Stress-induced Gene Expression in Candida albicans : Absence of a General Stress Response

125

127

Candida albicans is a ubiquitous opportunistic pathogen that is the most prevalent cause of hospital-acquired fungal infections. In mammalian hosts, C. albicans is engulfed by phagocytes that attack the pathogen with DNA-damaging reactive oxygen species (ROS). Acetylation of histone H3 lysine 56 (H3K56) by the fungal-specific histone acetyltransferase Rtt109 is important for yeast model organisms to survive DNA damage and maintain genome integrity. To assess the importance of Rtt109 for C. albicans pathogenicity, we deleted the predicted homolog of Rtt109 in the clinical C. albicans isolate, SC5314. C. albicans rtt109 −/− mutant cells lack acetylated H3K56 (H3K56ac) and are hypersensitive to genotoxic agents. Additionally, rtt109 −/− mutant cells constitutively display increased H2A S129 phosphorylation and elevated DNA repair gene expression, consistent with endogenous DNA damage. Importantly, C. albicans rtt109 −/− cells are significantly less pathogenic in mice and more susceptible to killing by macrophages in vitro than are wild-type cells. Via pharmacological inhibition of the host NADPH oxidase enzyme, we show that the increased sensitivity of rtt109 −/− cells to macrophages depends on the host's ability to generate ROS, providing a mechanistic link between the drug sensitivity, gene expression, and pathogenesis phenotypes. We conclude that Rtt109 is particularly important for fungal pathogenicity, suggesting a unique target for therapeutic antifungal compounds.acetylation | chromatin | fungal pathogenesis | DNA damage resistance | macrophage

Section: Resultsmentioning

confidence: 99%

Histone acetyltransferase Rtt109 is required for Candida albicans pathogenesis

Rosa

Boyartchuk

Zhu

et al. 2010

125

127

“…These genes have been shown to be strongly corepressed in S. cerevisiae under environmental stress or nutrient limitation conditions (10,11). In contrast, a previous study in Candida albicans failed to show similar repression under environmental stress (12), suggesting that RP expression levels may have diverged between species. However, all of the RP regulatory circuits characterized to date have a similar functional organization with some components that are constitutively localized on the RP promoter (Tbf1 in C. albicans and Rap1 in S. cerevisiae; both are also associated with telomere maintenance), and some that are regulated by nutrient-and environmental-response pathways (e.g., Ifh1 and Sfp1) (6,(13)(14)(15)(16).…”

mentioning

confidence: 87%

Gene duplication and the evolution of ribosomal protein gene regulation in yeast

Wapinski

Pfiffner

French

et al. 2010

Coexpression of genes within a functional module can be conserved at great evolutionary distances, whereas the associated regulatory mechanisms can substantially diverge. For example, ribosomal protein (RP) genes are tightly coexpressed in Saccharomyces cerevisiae, but the cis and trans factors associated with them are surprisingly diverged across Ascomycota fungi. Little is known, however, about the functional impact of such changes on actual expression levels or about the selective pressures that affect them. Here, we address this question in the context of the evolution of the regulation of RP gene expression by using a comparative genomics approach together with cross-species functional assays. We show that an activator (Ifh1) and a repressor (Crf1) that control RP gene regulation in normal and stress conditions in S. cerevisiae are derived from the duplication and subsequent specialization of a single ancestral protein. We provide evidence that this regulatory innovation coincides with the duplication of RP genes in a whole-genome duplication (WGD) event and may have been important for tighter control of higher levels of RP transcripts. We find that subsequent loss of the derived repressor led to the loss of a stress-dependent repression of RPs in the fungal pathogen Candida glabrata. Our comparative computational and experimental approach shows how gene duplication can constrain and drive regulatory evolution and provides a general strategy for reconstructing the evolutionary trajectory of gene regulation across species. T he coordinated expression of modules of functionally related genes, such as ribosomal proteins or oxidative phosphorylation enzymes, is often conserved at great evolutionary distances (1). This is consistent with a selective pressure to conserve coordinated transcript levels to maintain functional cellular modules. Recent studies have shown that the regulatory mechanisms controlling conserved modules can diverge, most notably by switching from one regulatory system to another while preserving coregulation (1, 2). However, because previous studies have typically relied on functional expression data from only one or two species, it is unknown whether these changes in regulatory mechanisms affect the expression levels of a module's genes at all or whether both coexpression and expression levels are conserved.A prominent example of a conserved regulatory module is the ribosomal protein (RP) module. Genes encoding RPs are tightly coexpressed in organisms from bacteria to humans (3, 4), consistent with a selective pressure to conserve coordinated transcript levels to maintain a stoichoimetric balance in ribosome assembly. The transcription factors controlling RP gene expression have changed several times since the last common ancestor of the Ascomycota fungi, which span Saccharomyces cerevisiae and Schizosaccharomyces pombe (4-6). These dramatic changes include the loss of the ancestral regulator Tbf1, the emergence of Rap1 as a key activator among the Hemiascomycota (4, 5), as well as the add...

“…However, some of the organisms, for example C. albicans, employ a regulatory mechanism lacking both RAP1 and Homol-D elements (and using IFHL and RRPE elements). Indeed, a recent expression profiling study (22) indicates that the C. albicans RP module responds much more weakly to environmental stress than either S. cerevisiae or S. pombe (Supporting Materials and Methods, note 3).…”

Section: Conservation Of Spatial Configuration In Ribosomal Promotersmentioning

confidence: 99%

Conservation and evolvability in regulatory networks: The evolution of ribosomal regulation in yeast

Tanay

Regev

Shamir

2005

243

254

Transcriptional modules of coregulated genes play a key role in regulatory networks. Comparative studies show that modules of coexpressed genes are conserved across taxa. However, little is known about the mechanisms underlying the evolution of module regulation. Here, we explore the evolution of cis-regulatory programs associated with conserved modules by integrating expression profiles for two yeast species and sequence data for a total of 17 fungal genomes. We show that although the cis-elements accompanying certain conserved modules are strictly conserved, those of other conserved modules are remarkably diverged. In particular, we infer the evolutionary history of the regulatory program governing ribosomal modules. We show how a ciselement emerged concurrently in dozens of promoters of ribosomal protein genes, followed by the loss of a more ancient cis-element. We suggest that this formation of an intermediate redundant regulatory program allows conserved transcriptional modules to gradually switch from one regulatory mechanism to another while maintaining their functionality. Our work provides a general framework for the study of the dynamics of promoter evolution at the level of transcriptional modules and may help in understanding the evolvability and increased redundancy of transcriptional regulation in higher organisms.regulatory motifs ͉ transcriptional networks T ranscriptional modules, i.e., groups of coregulated genes, play a central role in the organization and function of regulatory networks (1-3). Comparative studies have demonstrated that various transcriptional modules are highly conserved across a wide variety of organisms from Escherichia coli to humans (4-6). A common tacit assumption is that conserved regulatory mechanisms underlie module conservation, because coregulation imposes tight constraints on the evolution of a module's promoters. Indeed, recent studies showed that orthologous transcriptional modules are often associated with conserved cis-elements (7).To gain new insights into the evolution of regulation of transcriptional modules, we developed an integrated method for comparative expression and sequence analysis. We applied our method to 17 fully sequenced yeast genomes and identified conserved transcriptional modules and the cis-elements that are associated with them in each species. Although the cis-elements associated with certain modules were conserved in all species, other modules were associated with distinct cis-elements in different species. Divergence of cis-elements in specific promoters has been documented, e.g., in refs. 8 and 9, but it is difficult to explain in a similar way the divergence we observed in a regulatory program associated with dozens of coexpressed genes. In particular, it is not clear how multiple promoters diverge in a coordinated way and how divergence occurs without adversely affecting the coexpression phenotype. To answer this question, we inferred the detailed evolutionary history of modules' regulatory programs and studied different evolutionary...