title: Regulation of yeast oscillatory dynamics.
abstract: When yeast cells are grown continuously at high cell density, a respiratory oscillation percolates throughout the population. Many essential cellular functions have been shown to be separated temporally during each cycle; however, the regulatory mechanisms involved in oscillatory dynamics remain to be elucidated. Through GC-MS analysis we found that the majority of metabolites show oscillatory dynamics, with 70% of the identified metabolite concentrations peaking in conjunction with NAD(P)H. Through statistical analyses of microarray data, we identified that biosynthetic events have a defined order, and this program is initiated when respiration rates are increasing. We then combined metabolic, transcriptional data and statistical analyses of transcription factor activity, identified the top oscillatory parameters, and filtered a large-scale yeast interaction network according to these parameters. The analyses and controlled experimental perturbation provided evidence that a transcriptional complex formed part of the timing circuit for biosynthetic, reductive, and cell cycle programs in the cell. This circuitry does not act in isolation because both have strong translational, proteomic, and metabolic regulatory mechanisms. Our data lead us to conclude that the regulation of the respiratory oscillation revolves around coupled subgraphs containing large numbers of proteins and metabolites, with a potential to oscillate, and no definable hierarchy, i.e., heterarchical control.
authors.affiliation: ERATO-SORST Kitano Symbiotic Systems Project, Japan Science and Technology Agency, 9S3 Shinanomachi Research Park, Keio University School of Medicine, 35 Shinanomachi, Tokyo 160-8582, Japan. dougie@symbio.jst.go.jp
authors.forename: Douglas B
authors.initials: DB
authors.lastname: Murray
authors.forename: Manfred
authors.initials: M
authors.lastname: Beckmann
authors.forename: Hiroaki
authors.initials: H
authors.lastname: Kitano
mesh_terms: D000596:Amino Acids / Q000096:biosynthesis; D001683:Biological Clocks; D053898:Biosynthetic Pathways; D008401:Gas Chromatography-Mass Spectrometry; D053858:Metabolic Networks and Pathways; D009249:NADP / Q000032:analysis; D014157:Transcription Factors / Q000032:analysis; D015003:Yeasts / Q000166:cytology* / Q000378:metabolism*
chemical_list: D000596:Amino Acids; D014157:Transcription Factors; D009249:NADP