Temporal Partitioning of the Yeast Cellular Network

Abstract

A plethora of data is accumulating from high throughput methods on metabolites, coenzymes, proteins, lipids and nucleic acids and their interactions as well as the signalling and regulatory functions and pathways of the cellular network. The frozen moment viewed in a single discrete time sample requires frequent repetition and updating before any appreciation of the dynamics of component interaction becomes possible. Even then in a sample derived from a cell population, time-averaging of processes and events that occur in out-of-phase individuals blur the detailed complexity of single cell. Continuously grown cultures of yeast spontaneously self-synchronise and provide resolution of detailed temporal structure. Continuous online monitoring (O-2 electrode and membrane-inlet mass spectrometry for O-2, CO2 and H2S; direct fluorimetry for NAD(P) H and flavins) gives dynamic information from timescales of minutes to hours. When these data are supplemented with mass spectrometry-based metabolomics and transcriptomics, the predominantly oscillatory behaviour of network components becomes evident, where respiration cycles between increased oxygen consumption (oxidative phase) and decreased oxygen consumption (reductive phase). This ultradian clock provides a coordinating function that links mitochondrial energetics and redox balance to transcriptional regulation, mitochondrial structure and organelle remodelling, DNA duplication and chromatin dynamics. Ultimately, anabolism and catabolism become globally partitioned: mediation is by direct feedback loops between the energetic and redox state of the cell and chromatin architecture via enzymatic co-factors and co-enzymes. Multi-oscillatory outputs were observed in dissolved gases with 12-h, 40-min and 4-min periods, and statistical self-similarity in Power Spectral and Relative Dispersional analyses: i.e. complex non-linear behaviour and a functional scale-free network operating simultaneously on several timescales. Fast sampling (at 10 or 1 Hz) of NAD(P) H fluorescence revealed subharmonic components of the 40-min signal at 20,10 and 3-5 min. The latter corresponds to oscillations directly observed and imaged by 2-photon microscopy in surface-attached cells. Signalling between time domains is suggested by studies with protonophore effectors of mitochondrial energetics. Multi-oscillatory states impinge on the complex reactome (where concentrations of most chemical species oscillate) and network functionality is made more comprehensible when in vivo time structure is taken into account.