interruption of metabolic pathways is a promising approach which could lead to the discovery of new antimicrobial drugs. However, nutrient availability strongly varies in respect to the infected host niche and pathogens may possess different strategies to acquire nutrients. This review focuses on the differences in regulation and use of key metabolic pathways during infection by pathogenic fungi, especially in the filamentous fungus Aspergillus fumigatus and the dimorphic yeast Candida albicans. Besides universal metabolic pathways, emphasis is given on pathways, which are absent in humans and might, therefore, suit as antifungal drug targets. Niche-specific nutrient availability and different physiological strategies complicate the identification of metabolic pathways, which are essential for all pathogens at each step of the infection process.

Fungal proteases and their pathophysiological effects

Proteolytic enzymes play an important role in fungal physiology and development. External digestion of protein substrates by secreted proteases is required for survival and growth of both saprophytic and pathogenic species. Extracellular serine, aspartic, and metalloproteases are considered virulence factors of many pathogenic species. New findings focus on novel membrane-associated proteases such as yapsins and ADAMs and their role in pathology. Proteases from fungi induce inflammatory responses by altering the permeability of epithelial barrier and by induction of proinflammatory cytokines through protease-activated receptors. Many fungal allergens possess proteolytic activity that appears to be essential in eliciting Th2 responses. Allergenic fungal proteases can act as adjuvants, potentiating responses to other allergens. Proteolytic enzymes from fungi contribute to inflammation through interactions with the kinin system as well as the coagulation and fibrinolytic cascades. Their effect on the host protease-antiprotease balance results from activation of endogenous proteases and degradation of protease inhibitors. Recent studies of the role of fungi in human health point to the growing importance of proteases not only as pathogenic agents in fungal infections but also in asthma, allergy, and damp building related illnesses. Proteolytic enzymes from fungi are widely used in biotechnology, mainly in food, leather, and detergent industries, in ecological bioremediation processes and to produce therapeutic peptides. The involvement of fungal proteases in diverse pathological mechanisms makes them potential targets of therapeutic intervention and candidates for biomarkers of disease and exposure.

Comparative and functional genomics provide insights into the pathogenicity of dermatophytic fungi

BACKGROUND

Millions of humans and animals suffer from superficial infections caused by a group of highly specialized filamentous fungi, the dermatophytes, which exclusively infect keratinized host structures. To provide broad insights into the molecular basis of the pathogenicity-associated traits, we report the first genome sequences of two closely phylogenetically related dermatophytes, Arthroderma benhamiae and Trichophyton verrucosum, both of which induce highly inflammatory infections in humans.

RESULTS

97% of the 22.5 megabase genome sequences of A. benhamiae and T. verrucosum are unambiguously alignable and collinear. To unravel dermatophyte-specific virulence-associated traits, we compared sets of potentially pathogenicity-associated proteins, such as secreted proteases and enzymes involved in secondary metabolite production, with those of closely related onygenales (Coccidioides species) and the mould Aspergillus fumigatus. The comparisons revealed expansion of several gene families in dermatophytes and disclosed the peculiarities of the dermatophyte secondary metabolite gene sets. Secretion of proteases and other hydrolytic enzymes by A. benhamiae was proven experimentally by a global secretome analysis during keratin degradation. Molecular insights into the interaction of A. benhamiae with human keratinocytes were obtained for the first time by global transcriptome profiling. Given that A. benhamiae is able to undergo mating, a detailed comparison of the genomes further unraveled the genetic basis of sexual reproduction in this species.

CONCLUSIONS

Our results enlighten the genetic basis of fundamental and putatively virulence-related traits of dermatophytes, advancing future research on these medically important pathogens.

Development of efficient tools for genetic manipulation of dermatophytes

Molecular biological approaches have recently begun to be applied to molecular genetics studies of dermatophytes. High-throughput gene analysis methodologies, such as EST sequencing, differential cDNA screening, and cDNA-based microarray analysis have been used to obtain information on many dermatophyte genes and their expression profiles under different experimental conditions. In addition, whole genome sequencing projects are underway for several important dermatophytes, such as Trichophyton rubrum and Microsporum canis. These studies will provide large amounts of valuable information for elucidating the molecular basis of host invasion by dermatophytes and their virulence. Targeted gene disruption by homologous recombination is one of the most common approaches for determining the functions and roles of numerous genes isolated from pathogenic fungi. However, the difficulty of genetic manipulation due to low transformation frequency of dermatophytes may limit the successful production of null mutants by targeted gene disruption via homologous recombination. To overcome these problems, our group has developed useful genetic manipulation systems for dermatophytes using the clinically important dermatophyte, T. mentagrophytes.

Comparative analysis of secreted enzymes between the anthropophilic-zoophilic sister species Trichophyton tonsurans and Trichophyton equinum

Trichophyton tonsurans (TT) and Trichophyton equinum (TE) are two closely related dermatophytes with very different host preferences. This study was designed to examine the genetic and transcript level variations of secreted enzymes between TT and TE. Thirty-one genes representing 10 gene families were selected for comparison and complete genomic and cDNA sequences were elucidated. Sequence analyses of the selected genes identified 104 polymorphisms between the two dermatophytes, 37 of which are expected to encode changes in their polypeptide sequence. Quantitative RT-PCR was used to examine the differences in levels of transcript between TT and TE grown over 14d in aqueous keratin medium. Differences in transcript expression between TT and TE were gene specific and ranged from 1.1-fold to 33-fold. Intra-specific variability across all genes ranged from 41% to 250%. Despite their overall genetic similarity, TT and TE exhibit a moderate degree of variability in the genomic make-up of their secreted enzymes and the extent to which they are transcribed when grown in an aqueous keratin medium. Such differences may contribute to how these genetically similar organisms have adapted to infect divergent host organisms.