Science Progress (2006), 89(3)
Subscribers may view full papers here
DNA
supercoiling and bacterial gene expression.
CHARLES
J. DORMAN
ABSTRACT
DNA
in bacterial cells is maintained in a negatively supercoiled state. This
contributes
to the organization of the bacterial nucleoid and also influences
the
global gene expression pattern in the cell through modulatory effects on
transcription.
Supercoiling arises as a result of changes to the linking number
of
the relaxed double-stranded DNA molecule and is set and reset by the
action
of DNA topoisomerases. This process is subject to a multitude of
influences
that are usually summarized as environmental stress. Responsiveness
of
linking number change to stress offers the promise of a mechanism for
the
wholesale adjustment of the transcription programme of the cell as the
bacterium
experiences different environments. Recent data from DNA
microarray
experiments support this proposition. The emerging picture is
one
of DNA supercoiling acting at or near the apex of a regulatory hierarchy
where
it collaborates with nucleoid-associated proteins and transcription
factors
to determine the gene expression profile of the cell.
Keywords: DNA
supercoiling, DNA topoisomerase, DNA gyrase, negative
supercoiling,
positive supercoiling, transcription, nucleoid-associated
proteins,
Fis, IHF, H–NS
The
role of Two-component regulation systems in the
physiology
of the bacterial cell
MARTIJN
BEKKER, M. JOOST TEIXEIRA DE MATTOS AND KLAAS J. HELLINGWERF
ABSTRACT
Two-component
regulation systems (TCRSs) are the dominant type of
signal
transduction system in prokaryotes that are used to inform the cellular
trancriptional
machinery (and additional targets for regulation, like the
motility
apparatus) about actual changes in the extracellular physicochemical
conditions.
We now review their molecular structure and enzymatic
characteristics,
their mutual interactions and its implications, and their role
in
cellular physiology. Specific emphasis is placed on the ArcByA
system, a
representative
of the phosphorelay type of TCRS, and a key player in the
adjustment
of the cellular make-up of enterobacteria in response to alterations
in
the oxygen availability. Also some applied aspects of the TCRSs are
discussed,
i.e. their role as a target to develop new
anti-bacterials and their
application
in biotechnology (or: ‘synthetic biology’).
Keywords: Two-component
system, TCRS, physiology, histidine protein
kinase,
response regulator, antimicrobials, signal transduction, synthetic
biology,
ArcB, oxygen regulation
Deciphering
a complex genetic regulatory network:
the Bacillus subtilis sw protein
and intrinsic
resistance
to antimicrobial compounds
JOHN
D. HELMANN
ABSTRACT
Bacillus
subtilis, a spore-forming soil bacterium, is the preeminent model
system
for the analysis of gene regulation in Gram-positive bacteria. Early
genetic
analyses established that this organism uses alternative sigma (s)
subunits
to reprogram RNA polymerase to activate genes required for
growth
phase transitions, motility, general stress response, and sporulation.
Unexpectedly,
the genome sequence predicts the presence of an additional
seven
s subunits: all members of the extracytoplasmic
function (ECF) s
subfamily
of regulators that typically respond to cell envelope stresses. Here,
we
review our current understanding of one of these s factors,
sW, with an
emphasis
on experimental strategies and approaches. Exposure to cell
envelope
active antibiotics and toxic peptides triggers a signaling cascade
that
releases sW from its cognate anti-s thereby
allowing transcription of
~60
sW-dependent genes. These genes encode proteins
that inactivate,
sequester,
or eliminate toxic compounds from the cell.
Keywords: gene
regulation, transcription, RNA polymerase, sigma, cell
wall,
antibiotic, bacteriocin, genomics, microarray
Variations
on a theme: diverse N-acyl homoserine
lactone-mediated quorum sensing mechanisms in
Gram-negative bacteria
DEBRA
SMITHa, JIN-HONG WANGb,
JANE E. SWATTONa,
PETER
DAVENPORTa, BIANCA PRICEa,
HELGA MIKKELSENa,
HANNAH
STICKLANDa, KAHOKO NISHIKAWAa,c,
NOE´MIE
GARDIOLa,
DAVID R. SPRINGd AND MARTIN WELCHa
ABSTRACT
Many
Gram-negative bacteria employ a mechanism of cell – cell communication
known
as quorum sensing (QS). The role of QS is to enable the cells in a
culture
to coordinate their gene expression profile with changes in the
population
cell density. The best characterized mechanisms of QS employ
N-acylated
homoserine lactones (AHLs) as signalling molecules. These
AHLs
are made by enzymes known as LuxI homologs, and accumulate in
the
culture supernatant at a rate proportional to the increase in cell density.
Once
the AHL concentration exceeds a certain threshold value, these ligands
bind
to intracellular receptors known as LuxR homologs. The latter are
transcriptional
regulators, whose activity alters upon binding the AHL
ligand,
thereby eliciting a change in gene transcription. Over the last five
years,
it has become increasingly obvious that this is a rather simplistic view
of
AHL-dependent QS, and that in fact, there is considerable diversity in the
way
in which LuxI-R homologs operate. The aim of the current review is to
describe
these variations on the basic theme, and to show how functional
genomics
is revolutionizing our understanding of QS-controlled regulons.
Keywords: N-acyl
homoserine lactones, biofilms, cell-cell
communication,
LuxI, LuxR, quorum sensing, signal transduction