Document Detail


Free energy rhythms in Saccharomyces cerevisiae: a dynamic perspective with implications for ribosomal biogenesis.
MedLine Citation:
PMID:  23379300     Owner:  NLM     Status:  MEDLINE    
Abstract/OtherAbstract:
To describe the time course of cellular systems, we integrate ideas from thermodynamics and information theory to discuss the work needed to change the state of the cell. The biological example analyzed is experimental microarray transcription level oscillations of yeast in the different phases as characterized by oxygen consumption. Surprisal analysis was applied to identify groups of transcripts that oscillate in concert and thereby to compute changes in free energy with time. Three dominant transcript groups were identified by surprisal analysis. The groups correspond to the respiratory, early, and late reductive phases. Genes involved in ribosome biogenesis peaked at the respiratory phase. The work to prepare the state is shown to be the sum of the contributions of these groups. We paid particular attention to work requirements during ribosomal building, and the correlation with ATP levels and dissolved oxygen. The suggestion that cells in the respiratory phase likely build ribosomes, an energy intensive process, in preparation for protein production during the S phase of the cell cycle is validated by an experiment. Surprisal analysis thereby provided a useful tool for determining the synchronization of transcription events and energetics in a cell in real time.
Authors:
A Gross; Caroline M Li; F Remacle; R D Levine
Publication Detail:
Type:  Journal Article; Research Support, N.I.H., Extramural; Research Support, Non-U.S. Gov't     Date:  2013-02-20
Journal Detail:
Title:  Biochemistry     Volume:  52     ISSN:  1520-4995     ISO Abbreviation:  Biochemistry     Publication Date:  2013 Mar 
Date Detail:
Created Date:  2013-03-05     Completed Date:  2013-04-22     Revised Date:  2014-03-06    
Medline Journal Info:
Nlm Unique ID:  0370623     Medline TA:  Biochemistry     Country:  United States    
Other Details:
Languages:  eng     Pagination:  1641-8     Citation Subset:  IM    
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MeSH Terms
Descriptor/Qualifier:
Biological Clocks*
Computer Simulation
Gene Expression Regulation, Fungal*
Information Theory
Models, Biological
Oxygen Consumption
Ribosomes / genetics*,  metabolism
Saccharomyces cerevisiae / cytology,  genetics*,  metabolism
Saccharomyces cerevisiae Proteins / genetics,  metabolism
Thermodynamics
Transcription, Genetic
Grant Support
ID/Acronym/Agency:
R01 GM081757/GM/NIGMS NIH HHS; R01 GM81757/GM/NIGMS NIH HHS
Chemical
Reg. No./Substance:
0/Saccharomyces cerevisiae Proteins
Comments/Corrections

From MEDLINE®/PubMed®, a database of the U.S. National Library of Medicine


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