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Expansion of a pivotal functional genomics resource identifies novel regulators of temperature-dependent fitness in the fungal pathogen Candida albicans

ABSTRACT: Functional genomic screens in Candida albicans are fundamental to uncover novel gene functions and the molecular mechanisms of virulence. In this study, expansion of the Gene Replacement and Conditional Expression (GRACE) library, covering now ~73% of the C. albicans genome, revealed genes relevant for fitness at cold or heat stress. From an initial screen at 30°C and 39°C, strains with moderate to severe growth defects were further assayed for growth under six different temperatures. Assessment of growth scores revealed enrichment of genes associated with RNA metabolism and regulatory-related processes as important during cold stress, whereas genes involved in cell cycle, filamentation and stress response were essential during elevated temperature. Here, we describe the function of cold-essential gene C1_11680C (or YSF3), which is involved in splicing and branchpoint recognition. RNA-Seq was conducted for functional analysis of C1_11680C, by investigating transcriptomic changes upon deletion at host (37°C) and cold stress (22°C) temperatures. This revealed major global splicing defects and confirmed its identity as the homolog of S. cerevisieae Ysf3 (Yeast splicing factor 3). We also found particular importance of this gene for splicing of introns with non-consensus branchpoints. In summary, this study describes the temperature-dependance of previously uncharazterized genes through a significant expansion of a pivotal genomics resource.

ORGANISM(S): Candida albicans

PROVIDER: GSE294776 | GEO | 2025/09/24

REPOSITORIES: GEO

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Project description:Purpose: We aimed at i) obtaining insight into how a thermophile organism reacts to cold stress, and ii) evaluating the impact of HGT candidates on the acclimation process to temperature decrease. Methods: The experimental design followed a temperature shift timeline: after two weeks of cultivation at 42°C, constant illumination (90 μE) and constant shaking (160 rpm) in photoautotrophic conditions the first sampling took place (Hot_T48_1) and the cultures of G.sulphuraria were swiftly moved to 28°C ( = cold temperature). "Cold" samples were taken after 3h (Cold_T3_2), 12h (Cold_T12_3) and 48h (Cold_T48_4). After cold treatment at 28°C for 48 hours, the G. sulphuraria was then switched to 46°C for 48 hours (="Hot"). Again, samples were taken after 3h (Hot_T3_5), 12h (Hot_T12_6) and 48h (Hot_T48_7). Altogether, a 48h temperature timeshift at 28°C and successive recovery at 46°C were targeted for sampling. Results: Galdieria sulphuraria is a unicellular red alga that lives in hot, acidic, toxic metal-rich, volcanic environments, where few other organisms survive. Its genome harbours up to 5% of genes most likely acquired through horizontal gene transfer. These genes probably contributed to G. sulphuraria’s adaptation to its extreme habitats, resulting in today’s polyextremophilic traits. Here, we applied RNA-sequencing to obtain insights into the acclimation of a thermophilic organism towards temperatures below its growth optimum and to study how horizontally acquired genes contribute to cold acclimation. A decrease in growth temperature from 42 °C/46 °C to 28 °C resulted in an upregulation of ribosome biosynthesis, while excreted proteins, probably components of the cell wall, were downregulated. Photosynthesis was suppressed at cold temperatures, and transcript abundances indicated that C-metabolism switched from gluconeogenesis to glycogen degradation. Folate cycle and S-adenosylmethionine cycle (one-carbon metabolism) were transcriptionally upregulated, probably to drive the biosynthesis of betaine. All these cold-induced changes in gene expression were reversible upon temperature increase. Numerous genes acquired by horizontal gene transfer displayed pronounced temperature-dependent expression changes, corroborating the view that these genes contributed to adaptive evolution in G. sulphuraria.

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Expansion of a pivotal functional genomics resource identifies novel regulators of temperature-dependent fitness in the fungal pathogen Candida albicans

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