Diverse two-dimensional input functions control bacterial sugar genes.
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.
Kaplan
Shai
S
Department of Molecular Cell Biology, Weizmann Institute of Science, Rehovot 76100, Israel.
Bren
Anat
A
Zaslaver
Alon
A
Dekel
Erez
E
Alon
Uri
U
D001426:Bacterial Proteins / Q000235:genetics / Q000378:metabolism; D002241:Carbohydrates / Q000235:genetics* / Q000502:physiology; D004926:Escherichia coli / Q000235:genetics* / Q000502:physiology; D015964:Gene Expression Regulation, Bacterial; D005798:Genes, Bacterial; D009005:Monosaccharides / Q000378:metabolism; D015398:Signal Transduction; D014157:Transcription Factors / Q000378:metabolism; D014158:Transcription, Genetic
D001426:Bacterial Proteins; D002241:Carbohydrates; D009005:Monosaccharides; D014157:Transcription Factors