Biology Reference
In-Depth Information
Gilles-Gonzalez &Gonzalez, 1993; Iniesta, Hillson, & Shapiro, 2010; Sousa,
Tuckerman, Gondim, Gonzalez, & Gilles-Gonzalez, 2013; Virts, Stanfield,
Helinski, & Ditta, 1988
); and (iii) modulation of the local concentration of
the second messenger cyclic-di-GMP by the concerted activity of DGCs
and phosphodiesterases (PDEs), for example, haem-containing phosphodi-
esterase A1 (PDEA1), DOS, and GCS proteins (
Chang et al., 2001;
Delgado-Nixon, Gonzalez, & Gilles-Gonzalez, 2000; Sasakura et al.,
2002; Tal et al., 1998; Weinhouse et al., 1997; Zhao, Brandish,
Ballou, & Marletta, 1999
).
Each one of these families has been studied during the past years and data
are available on their activity pathways and their protein structures.
2.2.1 Regulation of gene expression via protein
-
DNA interaction
The first mechanism that can influence the expression of selected genes is the
direct interaction between the transcription regulator and the gene pro-
moter. When a certain group of genes is regulated, a univocal recognition
between the protein and the DNA sequence occurs. The haem-based sen-
sors that regulate gene expression are activated, or inactivated, upon binding
of a given diatomic gas. Therefore, the nature and the concentration of the
gas is the signal that triggers gene-transcription.
2.2.1.1 The carbon monoxide oxidation activator
The CooA is a transcription regulator first reported in
Rhodospirillum rubrum
(
Rr
CooA) whose action is specifically activated upon binding of CO
(
Shelver, Kerby, He, & Roberts, 1995; Shelver et al., 1997; Uchida
et al., 1998
). In the presence of CO, it activates the expression of enzymes
involved in the CO oxidation pathway by direct binding to specific DNA
regions (
Aono et al., 1996; He et al., 1996
).
Evolutionary studies on the CooA coding sequence identified homology
with the cyclic-AMP receptor protein (CRP) family, in particular with
CRP (28% identity and 51% similarity) and FNR (18% identity and 45%
similarity) from
Escherichia coli
(
Shelver et al., 1995
).
In vivo
and
in vitro
studies show that CooA alone is sufficient to activate
the RNA polymerase (RNAP) and to start the DNA transcription process;
no other factors are required. The interaction between CooA and the
RNAP happens at the level of the C-terminal domain of the
a
subunit of
the polymerase (
He et al., 1999
) and is mediated by Glu167, a key residue
in the E-helix of CooA (
Youn, Thorsteinsson, Conrad, Kerby, &
Roberts, 2005
).
