Editorial: Candida glabrata, the other yeast pathogen

FEMS Yeast Research, 16, 2016, fov116 doi: 10.1093/femsyr/fov116 Advance Access Publication Date: 21 January 2016 Editorial

Editorial: Candida glabrata, the other yeast pathogen The ascomycete yeast Candida glabrata ranks second, in many studies, after Candida albicans as the most frequent yeast pathogen of humans, responsible for many types of opportunistic infections, and most notable for the high mortality it provokes in immuno-compromised patients. It was first described as Cryptococcus glabratus, isolated from human faeces in 1917 (Anderson, 1917). Major breakthroughs in understanding the phylogeny and population structure of yeast and other fungal pathogens, and indeed, many domains of the tree of life, were brought about by recent progress in sequencing technologies. Since Saccharomyces cerevisiae opened the way by becoming the first eukaryote to have its genome entirely sequenced, by an international consortium (Goffeau et al. 1996), many full genomes have been released, and yeast species account for a good number among eukaryotes, owing to the compactness and small size of their genomes. The genome of C. glabrata was published in 2004 (Dujon et al. 2004), as part of the Genolevures effort (http://gryc.inra.fr/). Genomics confirmed previous gene analyses (Kurtzman and Robnett, 1998), that showed that C. glabrata is much more closely phylogenetically related to S. cerevisiae than to C. albicans, descending from the same ancestor that underwent a whole genome duplication event. It remains one of the few pathogens from this branch of the phylogenetic tree of the Saccharomycetaceae. This is another demonstration of the fact that genus names are not monophyletic in yeasts, and do not represent true lineages. Since then, two new pathogens have been described, Candida nivariensis (Alcoba-Florez et al. 2005) and Candida bracarensis (Correia et al. 2006), that are part of the Nakaseomyces, the clade described by C. Kurtzman to contain C. glabrata, and up to that point, only three additional environmental species, Nakaseomyces (Kluyveromyces) bacillisporus, Nakaseomyces (Kluyveromyces) delphensis, Nakaseomyces (Candida) castellii, but no other pathogen (Kurtzman, 2003). The genomes of the five known additional Nakaseomyces were published in 2013 (Gabaldon et al. 2013). This, in addition to the development of molecular tools, should allow easier experimental studies in all Nakaseomyces; but at this point in time, obviously, most work has been performed on C. glabrata. Analysis of all Nakaseomyces genomes is reviewed in Angoul´ this issue. All genomes vant et al., and in Gabaldon and Carrete, of the Nakaseomyces are small, especially those of the species closely related to and including C. glabrata. All have lost most gene copies resulting from the past Whole Genome Duplication event, and genes involved in specific metabolic pathways. The one feature that distinguishes pathogenic species from non pathogens is the expansion of the EPA gene family,

specifically in pathogens. Finally, C. glabrata contains more tandem repeats of genes than the other Nakaseomyces, at least when examining the type strains (Gabaldon et al. 2013), and they mostly encode cell wall proteins, and, at least in the case of the YPS tandem family, have been shown to be involved in virulence (Kaur et al. 2007). It is likely that all Nakaseomyces are fortuitously pre-adapted to the human host, and commensalitypathogenicity emerged independently in three species (Gabaldon et al. 2013). Although genus names are not to be trusted for phylogeny, they do reveal interesting features. Nakaseomyces species used to be called “Kluyveromyces” and “Candida”. The name “Candida” is given to ascomycetous yeasts that have no apparent sexual forms, i.e. no teleomorph. Remarkably, this name has been mostly given to species which are pathogens of humans, highlighting this common character of these pathogens, that they seem to lose the ability to reproduce sexually, and seem to be mostly “stuck” in a given ploidy. Availability of genome sequences was instrumental in kicking off new research into sexual and parasexual cycles. Indeed, genomes reveal that they contain homologs of all genes needed for mating, for meiosis, sporulation and so forth. The iconic major yeast pathogen, the diploid Candida albicans was long thought asexual, but examination of its gene content encouraged efforts to search for mating forms. This led to the discovery of a parasexual cycle (Hull et al. 2000; Magee and Magee, 2000). More recently, C. albicans has been shown to exist in the haploid phase (Hickman et al. 2013). It remains to be understood when and how the species goes through these stages in its natural environment. Contrary to C. albicans, C. glabrata is isolated as haploid cells, and it has no described sexual cycle. As it is related to S. cerevisiae, the sexual cycle of this latter species must give us some clues as to what we should search for in C. glabrata. Some wildtype S. cerevisiae isolates are homothallic (Katz-Ezov et al. 2010) which means that a single cell isolated after sporulation can give rise to diploid cells without having to encounter a cell of the opposite mating-type. This peculiar ability is shared by many fungal species, but mechanisms vary and it is most well-studied in S. cerevisiae. Homothallism in S. cerevisiae involves fusion of cells of opposite mating-types, but haploid cells can undergo matingtype switching, which leads to mixed populations of cells, which can then mate to produce diploids. The underlying mechanisms depend on the existence of a selfish gene, of the intein family, that has been domesticated by S. cerevisiae. This gene encodes an endonuclease, called Ho, that cuts the MAT locus, generating a dangerous double-strand break that is repaired by Homologous Recombination involving two additional loci, HMR (Hidden Mat

 C FEMS 2016. All rights reserved. For permissions, please e-mail: [email protected]

1 Downloaded from https://academic.oup.com/femsyr/article-abstract/16/2/fov116/2570119/Editorial-Candida-glabrata-the-other-yeast by guest on 21 October 2017

2

FEMS Yeast Research, 2016, Vol. 16, No. 2

Right) and HML (Hidden Mat Left), containing type a and type alpha information, respectively. All Nakaseomyces genomes contain homologs of genes necessary for mating-type switching, mating and meiosis (Fabre et al. 2005; Muller et al. 2007; Gabaldon et al. 2013 and our unpublished results), although none of the Candida species are known to mate, or switch naturally (our own unpublished results). The HO gene from C. glabrata was over-expressed constitutively in the type strain, of MATalpha type, and MATa strains were obtained (Edskes and Wickner 2013). Our results (Boisnard et al. 2015) show that inducible expression of HO genes of various origins in C. glabrata can induce switching in both directions, from MATalpha to MATa and back. We have also shown that expression of mating-related genes seems less tightly regulated in C. glabrata, so that several steps of the mating pathway may not be functioning at optimal levels in experimental conditions (Muller et al. 2008). Nonetheless, it is likely that conditions for mating will be found for the Candida species of the Nakaseomyces, as observation of mating-related forms in C. glabrata has been reported (Usher and Haynes, 2014). It was thus untimely to include a review on mating in this special issue, and we have focused on papers that deal with recent advances and hypotheses. Phylogeny, the emergence of pathogeny and epidemiology of C. glabrata, but also of the two newly described pathogens, C. nivariensis and C. bracarensis are discussed in Gabaldon and Carrete´ and in Angoulvant et al. Modern medical devices are major points of entry for opportunistic pathogens, and the formation of biofilms is essential for such infections to occur, but genes encoding adhesins are often subjected to sub-telomeric silencing. This is examined in the article by d’Enfert and Janbon, in which they describe how silencing can be relieved by chromatin remodelling complexes. Molecular mechanisms for silencing are also discussed in Castano et al., in relation to virulence genes. The adhesins themselves are adressed in Gomez-Molero et al.: many genes are present in the genome of C. glabrata, but it seems few such proteins are indeed incorporated into the cell wall. Their work shows that hyperadherent strains do address more of these proteins to their cell wall. Biofilm formation is also related to C. glabrata’s resistance to azoles, which seems not to be associated to fitness costs in this species, as discussed in Vale-Silva and Sanglard. Another major aspect of virulence in C. glabrata is the fact that the yeast cells can divide within macrophages without causing too much damage to them, before being released, and this is addressed in the article by Kasper et al. The yeasts’ metabolism must therefore adapt to the hostile environment inside the macrophage. The phylogenetic proximity of the Nakaseomyces with S. cerevisiae led to the assumption that carbon metabolism is probably very similar in all these species. It is usually assumed that S. cerevisiae’s metabolic pathways for sugar consumption are extremely well-adapted to the high suger content of grape juice, a very specialized ecological niche, and that is correlated with a high number of duplicated genes involved in glycolysis. Legrand et al. examine these genes in all Nakaseomyces’ genomes, and experimentally determine glucose consumption rates. This shows that the relationship between gene number and glucose metabolism is not as straightforward as was hypothesized based on the genome and biology of the model yeast S. cerevisiae, highlighting again the precautions one must take when inferring evolutionary events from partial phylogenetic exploration of genomes, and the fact that no species can be a “model” for all aspects of a cell’s biology.

Finally, sequencing in addition to high-throughput genetical and biochemical tools in S. cerevisiae had led to an unprecedented level of understanding of this model yeast. It is essential that such methodology be applied on other species, and especially on pathogens, where comparisons to a non-pathogenic model may be the least appropriate. Papers by Roy and Thompson, and Usher et al., adress these issues, with the comparative analysis of regulatory pathways and the development of synthetic lethal screens in C. glabrata. All of these recent advances should help us understand the emergence of yeast pathogens related to baker’s yeast. This special issue (http://femsyr.oxfordjournals.org/content/ thematic-issue-candida-glabrata) is therefore an opportunity to put forward all progress which has been made recently thanks mostly to the genome sequences basis now available, and aims to give an overview of future directions to explore.

REFERENCES Alcoba-Florez J, Mendez-Alvarez S, Cano J et al. Phenotypic and molecular characterization of Candida nivariensis sp. nov., a possible new opportunistic fungus. Journal of clinical microbiology 2005;43:4107–11. Anderson HW. Yeast-like fungi of the human intestinal tract. Journal of infectious diseases 1917;21:341–85. Boisnard S, Zhou Li Y, Arnaise S et al. Efficient Mating-Type Switching in Candida glabrata Induces Cell Death. PLoS One 2015;10:e0140990. Correia A, Sampaio P, James S et al. Candida bracarensis sp. nov., a novel anamorphic yeast species phenotypically similar to Candida glabrata. International journal of systematic and evolutionary microbiology 2006;56(Pt 1):313–7. Dujon B, Sherman D, Fischer G et al. Genome evolution in yeasts. Nature 2004;430:35–44. Edskes HK, Wickner RB. The [URE3] prion in Candida. Eukaryot Cell 2013;12:551–8. Fabre E, Muller H, Therizols P et al. Comparative genomics in hemiascomycetous yeasts: evolution of sex, silencing and subtelomeres. Mol Biol Evol 2005;22:856–73. ´ T, Martin T, Marcet-Houben M et al. Comparative geGabaldon nomics of emerging pathogens in the Candida glabrata clade. BMC Genomics 2013;14:623. Goffeau A, Barrell BG, Bussey H et al. Life with 6000 genes. Science 1996;274:546, 563–7. Hickman MA, Zeng G, Forche A et al. The “obligate diploid” C. albicans forms mating-competent haploids. Nature 2013;494: 55–9. Hull CM, Raisner RM, Johnson AD. Evidence for mating of the “asexual” yeast Candida albicans in a mammalian host. Science 2000;289:307–10. Katz Ezov T, Chang SL, Frenkel Z et al. Heterothallism in Saccharomyces cerevisiae isolates from nature: effect of HO locus on the mode of reproduction. Mol Ecol 2010;19:121–31. Kaur R, Ma B, Cormack BP. A family of glycosylphosphat idylinositol-linked aspartyl proteases is required for virulence of Candida glabrata. Proc Natl Acad Sci U S A. 2007;104:7628–33. Kurtzman CP. Phylogenetic circumscription of Saccharomyces, Kluyveromyces and other members of the Saccharomycetaceae, and the proposal of the new genera Lachancea, Nakaseomyces, Naumovia, Vanderwaltozyma and Zygotorulaspora. FEMS yeast research 2003;4:233–45.

Downloaded from https://academic.oup.com/femsyr/article-abstract/16/2/fov116/2570119/Editorial-Candida-glabrata-the-other-yeast by guest on 21 October 2017

Bolotin-Fukuhara and Fairhead

Kurtzman CP, Robnett CJ. Identification and phylogeny of ascomycetous yeasts from analysis of nuclear large subunit (26S) ribosomal DNA partial sequences. Antonie Van Leeuwenhoek 1998;73:331–71. Magee BB, Magee PT. Induction of mating in Candida albicans by construction of MTLa and MTLalpha strains. Science 2000;289:310–3. Muller H, Hennequin C, Dujon B et al. Comparing MAT in the genomes of hemiascomycetous yeasts. In Heitman J, Kronstad J, Taylor J et al. (eds). “Sex in Fungi: Molecular Determination and Evolutionary Implications”, ASM Press, 2007.

3

Muller H, Hennequin C, Gallaud J et al. The asexual yeast C. glabrata maintains distinct a and alpha haploid mating types. Eukaryot Cell 2008;7:848–58. Usher J, Haynes K. Engineering a complete sexual cycle in Candida glabrata. S5: 5. 12th ASM Conference on Candida and Candidiasis, 2014.

Monique Bolotin-Fukuhara and C´ecile Fairhead, Universit´e Paris Sud, Facult´e des Sciences d’Orsay, F 91405 Orsay Cedex, France. E-mail: [email protected]

Downloaded from https://academic.oup.com/femsyr/article-abstract/16/2/fov116/2570119/Editorial-Candida-glabrata-the-other-yeast by guest on 21 October 2017