Regulation of carotenogenesis in the red yeast Xanthophyllomyces dendrorhous: the role of the transcriptional co-repressor complex Cyc8–Tup1 involved in catabolic repression

Abstract

BackgroundThe yeast Xanthophyllomyces dendrorhous produces carotenoids of commercial interest, including astaxanthin and β-carotene. Although carotenogenesis in this yeast and the expression profiles of the genes controlling this pathway are known, the mechanisms regulating this process remain poorly understood. Several studies have demonstrated that glucose represses carotenogenesis in X. dendrorhous, suggesting that this pathway could be regulated by catabolic repression. Catabolic repression is a highly conserved regulatory mechanism in eukaryotes and has been widely studied in Saccharomyces cerevisiae. Glucose-dependent repression is mainly observed at the transcriptional level and depends on the DNA-binding regulator Mig1, which recruits the co-repressor complex Cyc8–Tup1, which then represses the expression of target genes. In this work, we studied the regulation of carotenogenesis by catabolic repression in X. dendrorhous, focusing on the role of the co-repressor complex Cyc8–Tup1.ResultsThe X. dendrorhous CYC8 and TUP1 genes were identified, and their functions were demonstrated by heterologous complementation in S. cerevisiae. In addition, cyc8 − and tup1 − mutant strains of X. dendrorhous were obtained, and both mutations were shown to prevent the glucose-dependent repression of carotenogenesis in X. dendrorhous, increasing the carotenoid production in both mutant strains. Furthermore, the effects of glucose on the transcript levels of genes involved in carotenogenesis differed between the mutant strains and wild-type X. dendrorhous, particularly for genes involved in the synthesis of carotenoid precursors, such as HMGR, idi and FPS. Additionally, transcriptomic analyses showed that cyc8 − and tup1 − mutations affected the expression of over 250 genes in X. dendrorhous. ConclusionsThe CYC8 and TUP1 genes are functional in X. dendrorhous, and their gene products are involved in catabolic repression and carotenogenesis regulation. This study presents the first report involving the participation of Cyc8 and Tup1 in carotenogenesis regulation in yeast.Electronic supplementary materialThe online version of this article (doi:10.1186/s12934-016-0597-1) contains supplementary material, which is available to authorized users.

Production of astaxanthin at moderate temperature in Xanthophyllomyces dendrorhous using a two‐step process

“…Astaxanthin generated from the beginning of the exponential phase and reached to the maximal value when the glucose consumed up. It seemed different from a theory that in cultures supplemented with glucose, carotenogenesis was induced only after the culture medium ran out of glucose [16]. The reason might be starch or other organic carbon source existing in the potato dextrose medium weakened the catabolic repression of glucose.…”

Convergence between Regulation of Carbon Utilization and Catabolic Repression in Xanthophyllomyces dendrorhous

“…To correlate the effect of assimilation of different carbon sources on central metabolism, we analyzed the proteome and transcriptome of strains cyc8 Ϫ/Ϫ , tup1 Ϫ/Ϫ , and mig1 Ϫ/Ϫ , encoding principal transcriptional regulators. Glucose repression and derepression essentially concern genes involved in oxidative metabolism and the TCA cycle, genes coding for the metabolism of alternative carbon sources, or genes coding for gluconeogenesis (11)(12)(13)(14)(15)(16)(17)(18)(19)(20). The most common mechanisms regulating gene products involve a decrease in transcription or translation at the gene level or an increase in protein degradation at the protein level (12).…”

“…RNA extraction and transcriptome sequencing. The total RNA extraction protocol was performed according to a modified protocol previously described (13).…”

“…In agreement with the above, our team showed that X. dendrorhous has a functional catabolic repression mechanism. Moreover, carotenogenesis is inhibited in the presence of glucose, but the inhibition is alleviated in the mig1 Ϫ/Ϫ , cyc8 Ϫ/Ϫ , and tup1 Ϫ/Ϫ mutant strains (9,13). Additionally, transcriptomic studies of X. dendrorhous mutant strains cyc8 Ϫ/Ϫ and tup1 Ϫ/Ϫ have shown that these mutations have a pleiotropic effect, affecting the expression of over 200 genes involved in different biological processes (13).…”

Microbiological Synthesis of Carotenoids: Pathways and Regulation

“…Then, Mig1 recruits a co-repressor complex formed by the Cyc8 and Tup1 proteins that represses the transcription of the target genes. In the absence of glucose, Mig1 is phosphorylated by the Snf1 kinase complex, loses its interaction with the Cyc8-Tup1 complex, and it is exported to the cytoplasm [57][58][59]. In S. cerevisiae, the co-repressor complex Cyc8-Tup1 is considered as a global transcriptional co-repressor, because it regulates the expression of more than 180 genes, including those regulated by glucose.…”