Biology Reference
In-Depth Information
Chapter 12
Temporal Partitioning of the Yeast Cellular
Network
Douglas B. Murray, Cornelia Amariei, Kalesh Sasidharan, Rainer Machn
´
,
Miguel A. Aon, and David Lloyd
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 net-
work. 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
,CO
2
and H
2
S; 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 consump-
tion (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 chroma-
D.B. Murray (
*
) • C. Amariei • K. Sasidharan
Institute for Advanced Biosciences, Keio University, Tsuruoka, Japan
e-mail:
dougie@ttck.keio.ac.jp
R. Machn´
Institute for Theoretical Biochemistry, University of Vienna, Vienna, Austria
M.A. Aon
School of Medicine, Johns Hopkins University, Baltimore, MD, USA
e-mail:
maon1@jhmi.edu
D. Lloyd
School of Biosciences, Cardiff University, Wales, UK
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