Proteomic and metabolomic analysis of the carotenogenic yeast Xanthophyllomyces dendrorhous using different carbon sources

Abstract

BackgroundAstaxanthin is a potent antioxidant with increasing biotechnological interest. In Xanthophyllomyces dendrorhous, a natural source of this pigment, carotenogenesis is a complex process regulated through several mechanisms, including the carbon source. X. dendrorhous produces more astaxanthin when grown on a non-fermentable carbon source, while decreased astaxanthin production is observed in the presence of high glucose concentrations. In the present study, we used a comparative proteomic and metabolomic analysis to characterize the yeast response when cultured in minimal medium supplemented with glucose (fermentable) or succinate (non-fermentable).ResultsA total of 329 proteins were identified from the proteomic profiles, and most of these proteins were associated with carotenogenesis, lipid and carbohydrate metabolism, and redox and stress responses. The metabolite profiles revealed 92 metabolites primarily associated with glycolysis, the tricarboxylic acid cycle, amino acids, organic acids, sugars and phosphates. We determined the abundance of proteins and metabolites of the central pathways of yeast metabolism and examined the influence of these molecules on carotenogenesis.Similar to previous proteomic-stress response studies, we observed modulation of abundance from several redox, stress response, carbohydrate and lipid enzymes. Additionally, the accumulation of trehalose, absence of key ROS response enzymes, an increased abundance of the metabolites of the pentose phosphate pathway and tricarboxylic acid cycle suggested an association between the accumulation of astaxanthin and oxidative stress in the yeast. Moreover, we observed the increased abundance of late carotenogenesis enzymes during astaxanthin accumulation under succinate growth conditions.ConclusionsThe use of succinate as a carbon source in X. dendrorhous cultures increases the availability of acetyl-CoA for the astaxanthin production compared with glucose, likely reflecting the positive regulation of metabolic enzymes of the tricarboxylic acid and glyoxylate cycles. The high metabolite level generated in this pathway could increase the cellular respiration rate, producing reactive oxygen species, which induces carotenogenesis.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1484-6) contains supplementary material, which is available to authorized users.

Comparative genomics provides new insights into the diversity, physiology, and sexuality of the only industrially exploited tremellomycete: Phaffia rhodozyma

“…The presence of Mn-SOD and the absence of Cu/Zn-SOD in P. rhodozyma was previously described reported [45, 46]. Given that it has been reported that Mn-SOD is present only in the mitochondria, while Cu/Zn-SOD is cytosolic [47], it was proposed that P. rhodozyma would be hypersensitive to oxidative stress.…”

Proteomic analysis of Rhodotorula mucilaginosa: dealing with the issues of a non‐conventional yeast

“…Thus, the increase in the expression level of enzymes involved in the biosynthesis of cytosolic acetyl‐CoA is in accordance with the accumulation of carotenoids in stationary phase. Moreover, in accordance with the upregulation of enzymes involved in the stress response during carotenogenesis (Barbachano‐Torres et al ., ; Martinez‐Moya et al ., ), at the stationary phase of growth there was a slight but consistent increase in the expression levels of catalase and heat shock protein HSP70. According to Martinez‐Moya et al .…”

“…According to Martinez‐Moya et al . (), the higher abundance of enzymes involved in the response to stress in stationary phase would be related to the induction of carotenogenesis.…”

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).…”

“…Previously, Martinez-Moya and collaborators carried out proteomic studies in which they analyzed protein profiles present before and during the induction of carotenogenesis with glucose or succinate carbon sources. In those studies, differentially abundant proteins (DAPs) were identified by two-dimensional polyacrylamide gel electrophoresis (PAGE) followed by mass spectrometry (MS), and the data were corre-lated with the metabolomic profiles of central metabolic pathways (14,15). These works showed significant differences in the protein profiles related to the time of analysis and carbon source employed.…”