bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Дек. 2, 2023
Abstract
Optogenetics
is
a
powerful
tool
for
spatiotemporal
control
of
gene
expression.
Several
light-inducible
regulators
have
been
developed
to
function
in
bacteria,
and
these
regulatory
circuits
ported
into
new
host
strains.
Here,
we
adapted
red
transcription
factor
Shewanella
oneidensis
.
This
circuit
based
on
the
iLight
optogenetic
system,
which
controls
expression
using
light.
Promoter
engineering
thermodynamic
model
were
used
adapt
this
system
achieve
differential
light
dark
conditions
within
S.
strain.
We
further
improved
by
adding
repressor
invert
genetic
activate
under
illumination.
The
inverted
was
extracellular
electron
transfer
(EET)
ability
use
both
blue
light-induced
simultaneously
demonstrated.
Our
work
expands
synthetic
biology
toolbox
,
could
facilitate
future
advances
applications
with
electrogenic
bacteria.
ACS Synthetic Biology,
Год журнала:
2025,
Номер
unknown
Опубликована: Май 6, 2025
Optogenetics
has
emerged
as
a
powerful
tool
for
regulating
cellular
processes
due
to
its
noninvasive
nature
and
precise
spatiotemporal
control.
Far-red
light
(FRL)
increasingly
been
used
in
the
optogenetic
control
of
mammalian
cells
low
toxicity
high
tissue
penetration.
However,
robust
orthogonal
FRL
sensors
are
lacking
bacteria.
Here,
we
established
an
sensor
Escherichia
coli
with
maximum
dynamic
range
exceeding
230-fold
based
on
RfpA-RfpC-RfpB
(RfpABC)
signaling
system
that
regulates
far-red
photoacclimation
(FaRLiP)
cyanobacteria.
We
identified
conserved
DNA
motif
promoter
sequences
Chl
f
synthase
gene
other
genes
FaRLiP
clusters,
termed
light-regulatory
(FLR)
motif,
which
enables
light-responsive
activation
expression
through
interaction
RfpB.
Based
FLR
simplified
FLR-containing
promoters
characterized
their
abilities
ranges,
can
be
utilized
different
synthetic
biology
scenarios.
Additionally,
one
or
two
motifs
present
at
loci
within
cluster,
providing
further
FRL-inducible
resources.
The
exhibits
effective
suppression
under
low-intensity
white
light,
respectively,
remains
functional
darkness.
In
conclusion,
this
study
advances
understanding
regulatory
mechanisms
cyanobacteria
provides
applications.
ACS Synthetic Biology,
Год журнала:
2022,
Номер
11(10), С. 3482 - 3492
Опубликована: Сен. 21, 2022
Sensory
photoreceptors
mediate
numerous
light-dependent
adaptations
across
organisms.
In
optogenetics,
achieve
the
reversible,
non-invasive,
and
spatiotemporally
precise
control
by
light
of
gene
expression
other
cellular
processes.
The
light-oxygen-voltage
receptor
PAL
binds
to
small
RNA
aptamers
with
sequence
specificity
upon
blue-light
illumination.
By
embedding
responsive
aptamer
in
ribosome-binding
genes
interest,
their
can
be
downregulated
light.
We
developed
pCrepusculo
pAurora
optogenetic
systems
that
are
based
on
allow
down-
upregulate,
respectively,
bacterial
using
blue
Both
realized
as
compact,
single
plasmids
exhibit
stringent
responses
low
basal
activity
up
several
10-fold
dynamic
range.
As
exerts
at
level,
it
combined
circuits
transcription
initiation.
integrating
regulatory
mechanisms
operating
DNA
mRNA
levels,
emergent
properties
thus
devised.
a
case
point,
pEnumbra
setup
permits
upregulate
under
moderate
whereas
strong
shuts
off
again.
Beyond
providing
novel
signal-responsive
for
diverse
applications
biotechnology
synthetic
biology,
our
work
also
illustrates
how
PAL-aptamer
interaction
harnessed
interrogation
RNA-based
ACS Synthetic Biology,
Год журнала:
2024,
Номер
13(5), С. 1467 - 1476
Опубликована: Май 2, 2024
Optogenetics
is
a
powerful
tool
for
spatiotemporal
control
of
gene
expression.
Several
light-inducible
regulators
have
been
developed
to
function
in
bacteria,
and
these
regulatory
circuits
ported
new
host
strains.
Here,
we
adapted
red-light-inducible
transcription
factor
Shewanella
oneidensis.
This
circuit
based
on
the
iLight
optogenetic
system,
which
controls
expression
using
red
light.
A
thermodynamic
model
promoter
engineering
were
used
adapt
this
system
achieve
differential
light
dark
conditions
within
S.
oneidensis
strain.
We
further
improved
by
adding
repressor
invert
genetic
activate
under
illumination.
The
inverted
was
extracellular
electron
transfer
ability
use
both
red-
blue-light-induced
simultaneously
also
demonstrated.
Our
work
expands
synthetic
biology
capabilities
oneidensis,
could
facilitate
future
advances
applications
with
electrogenic
bacteria.
Nucleic Acids Research,
Год журнала:
2024,
Номер
52(16), С. 10017 - 10028
Опубликована: Авг. 10, 2024
Abstract
Vital
organismal
processes,
including
development,
differentiation
and
adaptation,
involve
altered
gene
expression.
Although
expression
is
frequently
controlled
at
the
transcriptional
stage,
various
regulation
mechanisms
operate
downstream
levels.
Here,
we
leverage
photoreceptor
NmPAL
to
optogenetically
induce
RNA
refolding
translation
of
bacterial
mRNAs.
Blue-light-triggered
binding
disrupts
a
cis-repressed
mRNA
state,
thereby
relieves
obstruction
initiation,
upregulates
Iterative
probing
optimization
circuit,
dubbed
riboptoregulator,
enhanced
induction
30-fold.
Given
action
level,
riboptoregulator
can
differentially
regulate
individual
structural
genes
within
polycistronic
operons.
Moreover,
it
orthogonal
be
wed
with
other
gene-regulatory
circuits
for
nuanced
more
stringent
gene-expression
control.
We
thus
advance
pAurora2
circuit
that
combines
translational
increase
by
>1000-fold.
The
strategy
stands
upgrade
numerous
regulatory
widely
applies
control
in
microbial
biotechnology,
synthetic
biology
materials
science.
Nonlinear Dynamics,
Год журнала:
2023,
Номер
111(9), С. 7975 - 7992
Опубликована: Фев. 15, 2023
Abstract
Control-based
continuation
(CBC)
is
an
experimental
method
that
can
reveal
stable
and
unstable
dynamics
of
physical
systems.
It
extends
the
path-following
principles
numerical
to
experiments
provides
systematic
dynamical
analyses
without
need
for
mathematical
modelling.
CBC
has
seen
considerable
success
in
studying
bifurcation
structure
mechanical
Nevertheless,
not
practical
relaxation
oscillations.
Large
numbers
Fourier
modes
are
required
describe
them,
length
experiment
significantly
increases
when
many
used,
as
system
must
be
run
convergence
times.
Furthermore,
oscillations
often
arise
autonomous
systems,
which
appropriate
phase
constraint
required.
To
overcome
these
challenges,
we
introduce
adaptive
B-spline
discretisation
produce
a
parsimonious
description
responses
would
otherwise
require
modes.
We
couple
this
novel
phase-locks
control
target
solution
phase.
Results
demonstrated
on
simulations
slow-fast
synthetic
gene
network
Oregonator
model.
Our
methods
extend
much
broader
range
systems
than
have
been
studied
so
far,
opening
up
opportunities
Living
cells
are
exquisitely
tuned
to
sense
and
respond
changes
in
their
environment.
Repurposing
these
systems
create
engineered
biosensors
has
seen
growing
interest
the
field
of
synthetic
biology
provides
a
foundation
for
many
innovative
applications
spanning
environmental
monitoring
improved
biobased
production.
In
this
review,
we
present
detailed
overview
currently
available
methods
that
have
supported
development,
scale-up,
deployment.
We
focus
on
genetic
sensors
living
whose
outputs
affect
gene
expression.
find
emerging
high-throughput
experimental
assays
evolutionary
approaches
combined
with
advanced
bioinformatics
machine
learning
establishing
pipelines
produce
virtually
any
small
molecule,
protein,
or
nucleic
acid.
However,
more
complex
sensing
tasks
based
classifying
compositions
stimuli
reliable
deployment
into
real-world
settings
remain
challenges.
suggest
recent
advances
our
ability
precisely
modify
nonmodel
organisms
integration
proven
control
engineering
principles
(e.g.,
feedback)
broader
design
will
be
necessary
overcome
hurdles
realize
immense
potential
field.
Structure,
Год журнала:
2024,
Номер
32(11), С. 1952 - 1962.e3
Опубликована: Авг. 30, 2024
Highlights•Cryo-EM
structures
of
a
bathy
bacteriophytochrome
at
near-atomic
resolution•Large
structural
changes
between
states
lead
to
strong
on-off
switching
mechanism•Connector
region
length
responsible
for
adjusting
photoresponseSummaryPhytochromes
are
photoreceptor
proteins
in
plants,
fungi,
and
bacteria.
They
can
adopt
two
photochromic
with
differential
biochemical
responses.
The
transducing
the
signal
from
chromophore
output
modules
poorly
understood
due
challenges
capturing
dynamic,
full-length
protein.
Here,
we
present
cryoelectron
microscopy
(cryo-EM)
phytochrome
Pseudomonas
aeruginosa
(PaBphP)
its
resting
(Pfr)
photoactivated
(Pr)
state.
kinase-active
Pr
state
has
an
asymmetric,
dimeric
structure,
whereas
kinase-inactive
Pfr
opens
up.
This
behavior
is
different
other
known
phytochromes
explain
it
unusually
short
connection
photosensory
modules.
Multiple
sequence
alignment
this
suggests
evolutionary
optimization
modes
transduction
sensor
proteins.
results
establish
new
mechanism
light-sensing
by
histidine
kinases
provide
input
design
optogenetic
variants.Graphical
abstract
Journal of Molecular Biology,
Год журнала:
2023,
Номер
436(5), С. 168257 - 168257
Опубликована: Авг. 31, 2023
Sensory
photoreceptors
abound
in
nature
and
enable
organisms
to
adapt
behavior,
development,
physiology
environmental
light.
In
optogenetics,
allow
spatiotemporally
precise,
reversible,
non-invasive
control
by
light
of
cellular
processes.
Notwithstanding
the
development
numerous
optogenetic
circuits,
an
unmet
demand
exists
for
efficient
circuits
sensitive
red
light,
given
its
superior
penetration
biological
tissue.
Bacteriophytochrome
sense
ratio
far-red
regulate
activity
enzymatic
effector
modules.
The
recombination
bacteriophytochrome
photosensor
modules
with
cyclase
effectors
underlies
photoactivated
adenylyl
cyclases
(PAC)
that
catalyze
synthesis
ubiquitous
second
messenger
3',
5'-cyclic
adenosine
monophosphate
(cAMP).
Via
homologous
exchanges
unit,
we
devised
novel
PACs,
variant
DmPAC
exhibiting
40-fold
activation
under
thus
surpassing
previous
red-light-responsive
PACs.
Modifications
PHY
tongue
modulated
responses
Exchanges
offer
avenue
further
enhancing
PACs
but
require
optimization
linker
photosensor.
a
derivative
guanosine
manipulation
cyclic-nucleotide-dependent
processes
mammalian
cells
Taken
together,
advance
second-messenger
signaling
provide
insight
into
design
receptors.
