Comparative Genomics and Functional Genomics of Candida species

Christophe d'Enfert and Bernhard Hube, from "Candida : Comparative and Functional Genomics" Eds: d'Enfert, C. and Hube, B. (2007) Caister Academic Press.

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Candida Genomics

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The last decade has seen the sustained medical importance of opportunistic infections due to different Candida species. Meanwhile, the genome sequence of several Candida species has been completed, enabling the detailed investigation of some aspects of their biology with the aid of post-genomic approaches. The basic knowledge gained from these investigations of pathogenic Candida, and related yeasts, can translate into innovations in the development of novel antifungal therapies, original approaches for targeted immuno-interventions, or highly sensitive diagnosis of fungal infections.

Candida Comparative and Functional Genomics

Fungal infections have become a prominent problem over the last 25 years (Martin et al., 2003). This is mainly due to the worldwide increase in the number of immunocompromised patients, who are highly susceptible to opportunistic infections, including mycoses (Fridkin and Jarvis, 1996). Indeed, the AIDS epidemic has been accompanied by a sharp increase in the number of patients who develop opportunistic fungal infections, and these remain a serious concern in poor countries unable to provide widespread access to HAART (highly active antiretroviral therapy). In developed countries, patients with underlying pathologies such as cancer or those who receive immunosuppressive regimens or broad-spectrum antimicrobial therapy are at high risk of developing disseminated fungal infections. The use of indwelling catheters, artificial implants, and surgical trauma, particularly abdominal, increase the risk of patients contracting systemic infections. Consequently, fungi are frequently the cause of nosocomial infections, representing a serious threat because of their associated high mortality rate (Lin et al., 2001; Ruhnke, 2006). This is despite the availability of antifungal treatments, including some based on molecules with a new mode of action such as echinocandins, and other therapeutic approaches (Boucher et al., 2004; Segal et al., 2006). High mortality rates associated with disseminated fungal infections are in part due to late diagnosis and the relative inefficiency of currently available antifungals in some situations, e.g. infections by certain Candida species that are inherently resistant to some classes of drugs (Ruhnke, 2006; Segal and Walsh, 2006).

Among fungal pathogens responsible for opportunistic infections, species of the genus Candida have a central contribution. These species can infect most patients to some degree and are responsible for superficial infections such as oropharyngeal candidiasis and vulvovaginal candidiasis. These types of infection can be cured efficiently with the current antifungal arsenal although they represent a concern in AIDS patients. However, species of the genus Candida are also responsible for life-threatening systemic infections, particularly in patients treated in intensive care units (ICUs), cancer patients receiving chemotherapy, and organ transplant patients (Wenzel, 1995; George et al., 1997; Maertens et al., 2001; Kullberg and Oude Lashof, 2002; Safdar et al., 2004). Among Candida species, C. albicans, which can also be a commensal of the skin and the gastrointestinal and genitourinary tracts, is responsible for the majority of Candida bloodstream infections (candidemia) (Pfaller et al., 1999; Viscoli et al., 1999; Kibbler et al., 2003; Wisplinghoff et al., 2004). Yet, there is an increasing incidence of infections caused by C. glabrata, which could be due to the fact that it is frequently less susceptible to the currently used azole antifungals (Kibbler et al., 2003; Snydman, 2003; Wisplinghoff et al., 2004). Other medically important Candida species include C. parapsilosis, C. tropicalis, and C. dubliniensis (Wingard et al., 1980; Pfaller, 1996; Viscoli et al., 1999; Krcmery and Barnes, 2002). Each of these species represents a therapeutic challenge that will be surmounted through a better understanding of its specific biology, physiopathology, and epidemiology. Undoubtedly, our understanding will benefit from both focused and comparative approaches.

All Candida species fall within the hemiascomycete group, which contains most of the known yeast species (see Candida: Comparative and Functional Genomics). An emblematic representative of the hemiascomycete group is the yeast Saccharomyces cerevisiae, which has become one of the main models for the study of eukaryotic organisms. This is in part due to the ease with which the genome of S. cerevisiae can be manipulated through both classical and molecular genetics, but in part because S. cerevisiae was the first eukaryotic organism to have its genome sequenced (Goffeau et al., 1996). The combination of these assets has placed S. cerevisiae at the forefront of research on eukaryotic cell biology. In addition, S. cerevisiae provides an unequaled reference for the study of pathogenic hemiascomycetous yeasts, such as C. glabrata, which is closely related to S. cerevisiae, and also for other Candida species that are more distantly related. Therefore, S. cerevisiae continues to serve as a model for the study of Candida biology and pathogenicity, although recent investigations supported by the development of the genomics and post-genomics of different Candida species have shown that there is an intense rewiring of gene function and regulation over the hemiascomycete group (see Candida: Comparative and Functional Genomics).

C. albicans is responsible for the majority of Candida infections. This fungus has therefore become a central focus of molecular research on fungal pathogens of humans. Many tools developed to engineer the genome of S. cerevisiae have now been adapted to study C. albicans and allow exquisite dissection of the function of a gene or group of genes in this species. Yet, two peculiarities of C. albicans have somehow limited the speed at which its biology could be investigated through molecular genetic approaches. First, C. albicans is a diploid species and lacks an exploitable sexual cycle with a haploid phase (Candida: Comparative and Functional Genomics). Therefore, the construction of knock-out mutant strains remains tedious and this slows the pace at which biological processes can be studied. Several approaches have been developed to circumvent this limitation. Second, C. albicans and other phylogenetically related Candida species share an alteration of the genetic code: the CUG codon in these species is translated into a serine residue instead of leucine. Much progress has now been made in the understanding of this evolutionary trait of the Candida clade and its biological impact (see Candida: Comparative and Functional Genomics). Importantly, this alteration has prevented a straightforward implementation of standard reporter genes, and novel reporters have had to be developed or adapted for the investigation of Candida. These are now available and should contribute to post-genomic analysis of C. albicans and related species. Yet, some approaches such as the production of C. albicans proteins in heterologous hosts or two-hybrid screens still suffer from the difference in codon usage, indicating that novel molecular tools remain to be developed for the study of Candida species.

Despite these technical limitations, important progress was made during the last decade of the twentieth century in understanding the biology of C. albicans and its interaction with host cells at the molecular level (Berman and Sudbery, 2002). Yet, the sequencing of the C. albicans genome and subsequently of the genomes of several other medically relevant Candida species has marked the turn of the century and has profoundly and irreversibly changed the way Candida species are now investigated and understood. The C. albicans genome sequencing effort was launched in October 1996 by the Stanford Genome Technology Center, mostly at the initiative of Stewart Scherer. Successive releases of the sequencing data and genome assemblies have marked the last 10 years, culminating with the release of the diploid assembly 19 that provided a haploid version of the genome along with data on allelic regions in the genome ( Jones et al., 2004). A refined assembly 20 with the eight assembled C. albicans chromosomes has been released in the summer of 2006. Importantly, the availability of sequencing data prior to the completion of the genome sequence has made it possible to start C. albicans post-genomics early on. In this regard, genome databases have been made available to the research community providing different forms of genome annotation (d'Enfert et al., 2005; Guldener et al., 2005). These have been merged in a community-based annotation (Braun et al., 2005) hosted by the Candida Genome Database (Arnaud et al., 2005) addresses the different databases that are currently available and the challenges that their curators are facing. Moreover, the availability of the genome sequence has paved the way for the implementation of post-genomic approaches to the study of C. albicans: macroarrays and then microarrays have been developed and used to study the C. albicans transcriptome (see Candida: Comparative and Functional Genomics); proteomics has also been developed and complements transcriptional analyses; furthermore, systematic approaches are becoming available to study the contribution of each C. albicans gene in different contexts (see Candida: Comparative and Functional Genomics). Other Candida genome sequences have been, or are being, determined: C. glabrata (Dujon et al., 2004), C. dubliniensis, C. parapsilosis, C. guilliermondii, C. lusitaniae, and C. tropicalis. Thus, these species will soon enter the post-genomic era as well and provide interesting comparative data. The genome sequences obtained for the different Candida species along with those of non-pathogenic hemiascomycetes provide a wealth of knowledge on the evolutionary processes that have shaped the hemiascomycete group as well as those that may have contributed to the success of different Candida species as pathogens (see Candida: Comparative and Functional Genomics). Interestingly, the genome of C. albicans is highly dynamic, and this variability has been used advantageously for molecular epidemiological studies of C. albicans and population studies in this species (see Candida: Comparative and Functional Genomics). A remarkable discovery that has arisen from the genome sequence is the presence of a parasexual cycle in C. albicans. This parasexual cycle is under the control of mating-type loci and switching between white and opaque phenotypes (see Candida: Comparative and Functional Genomics). Investigating the role that the mating process plays in the dynamics of the C. albicans population or in other aspects of C. albicans biology and pathogenicity will undoubtedly represent an important focus for future research.

C. albicans and also C. glabrata have entered the post-genomic era. Comparative analysis of transcript profiles obtained in C. albicans and S. cerevisiae provides unique insights into the gene expression pattern of pathogenic versus non-pathogenic species (see Candida: Comparative and Functional Genomics). Moreover, post-genomic functional analyses are bringing insights into key topics of Candida research such as stress responses, morphogenesis, the cell wall and cell surface components, antifungal resistance, or interaction with host cells (see Candida: Comparative and Functional Genomics).

The knowledge of the genome sequence of C. albicans and C. glabrata has contributed to the increase in our understanding of the biology of these species and their interactions with host cells. Surely, this is just the beginning!! Post-genomic approaches are generating huge amounts of data on these central topics as well as on other important topics. There is no doubt that one of the future challenges for the Candida research community will be to integrate these data into a meaningful picture that explains why certain Candida species are so successful as pathogens in contrast to other yeast species and how their genetic arsenal is mobilized to establish the various forms of Candida diseases. The hope is that this system biology of the host-pathogen interaction will provide the foundation for better management of Candida infections.

Christophe d'Enfert and Bernhard Hube, from "Candida : Comparative and Functional Genomics" Eds: d'Enfert, C. and Hube, B. (2007) Caister Academic Press.

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Christophe d'Enfert and Bernhard Hube, from "Candida : Comparative and Functional Genomics" Eds: d'Enfert, C. and Hube, B. (2007) Caister Academic Press.