Transcription factor concentrations versus binding site affinities in the yeast S. cerevisiae

Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics, and the binding to functional sites must be controlled with a certain specificity for living organisms to be able to elicit s...

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Bibliographic Details
Published in:Physical biology 2007-06, Vol.4 (2), p.134-143
Main Authors: Aurell, Erik, d'Hérouël, Aymeric Fouquier, Malmnäs, Claes, Vergassola, Massimo
Format: Article
Language:English
Subjects:
Binding Sites
Biological physics
Biologisk fysik
Biophysics - methods
Cell Cycle
Condensed matter physics
DNA - chemistry
DNA INTERACTION
ESCHERICHIA-COLI
EXPRESSION
FACILITATED TARGET LOCATION
Fungal Proteins
Fysik
Gene Expression Regulation, Fungal
GENE-REGULATION
Kondenserade materiens fysik
Models, Biological
Models, Statistical
Models, Theoretical
NATURAL SCIENCES
NATURVETENSKAP
NETWORK MOTIFS
NUMBERS
Physics
PROTEIN
Protein Binding
REGULATORY NETWORK
Saccharomyces cerevisiae - metabolism
SINGLE-CELL
Software
Transcription Factors - metabolism
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Summary:Transcription regulation is largely governed by the profile and the dynamics of transcription factors' binding to DNA. Stochastic effects are intrinsic to this dynamics, and the binding to functional sites must be controlled with a certain specificity for living organisms to be able to elicit specific cellular responses. Specificity stems here from the interplay between binding affinity and cellular abundance of transcription factor proteins, and the binding of such proteins to DNA is thus controlled by their chemical potential. We combine large-scale protein abundance data in the budding yeast with binding affinities for all transcription factors with known DNA binding site sequences to assess the behavior of their chemical potentials in an exponential growth phase. A sizable fraction of transcription factors is apparently bound non-specifically to DNA, and the observed abundances are marginally sufficient to ensure high occupations of the functional sites. We argue that a biological cause of this feature is related to its noise-filtering consequences: abundances below physiological levels do not yield significant binding of functional targets and mis-expressions of regulated genes may thus be tamed.
ISSN:1478-3975
1478-3975
DOI:10.1088/1478-3975/4/2/006