Functional and regulatory profiling of energy metabolism in fission yeast

Abstract

BackgroundThe control of energy metabolism is fundamental for cell growth and function and anomalies in it are implicated in complex diseases and ageing. Metabolism in yeast cells can be manipulated by supplying different carbon sources: yeast grown on glucose rapidly proliferates by fermentation, analogous to tumour cells growing by aerobic glycolysis, whereas on non-fermentable carbon sources metabolism shifts towards respiration.ResultsWe screened deletion libraries of fission yeast to identify over 200 genes required for respiratory growth. Growth media and auxotrophic mutants strongly influenced respiratory metabolism. Most genes uncovered in the mutant screens have not been implicated in respiration in budding yeast. We applied gene-expression profiling approaches to compare steady-state fermentative and respiratory growth and to analyse the dynamic adaptation to respiratory growth. The transcript levels of most genes functioning in energy metabolism pathways are coherently tuned, reflecting anticipated differences in metabolic flows between fermenting and respiring cells. We show that acetyl-CoA synthase, rather than 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 from mitochondrial malfunction.ConclusionsThis study provides a rich framework of the genetic and regulatory basis of energy metabolism in fission yeast and beyond, and it pinpoints weaknesses of commonly used auxotroph mutants for investigating metabolism. As a model for cellular energy regulation, fission yeast provides an attractive and complementary system to budding yeast.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-016-1101-2) contains supplementary material, which is available to authorized users.

Mitochondrial respiration is required to provide amino acids during fermentative proliferation of fission yeast

“…We have shown that antimycin A, an inhibitor of the respiratory chain, slows down the growth of S. pombe cells in defined minimal medium, but much less so in rich yeast extract medium with the same glucose concentration [35] (Fig. S1A).…”

“…The S. pombe laboratory strain is part of a group of natural isolates that show higher respiration during fermentative growth, which is caused by a naturally occurring mutation in pyruvate kinase that limits glycolytic flux [34]. We have also reported that respiration is required for rapid cell proliferation during fermentation [35]. Here we define the respiratory functions in fission yeast that support rapid proliferation.…”

A natural variant of the sole pyruvate kinase of fission yeast lowers glycolytic flux triggering increased respiration and oxidative-stress resistance but decreased growth

“…The pdc101 and atd1 genes, on the other hand, were expressed more highly in the A-strain. These genes encode pyruvate decarboxylase and aldehyde dehydrogenase, respectively, and their induction is consistent with higher glycolytic flux and increased fermentation 29 . These expression changes are consistent with the central role of PYK in glycolysis and the observed metabolic effects mediated by the Pyk1 variants.…”

“…Resistance to antimycin A, which blocks the respiratory chain by inhibiting ubiquinol-cytochrome c oxidoreductase 42 , was used as a proxy readout for cellular dependence on oxidative phosphorylation. The standard laboratory strain 972 hshows a moderate reduction in maximum growth rate and biomass yield in this condition 29,43 . We applied a colony-based assay to determine relative fitness of each strain in rich glucose media with and without antimycin A.…”

“…S. cerevisiae cells without mitochondrial genome, and thus without respiratory capacity, feature a 'petite', slow-growth phenotype 25 . S. pombe cannot normally grow without a mitochondrial genome [26][27][28] , and blocking oxidative phosphorylation with antimycin A leads to moderate or strong growth inhibition, respectively, in rich or minimal glucose media 29 . In glucose-limiting conditions, such as stationary phase, the metabolism of yeast cells is reconfigured towards respiration 30,31 .…”