A genome-wide analysis of carbon catabolite repression in Schizosaccharomyces pombe

Abstract

Background Optimal glucose metabolism is central to the growth and development of cells. In microbial eukaryotes, carbon catabolite repression (CCR) mediates the preferential utilization of glucose, primarily by repressing alternate carbon source utilization. In fission yeast, CCR is mediated by transcriptional repressors Scr1 and the Tup/Ssn6 complex, with the Rst2 transcription factor important for activation of gluconeogenesis and sexual differentiation genes upon derepression. Through genetic and genome-wide methods, this study aimed to comprehensively characterize CCR in fission yeast by identifying the genes and biological processes that are regulated by Scr1, Tup/Ssn6 and Rst2, the core CCR machinery. Results The transcriptional response of fission yeast to glucose-sufficient or glucose-deficient growth conditions in wild type and CCR mutant cells was determined by RNA-seq and ChIP-seq. Scr1 was found to regulate genes involved in carbon metabolism, hexose uptake, gluconeogenesis and the TCA cycle. Surprisingly, a role for Scr1 in the suppression of sexual differentiation was also identified, as homothallic scr1 deletion mutants showed ectopic meiosis in carbon and nitrogen rich conditions. ChIP-seq characterised the targets of Tup/Ssn6 and Rst2 identifying regulatory roles within and independent of CCR. Finally, a subset of genes bound by all three factors was identified, implying that regulation of certain loci may be modulated in a competitive fashion between the Scr1, Tup/Ssn6 repressors and the Rst2 activator. Conclusions By identifying the genes directly and indirectly regulated by Scr1, Tup/Ssn6 and Rst2, this study comprehensively defined the gene regulatory networks of CCR in fission yeast and revealed the transcriptional complexities governing this system. Electronic supplementary material The online version of this article (10.1186/s12864-019-5602-8) contains supplementary material, which is available to authorized users.

Adaptation to Industrial Stressors Through Genomic and Transcriptional Plasticity in a Bioethanol Producing Fission Yeast Isolate

“…The Wilmar production isolate (Wilmar-P) was derived from an ancestral wild S. pombe strain (Wilmar-A) that was adapted for industrial use via repeated passaging through molasses fermentations ( Figure 1A). Given that carbon utilization is key to bioethanol production (Mohd Azhar et al 2017), we examined differences in the growth patterns of Wilmar-A and Wilmar-P to laboratory S. pombe and to mutants deficient in carbon catabolite repression (CCR), the predominant carbon-responsive transcriptional regulatory mechanism in S. pombe (Vassiliadis et al 2019). Wilmar-P and scr1 showed slightly improved growth compared to laboratory S. pombe Wilmar-A and scr1 tup11 tup12 strains when cultured at the optimal growth temperature of 32°C ( Figure 1B).…”

“…In contrast, the CCR mutants showed no appreciable growth on molasses. Given that sucrose is the primary carbon source within molasses (Jain and Venkatasubramanian 2017;Wythes et al 1978) and the CCR mutants are derepressed for inv1 + , which encodes the predominant sucrose invertase in S. pombe (Tanaka et al 1998;Vassiliadis et al 2019), this result suggests that factors other than sucrose metabolism are more important for successful growth on molasses. To simulate heat stress conditions which can occur during industrial fermentations, we repeated the experiment at 37°C.…”

“…To confirm the effect of these gene loss events on transcription, we performed RNA sequencing (RNA-seq) for Wilmar-A and Wilmar-P grown in glucose-sufficient (YES 3% glucose), glucosedeficient (YES 3% glycerol + 0.1% glucose) and glucose-starved (YES 3% glycerol) conditions and compared the expression of the coding regions overlapping regions of low coverage to previous RNA-seq data generated for laboratory S. pombe under the same conditions (Vassiliadis et al 2019). With few exceptions, most genes predicted as lost showed no evidence of expression in Wilmar-A or Wilmar-P in any condition confirming their absence in the Wilmar background ( Figure 3C).…”

“…In contrast, genes encoding ribosomal subunits and several transmembrane transporters including caf5 + (caffeine transport & drug efflux), amt1 + (ammonium transport) and nic1 + (heavy metal ion transport) were enriched in the glucose-starved condition. S. pombe is sensitive to nutrient deficient conditions and will undergo mating and meiosis in carbon or nitrogen deficient conditions (Mata et al 2007;Vassiliadis et al 2019). These results indicate that mating and meiosis pathways are more active in Wilmar-P growing in glucose-deficient conditions relative to laboratory S. pombe.…”

“…The RNA-seq data on laboratory media and molasses suggested improved carbon utiilisation within the Wilmar-P strain consistent with our earlier growth assays ( Figure 1B, 1C). Therefore, we further investigated the regulation of carbon metabolism pathway genes in Wilmar-P. Several previously defined targets of Scr1 (Vassiliadis et al 2019), a transcriptional repressor of carbon source utilisation genes in S. pombe, were among the differentially expressed genes in Wilmar-P on glucose or molasses ( Figure S7A). To investigate potential alterations to the Scr1 regulatory network in Wilmar-P globally, we tagged Scr1 with a tandem affinity purification (TAP) tag in laboratory S. pombe and Wilmar-P cells, and performed chromatin immunoprecipitation sequencing (ChIP-seq) on laboratory S. pombe and Wilmar-P Scr1-TAP cells cultured in YES + glucose or molasses conditions.…”