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BACKGROUND
E. coli is a free living, gram negative bacterium which colonizes
the lower gut of animals. Since it is a model organism, a lot of
experimental data is available. Furthermore, the complete
genome sequence (Blattner et al., 1997) of this microbe has
enormously helped to integrate a vast amount of biological
information. In this work we analyse an important class of
molecules namely transcription factors which regulate gene
expression. We study their domain architecture to understand
their evolution, their regulatory function as transcriptional
activators or repressors and the evolution of the regulatory
network.
DOMAINS are the structural and evolutionary unit of proteins
as defined in the SCOP database (Murzin et al., 1995) and a
FAMILY is a set of related domains which originated from a
common ancestor.
OBJECTIVES
What are the different protein families that
constitute the E. coli transcription factors?
Are regulatory functions related to domain
architecture or binding site position?
How complex is the gene regulatory network
in E. coli and how did it evolve?
RESULTS
There are 11 different DNA-binding domain (DBD) families and
46 different partner domains in 271 transcription factors (TFs)
On average each TF has 2 domains: one DBD and a
partner domain which is generally a control domain
73% of the TFs have arisen by gene duplication
Position of the TF binding site is the determining factor for
activation or repression rather than the DBD type, partner
domain or domain architecture
Transcription factors vary in the number of genes they
regulate. The dominant transcription factors that regulate
the largest number of genes also regulate the largest
number of TFs to amplify their influence
1/3 of the interactions have homologous transcription
factors that share a set of regulated genes or regulated
genes that share a set of transcription factors. This suggests
that duplication is a major mechanism in the
growth of the gene regulatory network
Domain Architectures of E. coli TFs
271 TFs have 74 distinct domain architecture
73% of E. coli TFs have arisen by gene duplication
Activators, Repressors and Dual
Regulators
Domain architecture, DNA
binding domain or partner
domain type is NOT indicative of
the regulatory function
Distance of the TF binding site
from the transcription start site is
the determining factor
33% of repressor binding sites
occur after the transcription start
site