Molecular strategies in Metazoan genomic evolution

Recent dermatophyte divergence revealed by comparative and phylogenetic analysis of mitochondrial genomes

Background

Dermatophytes are fungi that cause superficial infections of the skin, hair, and nails. They are the most common agents of fungal infections worldwide. Dermatophytic fungi constitute three genera, Trichophyton, Epidermophyton, and Microsporum, and the evolutionary relationships between these genera are epidemiologically important. Mitochondria are considered to be of monophyletic origin and mitochondrial sequences offer many advantages for phylogenetic studies. However, only one complete dermatophyte mitochondrial genome (E. floccosum) has previously been determined.

Results

The complete mitochondrial DNA sequences of five dermatophyte species, T. rubrum (26,985 bp), T. mentagrophytes (24,297 bp), T. ajelloi (28,530 bp), M. canis (23,943 bp) and M. nanum (24,105 bp) were determined. These were compared to the E. floccosum sequence. Mitochondrial genomes of all 6 species were found to harbor the same set of genes arranged identical order indicating that these dermatophytes are closely related. Genome size differences were largely due to variable lengths of non-coding intergenic regions and the presence/absence of introns. Phylogenetic analyses based on complete mitochondrial genomes reveals that the divergence of the dermatophyte clade was later than of other groups of pathogenic fungi.

Conclusion

This is the first systematic comparative genomic study on dermatophytes, a highly conserved and recently-diverged lineage of ascomycota fungi. The data reported here provide a basis for further exploration of interrelationships between dermatophytes and will contribute to the study of mitochondrial evolution in higher fungi.

Tprg, a gene predominantly expressed in skin, is a direct target of the transcription factor p63

p63 and p73 are highly homologous members of the p53 family that originated by gene duplication at the invertebrate-to-vertebrate transition. We characterize here a previously unreported gene, Transformation-related protein 63 regulated (Tprg), located upstream of the p63 gene in the vertebrate genome, with striking similarity to Transformation related protein 63 regulated like (Tprgl), an uncharacterized gene located upstream of p73, suggesting that p63/Tprg and p73/Tprgl are embedded in a paralogue region originated from a single duplication event. Tprg is predominantly expressed in the epithelial compartment of the skin, more abundantly in differentiated cells. Consistent with its relative higher expression in differentiated keratinocytes, finely tuned p63 expression levels are required for optimal Tprg expression in primary keratinocytes. p63 is essential for Tprg expression as shown in p63-knockdown keratinocytes; however, high levels of p63 result in Tprg downregulation. p63 directly binds in vivo to a canonical p63-binding site in an evolutionary conserved genomic region located in Tprg intron 4. This genomic region is sufficient to function as a p63-inducible enhancer in promoter studies. Thus, we demonstrate that the Tprg gene is predominantly expressed in skin, is physically associated with the p63 gene during evolution, and directly regulated by p63 through a long-distance enhancer located within the Tprg locus.

Jekyll and Hyde, the p53 protein, pleiotropics antagonisms and the thrifty aged hypothesis of senescence

Antagonistic pleiotropy theory holds that ageing is a not selected trait, and only the consequence of genes fixed in evolution by their reproductive advantage early in life, but with harmful effects in the post reproductive period. Although the existence of antagonistic pleiotropic genes has been controversial, recent molecular approaches seem to confirm them. One of the proposed examples is p53, a gene that plays a pivotal role in the cell stress response. It has been pointed that p53 driven programs, apoptosis and cellular senescence, protect organisms from cancer early in life, but promote ageing phenotype in older members. On the other hand, recent evidences suggest that ageing is not a random program, but a carefully orchestrated one. Accordingly, the antagonistic pleiotropy theory as well as the ageing purpose must be updated. In this issue the p53 candidature to be an antagonistic pleiotropic gene is revisited. Moreover, it has been postulated that these kinds of genes could be actively selected by both effects, and not only by their reproductive advantage early in life, because they improve fitness and they contribute to structure ageing, a program that optimise the energy availability in the post reproductive state.

Metazoan OXPHOS gene families: Evolutionary forces at the level of mitochondrial and nuclear genomes

Mitochondrial and nuclear DNAs contribute to encode the whole mitochondrial protein complement. The two genomes possess highly divergent features and properties, but the forces influencing their evolution, even if different, require strong coordination. The gene content of mitochondrial genome in all Metazoa is in a frozen state with only few exceptions and thus mitochondrial genome plasticity especially concerns some molecular features, i.e. base composition, codon usage, evolutionary rates. In contrast the high plasticity of nuclear genomes is particularly evident at the macroscopic level, since its redundancy represents the main feature able to introduce genetic material for evolutionary innovations. In this context, genes involved in oxidative phosphorylation (OXPHOS) represent a classical example of the different evolutionary behaviour of mitochondrial and nuclear genomes. The simple DNA sequence of Cytochrome c oxidase I (encoded by the mitochondrial genome) seems to be able to distinguish intra- and inter-species relations between organisms (DNA Barcode). Some OXPHOS subunits (cytochrome c, subunit c of ATP synthase and MLRQ) are encoded by several nuclear duplicated genes which still represent the trace of an ancient segmental/genome duplication event at the origin of vertebrates.

Evidence for p53-like-mediated stress responses in green algae

The tumor suppressor protein, p53, plays a major role in cellular responses to stress and DNA damage in animals; despite its critical function, p53 homologs have not been identified in any algal or plant lineage. This study employs a functional and evolutionary approach to test for a p53 functional equivalent in green algae. Specifically, the study: (i) investigated the effect of two synthetic compounds known to interfere with p53 activity; (ii) searched for sequences with similarity to known p53-induced genes; and (iii) analyzed the expression pattern of one such sequence. The findings reported here suggest that a p53 functional equivalent is present and mediates cellular responses to stress in green algae.

P63 deficiency: a failure of lineage commitment or stem cell maintenance?

A critical role for p63 in the development of stratified epithelia, such as the epidermis, has been recognized since the generation of mice lacking p63 expression. The molecular role of p63 in epidermal morphogenesis, however, remained controversial. The epidermal phenotype of p63-/- mice, which are born with a single-layered surface epithelium instead of a fully stratified epidermis, suggested that p63 could have a role in stem cell maintenance or in the commitment to stratification. In this review, we discuss evidence suggesting that p63 is required for the commitment to stratification, making p63 the earliest known gene expressed in the developing epidermis that is specific for the keratinocyte lineage.

Evolution of nuclearly encoded mitochondrial genes in Metazoa

All Metazoan nuclear genomes underwent a continuous process of both complete and partial genetic material gain and loss. The forces modulating these events are also subject to the strict interaction between nuclear and mitochondrial (mt) genome. In this context we investigate the evolution of nuclear genes encoding proteins which target the mitochondrion, with a particular attention to genes involved in oxidative phosphorylation (OXPHOS), one of the most ancient and conserved functions. To examine thoroughly the evolutionary strategies that preserve OXPHOS and coordinate the two cellular genomes, a comparative analysis has been carried out for 78 OXPHOS gene families in several Metazoa (insects, tunicates, fishes and mammals). We demonstrate that the duplication rate of OXPHOS genes increases passing from invertebrates to vertebrates consistently with the total increase in genome size, but all species are prone to negatively select OXPHOS duplicates compared to the general trend of nuclear gene families. These results are consistent with the 'balance hypothesis' and, at least in insects, the expression of duplicate genes is low and strongly testis-biased.

The role of p63 in development and differentiation of the epidermis

Expression of p63, a transcription factor that is transcribed into six isoforms, is required for proper development of stratified epithelia, such as the epidermis. In the absence of p63, epithelia remain single-layered. The molecular role of p63 in development and differentiation of stratified epithelia, however, remains controversial. Based on recent studies, we now believe that p63 has a dual role and is essential for development as well as maintenance of the epidermis. During embryogenesis, p63 may be the molecular switch required for initiation of epithelial stratification. This is based on our recent data demonstrating that ectopic expression of a p63 isoform in single-layered epithelia results in the induction of a stratification program. Furthermore, in the mature epidermis, p63 may maintain the proliferative potential of basal keratinocytes. This is suggested by the observation that p63 is primarily expressed in the basal compartment of the epidermis, that p63 expression induces hyperproliferation, and that its expression needs to be downregulated for terminal differentiation to take place. In this review, we discuss recent evidence supporting this dual role for p63 and place it in the context of our increasing knowledge of epidermal development and differentiation.

Genes involved in stem cell fate decisions and commitment to differentiation play a role in skin disease

Multipotent stem cells residing in the bulge region of the hair follicle give rise to cells of different fates including those forming hair follicles, interfollicular epidermis, and associated glands. Stem cell fate determination is regulated by genes involved in both proliferation and differentiation, which are tightly regulated processes. Understanding the molecular mechanisms by which proliferation and differentiation are regulated will provide useful insight into treating human diseases caused by the deregulation of these processes. Two genes involved in regulating proliferation and differentiation are c-Myc and p63, both of which have been found to be deregulated/mutated in several human diseases. Accelerating proliferation leads to neoplastic human diseases and deregulated c-Myc has been implicated in a variety of cancers. Evidence indicates that c-Myc also diverts stem cells to an epidermal and sebaceous gland fate at the expense of the hair follicle fate. Therefore, deregulation of c-Myc has the potential to not only accelerate tumorigenesis, but also influence skin tumor phenotype. In addition, the inhibition of differentiation may also predispose to the development of skin cancer. Recent evidence suggests that the transcription factor p63, is not only responsible for the initiation of an epithelial stratification program during development, but also the maintenance of the proliferative potential of basal keratinocytes in mature epidermis. Mutations in the p63 gene have been shown to cause ectodermal dysplasias and deregulated expression of p63 has been observed in squamous cell carcinomas. In this review, we will discuss recent data implicating a role for both c-Myc and p63 in human skin diseases.

Molecular clock and gene function

Molecular phylogenies based on the molecular clock require the comparison of orthologous genes. Orthologous and paralogous genes usually have very different evolutionary fates. In general, orthologs keep the same functions in species, whereas, particularly over a long time span, paralogs diverge functionally and may become pseudogenes or get lost. In eukaryotic genomes, because of the degree of redundancy of genetic information, homologous genes are grouped in gene families, the evolution of which may differ greatly between the various organisms. This implies that each gene in a species does not always have an ortholog in another species and thus, due to multiple duplication events following a speciation, many orthologous clades of paralogs are generated. We are often dealing with a one-to-many or many-to-many relationship between genes. In this paper, we analyze the evolution of two gene families, the p53 gene family and the porin gene family. The evolution of the p53 family shows a one-to-many gene relationship going from invertebrates to vertebrates. In invertebrates only a single gene has been found, while in vertebrates three members of the family, namely p53, p63, and p73, are present. The evolution of porin (VDAC) genes (VDAC1, VDAC2, and VDAC3) is an example of a many-to-many gene relationship going from yeast to mammals. However, the porin gene redundancy found in invertebrates and possibly in some fishes may indicate a tendency to duplicate the genetic material, rather than a real need for function innovation.

Adenosine deaminase, a key enzyme in DNA precursors control, is a new p73 target

The discovery of the p73 and p63 genes, homologous to p53 tumor suppressor has uncovered a family of transcription factors and widened the scenario of cell cycle control and apoptosis. We have identified a putative p53-responsive element in the human adenosine deaminase (ADA) gene, an important enzyme involved in nucleotide metabolism, the deficit of which causes the inhibition of DNA synthesis and repair. Here, we demonstrate that the ectopic expression of p73 isoforms leads to the ADA gene upregulation, showing for the first time a correlation between p73 and ADA. We found that p73 promotes ADA gene expression following a dNTP unbalance generated by ADA enzyme deficiency and 2'deoxyadenosine accumulation. The abrogation of p73 transcriptional activity by the specific dominant-negative p73DD abolishes ADA induction. By contrast, the ADA gene does not appear to be a functional p53 target in the physiological conditions we tested. On the whole, our results contribute to the emerging picture that p73 could play a different role from p53 in normal growth and development by inducing alternative target genes, which are not shared by p53.

In vivo and in vitro evidence for hydrogen peroxide (H2O2) accumulation in the epidermis of patients with vitiligo and its successful removal by a UVB-activated pseudocatalase

To date there is compelling in vitro and in vivo evidence for epidermal H2O2 accumulation in vitiligo. This paper reviews the literature and presents new data on oxidative stress in the epidermal compartment of this disorder. Elevated H2O2 levels can be demonstrated in vivo in patients compared with healthy controls by utilizing Fourier-Transform Raman spectroscopy. H2O2 accumulation is associated with low epidermal catalase levels. So far, four potential sources for epidermal H2O2 generation in vitiligo have been identified: (i) perturbed (6R)-L-erythro 5,6,7,8 tetrahydrobiopterin (6BH4) de novo synthesis/recycling/regulation; (ii) impaired catecholamine synthesis with increased monoamine oxidase A activities; (iii) low glutathione peroxidase activities; and (iv) "oxygen burst" via NADPH oxidase from a cellular infiltrate. H2O2 overproduction can cause inactivation of catalase as well as vacuolation in epidermal melanocytes and keratinocytes. Vacuolation was also observed in vitro in melanocytes established from lesional and nonlesional epidermis of patients (n = 10) but was reversible upon addition of catalase. H2O2 can directly oxidize 6BH4 to 6-biopterin, which is cytotoxic to melanocytes in vitro. Therefore, we substituted the impaired catalase with a "pseudocatalase". Pseudocatalase is a bis-manganese III-EDTA-(HCO3-)2 complex activated by UVB or natural sun. This complex has been used in a pilot study on 33 patients, showing remarkable repigmentation even in long lasting disease. Currently this approach is under worldwide clinical investigation in an open trial. In conclusion, there are several lines of evidence that the entire epidermis of patients with vitiligo is involved in the disease process and that correction of the epidermal redox status is mandatory for repigmentation.