Widespread Occurrence of Dosage Compensation in Candida albicans

Citation: Kravets A, Qin H, Ahmad A, Bethlendy G, Gao Q, et al. ( Widespread Occurrence of Dosage Compensation in Candida albicans Anatoliy Kravets 0 Hong Qin 0 Ausaf Ahmad 0 Gabor Bethlendy 0 Qinshan Gao 0 Elena Rustchenko 0 Michael Polymenis, Texas A&M University, United States of America 0 1 Department of Biochemistry and Biophysics, University of Rochester Medical Center , Rochester , New York, United States of America, 2 Department of Biology, Spelman College , Atlanta , Georgia , United States of America, 3 Roche Diagnostics Corporation, Indianapolis, Indiana, United States of America, 4 Department of Microbiology, Mount Sinai School of Medicine , New York, New York , United States of America The important human pathogen Candida albicans possesses an unusual form of gene regulation, in which the copy number of an entire specific chromosome or a large portion of a specific chromosome changes in response to a specific adverse environment, thus, insuring survival. In the absence of the adverse environment, the altered portion of the genome can be restored to its normal condition. One major question is how C. albicans copes with gene imbalance arising by transitory aneuploid states. Here, we compared transcriptomes from cells with either two copies or one copy of chromosome 5 (Ch5) in, respectively, a diploid strain 3153A and its representative derivative Sor55. Statistical analyses revealed that at least 40% of transcripts from the monosomic Ch5 are fully compensated to a disomic level, thus, indicating the existence of a genome-wide mechanism maintaining cellular homeostasis. Only approximately 15% of transcripts were diminished twofold in accordance with what would be expected for Ch5 monosomy. Another minor portion of approximately 6% of transcripts, unexpectedly, increased up to twofold and higher than the disomic level, demonstrating indirect control by monosomy. Array comparative genome hybridization revealed that only few out of approximately 500 genes on the monosomic Ch5b were duplicated, thus, not causing a global up regulation. Dosage compensation was confirmed with several representative genes from another monosomic Ch5a in the mutant Sor60. We suggest that C. albicans's unusual regulation of gene expression by the loss and gain of entire chromosomes is coupled with widespread compensation of gene dosage at the transcriptional level. - Funding: This work was supported in part by National Institutes of Health Grant AI29433 and Pfizer Global Pharmaceuticals, Pfizer Inc. to Fred Sherman, as well as partially supported by P30 AG18254 to Hong Qin. The authors are grateful to the University of Rochester funds that enabled this study. The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Competing Interests: Pfizer Inc., which gave a small grant some time ago to Fred Sherman, had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript. Candida albicans is a unicellular fungus that is a benign inhabitant of the mucosal surfaces of gastrointestinal tract in approximately two thirds of the healthy human population. In some healthy individuals, C. albicans causes merely superficial mucosal infections; however, in hospitals, C. albicans has emerged as an important pathogen of immunocompromized patients and is associated with significant morbidity, mortality, and high health-care costs. C. albicans is an obligate diploid organism with 8 pairs of chromosomes, whose unusual instability has been systematically investigated by us and others [1]. Throughout years, we have accumulated evidence that C. albicans generates aneuploidies as a response to environmental stresses [13], despite aneuploidy having detrimental effects on cell division and growth similar to other organisms [4,5]. Moreover, we have demonstrated that reversible loss or gain of specific chromosomes, or large portions of specific chromosomes, each occurring in a specific adverse environment, constitute unusual gene regulatory systems that allow C. albicans survival [1,2]. In the best-studied case, adaptation to the toxic sugar sorbose, the major mechanism conferring survival is the loss of an entire chromosome 5a (Ch5a) or an entire chromosome 5b (Ch5b). Here, we address an intriguing question of how C. albicans handles gene disbalance due to aneuploid chromosome by analyzing the expression of approximately 500 genes on the monosomic Ch5b. We found that at least 40% of transcripts were fully compensated to the disomic level, in contrast to another fungus Saccharomyces cerevisiae. This finding was supported with the analysis of limited number of genes from the alternative Ch5a. Using array comparative genome hybridization (aCGH), we demonstrated that widespread dosage compensation was not caused by gene duplication. This implies that epigenetic events may be responsible, similarly to compensatory mechanisms in higher eukaryotes, as elaborated in the Discussion. Evidence by pulsed-field gel electrophoresis (PFGE) that the mutant Sor55 is monosomic for Ch5b Electrophoretic karyotype [6] of the mutant Sor55, which we analyzed here with expression or CGH arrays, was previously reported [7]. Sor55 derived from the laboratory strain 3153A by exposure to toxic sorbose, which caused the loss of Ch5a. We have previously established that the loss of an entire Ch5a is a predominant mechanism for adaptation to toxic sorbose [1,2]. In this respect, Sor55 is a representative mutant. In order to assure that we are analyzing the transcriptom from cells with monosomic, but not with spontaneously duplicated Ch5b [7], we confirmed the electro-karyotype of Sor55. When cells of 3153A and Sor55 were grown to extract RNA for expression microarrays, an aliquot of cells was used to obtain native chromosomes for precise separation with PFGE [3] (Materials and Methods). As expected, Sor55 contained Ch5b, but lacked Ch5a, Fig. 1. The retained Ch5b was not duplicated, as determined by visual examination and densitometry [3]. In addition, consistently, PCR analysis showed that only MTLa1 on Ch5b, but not MTLa1 or MTLa2 on Ch5a, could be amplified from genomic DNA of Sor55 with the appropriate primers [Table S1 of supporting information (SI)]. As expected, all three genes, MTLa1, MTLa1 and MTLa2, could be amplified from 3153A. Also, monosomy of Ch5 has been reported to up regulate the SOU1 gene on Ch4 that is responsible for the growth on sorbose [7,8]. As expected, SOU1 in Sor55 was up regulated, as estimated by DNA microarray (Table S2) and Northern blot analysis (data not shown). We are, thus, confident that the Sor55 cells were monosomic for Ch5b at the time of transcriptom examination. Statistical analysis of the DNA microarray results reveals significantly diminished expression profile of monosomic Ch5b Genome-wide transcription profiles were determined with our custom microarrays (Materials a (...truncated)