E.coli aerobic/anaerobic switch study

1
E.coli aerobic/anaerobic switch study

• Chao Wang, Mar 1 2006

2
The bacterium E. coli possesses a large number of
sensing/regulation systems for rapid response to
environmental changes. Those regulation systems
allow variation in the way electrons are
channeled from donor to terminal acceptors such
that the overall potential difference is
maximized for any given growth condition. The
adaptive responses are coordinated by a group of
global regulators, which includes the one
component furmarate nitrate reduction (FNR)
protein, and the two-component anoxic redox
control (Arc) system. With the initial onset of
anaerobiosis ArcA is activated, and if these
conditions persist or become more anaerobic, FNR
is activated leading in turn to the upregulation
of ArcA and amplification of its effect
3
Fnr Modulon Fnr is a global transcription
regulator with similarity to CRP it has 4 Cys
residues that have been shown to bind a 4Fe-4S
cluster under some conditions and 2 2Fe-2S
centers under other conditions. Hence, a
redox-sensitive confirmational change can occur
that mediates control of transcription of 30
transcription units and gt70 genes. For nitrate
reductase, Fnr only potentiates expression.
Nitrate must be present to relieve repression by
NarX/NarL two component sensor-regulator system.
4
ArcA/B Modulon In this system, ArcB is the
sensor kinase, and is a membrane-bound protein
found in the cytoplasmic membrane. ArcA is the
response regulator of the system and is a
DNA-binding transcriptional regulator. The
signal that causes autophosphorylation of ArcB
and phosphotransfer to ArcA is not known, but is
presumed to be either the proton motive force or
a redox signal, possibly the redox state of the
quinone pool. Target genes include those
encoding quinol oxidase, succinate dehydrogenase,
superoxide dismutase and many others involved in
aerobic metabolism and energy production.
5
Metabolic network This system of connected
chemical reactions is a metabolic network. The
raw metabolic data collected at KEGG consist of a
detailed list of biochemical reactions. Besides
annotations for genes and genomes, KEGG contains
comprehensive information on biochemical
reactions, enzymes, and pathways.
Transcriptional Regulation Network Transcriptio
nal regulation is the mechanism that coordinates
the expression of genetic information coded on
the DNA with the needs of various life processes.
The regulation of transcription factors and
non-TF transcription units form a network of
transcriptional regulation. Gene Expression
Data The genome-scale cDNA microarray experiment
measures the expression differences under
different conditions for virtually all genes of
an organism.
6
To understand metabolic and transcriptional
regulation networks in term of their function in
the organism. One proper example in this respect
is the transcription regulated response of an E.
coli cell to oxygen availability.
7
Flux Balance Analysis of Metabolic Network Flux
balance analysis or FBA, is to find the flux for
each reaction in the network by linear
programming.
Mass balance equations accounting for all
reactions and transport mechanisms are written
for each species. These equations are then
rewritten in matrix form. At steady state, this
reduces to S V0.
8
Genetic network assisted flux balance analysis
9
Xoygen and redox sensing pathways in E.coli
10
Major central metabolic pathways
11
Main constituents of the Fnr ArcA/B regulon that
impact major metabolites
12
Major anaerobic and aerobic pathways
13
Fnr and AcrA have a set of overlapping target
genes. Mapping out this set of genes on the
metabolic net and combining some experimental
knowledge from literatures, we may learn more
about the crucial pathways. In Sans study,
only two state (O2 and O2) were investigated.
With glucose and oxygen as the controlling
variables, we want to characterize a continuous
activity of target enzymes, metabolites and
reactions. And using PhPP analysis, we may reveal
some phases about the changes in flux pattern.
With varying oxygen content, which are
different conditions, genes have different
expressions. We can map these involved genes to
proposed pathways. We can study the relation
among the expression, transcription regulation
and metabolic activities.
14
The End