Protein Science,
Journal Year:
2024,
Volume and Issue:
34(1)
Published: Dec. 11, 2024
H-NS,
a
nucleoid-associated
protein
(NAP)
from
enterobacteria,
regulates
gene
expression
by
dynamically
transducing
environmental
cues
to
conformational
assembly
and
DNA
binding.
In
this
work,
we
show
that
H-NS
Escherichia
coli,
which
can
assemble
into
octameric
tetrameric
oligomerization
states,
forms
spontaneous
micron-sized
liquid-like
condensates
with
at
sub-physiological
concentrations
in
vitro.
The
heterotypic
are
metastable
298
K,
partially
solubilizing
time,
while
still
retaining
their
properties.
display
UCST-like
phase
behavior
higher
temperatures,
but
large
decrease
droplet-assembly
propensities
310
K
ionic
strength.
Condensate
formation
be
tuned
cyclic
manner
between
the
extent
of
reversibility
determined
incubation
highlighting
strong
hysteresis.
An
engineered
phospho-mimetic
variant
(Y61E),
is
dimeric
only
weakly
binds
DNA,
unable
form
condensates.
Y61E
mutant
solubilizes
pre-formed
few
minutes
nearly
an
order
magnitude
speed-up
droplet
dissolution
relative
demonstrating
rapid
molecular
transport
dilute
condensed
phases.
Our
results
establish
intrinsically
tied
not
binding
also
its
phase-separation
tendencies,
showcasing
regulatable
programmable
nature
formed
archetypal
NAP
via
multiple
lifetimes.
Scientific Reports,
Journal Year:
2025,
Volume and Issue:
15(1)
Published: Jan. 19, 2025
Genome
organization
is
important
for
DNA
replication,
gene
expression,
and
chromosome
segregation.
In
bacteria,
two
large
families
of
proteins,
nucleoid-associated
proteins
(NAPs)
SMC
complexes,
play
roles
in
organizing
the
genome.
NAPs
are
highly
abundant
DNA-binding
that
can
bend,
wrap,
bridge,
compact
DNA,
while
complexes
load
onto
chromosome,
translocate
on
extrude
loops.
Although
capable
traversing
entire
bound
by
various
vivo,
it
unclear
whether
translocation
influenced
NAPs.
this
study,
using
Bacillus
subtilis
as
a
model
system,
we
expressed
collection
representative
bacterial
archaeal
introduce
distinct
structures
potentially
pose
different
challenges
movement.
By
fluorescence
microscopy
chromatin
immunoprecipitation,
observed
these
to
genome
characteristic
manners.
Using
genome-wide
conformation
capture
(Hi-C)
assays,
found
complex
traversed
without
slowing
down.
Our
findings
revealed
DNA-loop-extruding
activity
unaffected
exogenously
which
highlights
robustness
motors
busy
chromatin.
Molecular Microbiology,
Journal Year:
2025,
Volume and Issue:
123(2), P. 89 - 100
Published: Feb. 1, 2025
In
September
2023,
the
Biology
and
Physics
of
Prokaryotic
Chromosomes
meeting
ran
at
Lorentz
Center
in
Leiden,
The
Netherlands.
As
part
workshop,
those
attendance
developed
a
series
discussion
points
centered
around
current
challenges
for
field,
how
these
might
be
addressed,
field
is
likely
to
develop
over
next
10
years.
staff
facilitated
discussions
via
tools
aimed
optimizing
productive
interactions.
This
Perspective
article
summary
reflects
state-of-the-art
field.
It
expected
help
colleagues
advancing
their
own
research
related
prokaryotic
chromosomes
inspiring
novel
interdisciplinary
collaborations.
forward-looking
perspective
highlights
open
questions
driving
builds
on
impressive
recent
progress
areas
as
represented
by
accompanying
reviews,
perspectives,
articles
this
issue.
These
underline
multi-disciplinary
nature
multiple
length
scales
which
chromatin
studied
vitro
highlight
differences
similarities
bacterial
archaeal
chromatin-associated
processes.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Feb. 27, 2025
The
regulation
of
ribosomal
RNA
(rRNA)
is
closely
tied
to
nutrient
availability,
growth
phase,
and
global
gene
expression,
serving
as
a
key
factor
in
bacterial
adaptability
pathogenicity.
Mycobacterium
tuberculosis
(Mtb
)
stands
out
from
other
species
with
single
operon
controlled
by
two
promoters:
rrnA
P3
P1
high
ratio
sigma
(σ)
factors
genome
size.
While
the
primary
σ
A
known
drive
transcription,
alternative
B
has
been
proposed
contribute
transcription
housekeeping
genes,
including
rRNA
under
range
conditions.
However,
's
precise
role
remains
unclear.
Here,
we
quantify
steady-state
rates
reconstituted
reactions
establish
that
-mediated
dominates
production
almost
orders
magnitude
minimal
contributions
holoenzymes
and/or
all
conditions
tested.
We
measure
compare
kinetics
individual
initiation
steps
for
both
which,
taken
together
rate
measurements,
lead
us
model
where
exhibit
slower
DNA
unwinding
holoenzyme
recycling.
Our
data
further
demonstrate
CarD
RbpA
reverse
or
buffer
stimulatory
effect
negative
superhelicity
on
respectively.
Lastly,
show
major
determinant
increased
activity
due
its
N-terminal
205
amino
acids.
Taken
together,
our
reveal
intricate
interplay
promoter
sequence,
identity,
superhelicity,
shaping
and,
extension,
Mtb
.
mSystems,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 29, 2025
ABSTRACT
In
starving
Bacillus
subtilis
bacteria
,
the
initiation
of
two
survival
programs—biofilm
formation
and
sporulation—is
controlled
by
same
phosphorylated
master
regulator,
Spo0A~P.
Its
gene,
spo0A,
is
transcribed
from
promoters,
P
v
s,
that
are,
respectively,
regulated
RNA
polymerase
(RNAP)
holoenzymes
bearing
σ
A
H
.
Notably,
transcription
directly
autoregulated
Spo0A
~
binding
sites
known
as
0A1,
0A2,
0A3
box,
located
in
between
promoters.
It
remains
unclear
whether,
at
onset
starvation,
these
boxes
activate
or
repress
spo0A
expression,
whether
transcriptional
feedback
plays
a
role
increase
expression.
Based
on
experimental
data
promoter
activities
under
systematic
perturbation
architecture,
we
developed
biophysical
model
regulation
Spo0A~P
to
each
0A
boxes.
The
predicts
its
does
not
affect
RNAP
recruitment
promoters
but
instead
affects
rate.
Moreover,
effects
are
mainly
repressive
saturated
early
starvation.
Therefore,
expression
driven
holoenzyme
levels.
Additionally,
reveal
affinity
strongest
weakest
0A2
there
attractive
forces
occupied
Our
findings,
addition
clarifying
how
sporulation
regulator
controlled,
offer
framework
predict
regulatory
outcomes
complex
gene-regulatory
mechanisms.
IMPORTANCE
Cell
differentiation
often
critical
for
survival.
bacteria,
decisions
regulators
control.
understanding
transcriptionally
required
understand
differentiation.
However,
many
cases,
underlying
complex,
with
multiple
factor
making
it
challenging
dissect
exact
Here,
address
this
problem
Spo0A.
Using
model,
quantitatively
characterize
effect
individual
promoter.
Furthermore,
allows
us
identify
specific
step
affected
binding.
Such
promising
quantitative
study
wide
range
involved
feedback.
Applied Microbiology,
Journal Year:
2025,
Volume and Issue:
5(1), P. 17 - 17
Published: Feb. 7, 2025
The
transcription
of
genes
and
engineered
circuits
can
deeply
vary
when
inserted
into
different
genomic
loci.
This
unpredictable
performance,
termed
context
sensitivity,
complicates
strain
development.
Although
the
causes
mechanisms
sensitivity
are
emerging,
it
is
poorly
known
how
to
engineer
synthetic
pathways
isolated
from
it.
Using
tools
biology
for
designing
inserting
various
reporter
cassettes
in
Escherichia
coli
genome
RT-qPCR
directly
measuring
gene
transcription,
we
first
surveyed
landscape
at
214
positions
cells
grown
glucose
or
glycerol.
results
show
deep
variations
cassette
with
respect
position
(up
160-fold)
growth
condition
a
30-fold).
We
then
demonstrated
that
this
position-dependent
variability
strongly
reduced
insulated
an
artificial
protein-bound
DNA
loop.
Finally,
measured
two
loop-insulated
positions.
depends
on
relative
orientation
genes,
promoter
strength,
positive
supercoiling.
present
model
suggesting
looping
important
cause
be
used
better
controlling
circuits.
FEBS Letters,
Journal Year:
2024,
Volume and Issue:
unknown
Published: Nov. 24, 2024
DNA
replication
and
RNA
transcription
processes
compete
for
the
same
template
and,
thus,
frequently
collide.
These
transcription–replication
collisions
are
thought
to
lead
genomic
instability,
which
places
a
selective
pressure
on
organisms
avoid
them.
Here,
we
review
predisposing
causes,
molecular
mechanisms,
downstream
consequences
of
(TRCs)
with
strong
emphasis
prokaryotic
model
systems,
before
contrasting
findings
cases
in
eukaryotic
systems.
Current
research
points
structure
as
primary
determinant
steady‐state
TRC
levels
polymerase
regulation
inducer
excess
TRCs.
We
proposed
mechanisms
TRC‐induced
damage,
attempting
clarify
their
mechanistic
requirements.
Finally,
discuss
what
drives
genomes
select
against