Diverse Two-Dimensional Input Functions Control Bacterial Sugar Genes

Shai Kaplan, Anat Bren*, Alon Zaslaver, Erez Dekel, Uri Alon

*Corresponding author for this work

Research output: Contribution to journalArticlepeer-review

111 Scopus citations

Abstract

Cells respond to signals by regulating gene expression. The relation between the level of input signals and the transcription rate of the gene is called the gene's input function. Because most genes are regulated by more than one signal, the input functions are usually multidimensional. To understand cellular responses, it is essential to know the shapes of these functions. Here, we map the two-dimensional input functions of 19 sugar-utilization genes at high resolution in living E. coli cells. We find diverse, intricately shaped input functions, despite the similarity in the regulatory circuitry of these genes. Surprisingly, some of the input functions are nonmonotonic, peaking at intermediate signal levels. Furthermore, most of the input functions show separation of variables, in the sense that they can be described as the product of simple functions that depend on a single input. This first broad survey of two-dimensional input functions can be extended to map the logic of gene regulation in other systems.

Original languageAmerican English
Pages (from-to)786-792
Number of pages7
JournalMolecular Cell
Volume29
Issue number6
DOIs
StatePublished - 28 Mar 2008
Externally publishedYes

Bibliographical note

Funding Information:
We thank the US National Institutes of Health, Israel Science Foundation, Minerva, the Human Frontier Science Program, and the Kahn Family Foundation for support. S.K. is supported by Yeshaya Horowitz association through the Center for Complexity Science.

Keywords

  • DNA
  • SYSBIO

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