Functional and regulatory profiling of energy metabolism in fission yeast

The control of energy metabolism is fundamental for cell growth and function, and anomalies are implicated in complex diseases and ageing. Metabolism in yeast cells can be easily manipulated by supplying different carbon sources: on glucose yeast rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration. Fission yeast, unlike the remotely related budding yeast, has scarcely been used to study energy metabolism, although it features attractive mitochondrial and metabolic properties to make it a promising complementary model system. We screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth, which were enriched for mitochondrial functions. The presence of auxotrophic mutants strongly influenced the outcome of the genetic screens, and most genes uncovered here have not been implicated in respiration in budding yeast. We also applied gene expression profiling approaches to compare steady-state fermentative and respiratory growth and to analyse the dynamic adaptation to respiratory growth. Remarkably little overlap was evident between the genes identified in the functional screens and the genes regulated in response to different carbon sources. The transcript levels of most genes functioning in key energy metabolism pathways were coherently tuned, reflecting anticipated differences in metabolic flows between fermenting and respiring cells. We show that the acetyl-CoA synthase, rather than the citrate lyase, is essential for acetyl-CoA synthesis in fission yeast. We also investigated the transcriptional response to mitochondrial damage by genetic or chemical perturbations, defining a retrograde response that involves the concerted regulation of distinct groups of nuclear genes that may avert harm by mitochondrial malfunction. These systematic and targeted analyses provide a rich framework of the genetic and regulatory basis of fundamental metabolic states to guide future studies on energy metabolism in fission yeast and beyond.