A conserved regulator controls asexual sporulation in the fungal pathogen Candida albicans

Transcription factor Rme1 is conserved among ascomycetes and regulates meiosis and pseudohyphal growth in Saccharomyces cerevisiae. The genome of the meiosis-defective pathogen Candida albicans encodes an Rme1 homolog that is part of a transcriptional circuitry controlling hyphal growth. Here, we use chromatin immunoprecipitation and genome-wide expression analyses to study a possible role of Rme1 in C. albicans morphogenesis. We find that Rme1 binds upstream and activates the expression of genes that are upregulated during chlamydosporulation, an asexual process leading to formation of large, spherical, thick-walled cells during nutrient starvation. RME1 deletion abolishes chlamydosporulation in three Candida species, whereas its overexpression bypasses the requirement for chlamydosporulation cues and regulators. RME1 expression levels correlate with chlamydosporulation efficiency across clinical isolates. Interestingly, RME1 displays a biphasic pattern of expression, with a first phase independent of Rme1 function and dependent on chlamydospore-inducing cues, and a second phase dependent on Rme1 function and independent of chlamydospore-inducing cues. Our results indicate that Rme1 plays a central role in chlamydospore development in Candida species.

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-CisGenome to normalize ChIP-chip data and find peaks -Arraypipe 2.0 software to normalize expression microarray data, merge replicate spots from ChIP-chip GPR files and generate the corresponding median intensity data. -Integrated Genomics Viewer (IGV_2.3.68) software to visualize ChIP-chip results -realplex software version 2.2 (Eppendorf®) for qPCR data analysis -MUSCLE v3.8.311 for multiple alignment -trimAl v32 to trim the alignments -ProTest v2.43 to choose the best protein substitution models -PHYML v3.0.14 to reconstruct phylogenetic trees -Prism 8.4.3 (GraphPad) to draw graphs -Photoshop CS6 (Adobe) to create figures nature research | reporting summary

October 2018
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No sample size calculation was performed. Our study was based on the assumption that at least 3 independent biological replicates are sufficient to calculate statistical significance. On the other hand, based on the fact that off-target effects may occur during mutant construction in C. albicans, we usually construct mutants two times independently and verify the reproducibility of phenotypes.
No data were excluded from the analyses Experiments were replicated (or performed) at least 3 times independently. All attempts at replication were successful (or yielded statistically significant differences). When building mutant strains, several transformants were assessed for phenotypes.
No random sampling was performed since there were no selection steps with the potential for introducing bias in our study.
Since no randomization was used, blinding experiments were not relevant in our case. For chlamydosporulation scoring ( Figure S4), scores were assessed by two independent observers.