Abstract
Nutrient fluctuations in the cellular environment promote changes in cell metabolism and growth to adapt cell proliferation accordingly. The target of rapamycin (TOR) signalling network plays a key role in the coordination of growth and cell proliferation with the nutrient environment and, importantly, nutrient limitation reduces TOR complex 1 (TORC1) signalling. We have performed global quantitative fitness profiling of the collection of Schizosaccharomyces pombe strains from which non-essential genes have been deleted. We identified genes that regulate fitness when cells are grown in a nutrient-rich environment compared with minimal environments, with varying nitrogen sources including ammonium, glutamate and proline. In addition, we have performed the first global screen for genes that regulate fitness when both TORC1 and TORC2 signalling is reduced by Torin1. Analysis of genes whose deletions altered fitness when nutrients were limited, or when TOR signalling was compromised, identified a large number of genes that regulate transmembrane transport, transcription and chromatin organization/regulation and vesicle-mediated transport. The ability to tolerate reduced TOR signalling placed demands upon a large number of biological processes including autophagy, mRNA metabolic processing and nucleocytoplasmic transport. Importantly, novel biological processes and all processes known to be regulated by TOR were identified in our screens. In addition, deletion of 62 genes conserved in humans gave rise to strong sensitivity or resistance to Torin1, and 29 of these 62 genes have novel links to TOR signalling. The identification of chromatin and transcriptional regulation, nutritional uptake and transport pathways in this powerful genetic model now paves the way for a molecular understanding of how cells adapt to the chronic and acute fluctuations in nutrient supply that all eukaryotes experience at some stage, and which is a key feature of cancer cells within solid tumours.
Highlights
Cell proliferation is exquisitely sensitive to nutrient resources and requires metabolic adaption to meet the demands of dynamic changes in environmental conditions
The target of rapamycin (TOR) protein kinase forms two functionally distinct multi-protein complexes: TOR complex 1 (TORC1) and TOR complex 2 (TORC2), which are defined by unique components highly conserved across species; in mammals Raptor defines mTORC1, while Rictor defines mTORC2 [1]
Schizosaccharomyces pombe has the ability to proliferate on a diverse selection of nutrient environments, including complex ‘rich’ yeast extract with supplements (YES) and defined synthetic minimal medium based on Edinburgh minimal media (EMM) [18,19]
Summary
Cell proliferation is exquisitely sensitive to nutrient resources and requires metabolic adaption to meet the demands of dynamic changes in environmental conditions. Of rapamycin (TOR), a protein kinase, is one of the major energy and nutrient sensors in eukaryotic cells. In fission yeast Schizosaccharomyces pombe Mip defines TORC1 and Ste defines (TORC2) [2,3,4]. In all eukaryotes, it is rapamycin-sensitive TORC1 that is the major nutrient sensor that integrates environmental cues with cell growth and proliferation. Fission yeast TORC2 is not essential for cell proliferation [5], and TORC2 exerts distinct functions by phosphorylating distinct substrates that are required for sexual differentiation, actin organization and dynamics, to name just a few [1,4,5]
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