Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Ноя. 1, 2024
Spatial
organization
of
microbes
in
biofilms
enables
crucial
community
function
such
as
division
labor.
However,
quantitative
understanding
emergent
properties
remains
limited
due
to
a
scarcity
tools
for
patterning
heterogeneous
biofilms.
Here
we
develop
synthetic
optogenetic
toolkit
'Multipattern
Biofilm
Lithography'
rational
engineering
and
orthogonal
multi-strain
biofilms,
inspired
by
successive
adhesion
phenotypic
differentiation
natural
We
apply
this
profile
the
growth
dynamics
biofilm
communities,
observe
emergence
spatially
modulated
commensal
relationships
shared
antibiotic
protection
against
beta-lactam
ampicillin.
Supported
biophysical
modeling,
these
results
yield
in-vivo
measurements
key
parameters,
e.g.,
molecular
beta-lactamase
production
per
cell
length
scale
zone
protection.
Our
toolbox
associated
findings
provide
insights
into
spatial
distributed
within
with
direct
implications
future
research
engineering.
Biotechnology Advances,
Год журнала:
2024,
Номер
74, С. 108401 - 108401
Опубликована: Июнь 27, 2024
Metabolic
burden
is
defined
by
the
influence
of
genetic
manipulation
and
environmental
perturbations
on
distribution
cellular
resources.
The
rewiring
microbial
metabolism
for
bio-based
chemical
production
often
leads
to
a
metabolic
burden,
followed
adverse
physiological
effects,
such
as
impaired
cell
growth
low
product
yields.
Alleviating
imposed
undesirable
changes
has
become
an
increasingly
attractive
approach
constructing
robust
factories.
In
this
review,
we
provide
brief
overview
engineering,
focusing
specifically
recent
developments
strategies
diminishing
while
improving
robustness
yield.
A
variety
examples
are
presented
showcase
promise
engineering
in
facilitating
design
construction
Finally,
challenges
limitations
encountered
discussed.
Advanced Science,
Год журнала:
2025,
Номер
unknown
Опубликована: Март 16, 2025
Abstract
Dynamic
control
exhibits
increasing
significance
in
microbial
cell
factory
engineering
by
precisely
manipulating
gene
expression
over
time
and
levels.
However,
the
practical
uses
of
most
dynamic
tools
still
remain
challenging
because
poor
scale‐up
robustness,
especially
for
non‐model
chassis.
Herein,
a
quorum
sensing
(QS)‐based
collaborative
system
is
constructed
Halomonas
TD
regrouping
two
orthogonal
quorum‐sensing
modules
into
types,
namely
cell‐A
harboring
cinR‐luxI
cell‐B
luxR‐cinI
together
with
sfGFP
driven
P
cin
lux
promoters,
respectively.
Effective
15‐time
foldchange
achieved
mixing
cells
A
B
at
different
ratios
points
lab‐scale
fed‐batch
study.
Besides,
inhibitory
amplified
further
developed
cascading
CRISPRi/dCas9
MmP1
RNA
polymerase,
respectively,
yielding
up
to
80%
repression
efficiency
30‐time
amplification
under
high
density
fermentation.
Moreover,
500
mg
L
−1
indigo
4.7
g
superoxide
dismutase
(SOD)
are
obtained
engineered
using
QS‐based
study,
showing
1.5‐
1.0‐fold
higher,
than
yields
recombinants
induced
IPTG.
This
study
exemplifies
standardized
streamlined
inducer‐free
pattern
metabolic
promising
robustness
fermentation
contexts.
Journal of Applied Microbiology,
Год журнала:
2024,
Номер
135(7)
Опубликована: Июнь 27, 2024
Abstract
Microbiomes,
the
complex
networks
of
micro-organisms
and
molecules
through
which
they
interact,
play
a
crucial
role
in
health
ecology.
Over
at
least
past
two
decades,
engineering
biology
has
made
significant
progress,
impacting
bio-based
industry,
health,
environmental
sectors;
but
only
recently
begun
to
explore
microbial
ecosystems.
The
creation
synthetic
communities
presents
opportunities
help
us
understand
dynamics
wild
ecosystems,
learn
how
manipulate
interact
with
existing
microbiomes
for
therapeutic
other
purposes,
create
entirely
new
capable
undertaking
tasks
industrial
biology.
Here,
we
describe
ecosystems
can
be
constructed
controlled,
focusing
on
available
methods
interaction
mechanisms
facilitate
regulation
community
composition
output.
While
experimental
decisions
are
dictated
by
intended
applications,
vast
number
tools
suggests
great
opportunity
researchers
develop
diverse
array
novel
Current Opinion in Chemical Engineering,
Год журнала:
2024,
Номер
44, С. 101027 - 101027
Опубликована: Май 17, 2024
Clinical
advances
in
the
space
of
next-generation
vaccines
and
medicines,
together
with
advent
platform
technologies,
have
revolutionised
modus
operandi
biopharmaceutical
industry.
The
industry's
core
mission
for
uninterrupted
delivery
high-quality,
efficacious
drugs
is
now
further
challenged
by
bold
necessary
targets
to
operate
sustainably.
In
this
paper,
we
discuss
how
threefold
sustainability
that
integrates
economic,
environmental,
social
objectives
can
be
achieved
through
a
combination
technological
advances,
expert
knowledge
transparent
dialogue.
We
summarise
recent
biomanufacturing
terms
novel
intracellular
process-level
analytics,
computational
models
before
providing
an
outlook
on
Industry
5.0
principles
adopted
applied
advance
industrial
practice.
International Journal of Molecular Sciences,
Год журнала:
2024,
Номер
25(7), С. 4001 - 4001
Опубликована: Апрель 3, 2024
Light
is
a
key
environmental
component
influencing
many
biological
processes,
particularly
in
prokaryotes
such
as
archaea
and
bacteria.
control
techniques
have
revolutionized
precise
manipulation
at
molecular
cellular
levels
recent
years.
Bacteria,
with
adaptability
genetic
tractability,
are
promising
candidates
for
light
studies.
This
review
investigates
the
mechanisms
underlying
activation
bacteria
discusses
advancements
focusing
on
methods
controlling
We
delve
into
by
which
sense
transduce
signals,
including
engineered
photoreceptors
light-sensitive
actuators,
various
strategies
employed
to
modulate
gene
expression,
protein
function,
bacterial
motility.
Furthermore,
we
highlight
developments
light-integrated
of
microbial
responses,
upconversion
nanoparticles
optical
tweezers,
can
enhance
spatial
temporal
open
new
horizons
biomedical
applications.
Current Opinion in Biotechnology,
Год журнала:
2024,
Номер
89, С. 103193 - 103193
Опубликована: Авг. 28, 2024
Recent
advancements
in
plant
bioprinting
and
optogenetic
tools
have
unlocked
new
avenues
to
revolutionize
tissue
engineering.
Bioprinting
of
cells
has
the
potential
craft
intricate
3D
structures
incorporating
multiple
cell
types,
replicating
complex
microenvironments
found
plants.
Concurrently,
enable
control
biological
events
with
spatial,
temporal,
quantitative
precision.
Originally
developed
for
human
microbial
systems,
these
two
cutting-edge
methodologies
are
now
being
adapted
research.
Although
still
early
stages
development,
we
here
review
latest
progress
optogenetics
discuss
compelling
opportunities
biotechnology
research
arising
from
combination
technologies.
Scientific Reports,
Год журнала:
2024,
Номер
14(1)
Опубликована: Ноя. 18, 2024
The
discrepancy
between
model
predictions
and
actual
processes,
known
as
process-model
mismatch
(PMM),
remains
a
substantial
challenge
in
bioprocess
optimization.
We
previously
introduced
hybrid
silico/in-cell
controller
(HISICC)
that
combines
model-based
optimization
with
cell-based
feedback
to
address
this
problem.
Here,
we
extended
approach
regulate
key
enzyme
level
using
intracellular
biosensing.
HISICC
was
implemented
an
Escherichia
coli
strain
engineered
for
fatty
acid
production
(FA3).
This
contains
genetically
encoded
decelerates
the
expression
of
acetyl-CoA
carboxylase
(ACC)
response
malonyl-CoA
synthesized
through
enzymatic
reaction.
modeled
FA3
allow
optimize
inducer
input
accelerates
expression.
Simulations
showed
slowed
unexpectedly
rapid
accumulation
ACC
resulting
from
PMMs
before
it
reached
cytotoxic
levels,
thereby
improving
yields.
These
results
highlight
potential
our
approach,
particularly
cases
where
monitoring
biomolecules
is
required
handle
PMMs.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Фев. 29, 2024
Abstract
Discrepancy
between
model
predictions
and
actual
processes,
known
as
process–model
mismatch
(PMM),
remains
a
serious
challenge
in
bioprocess
optimization.
Previously,
we
proposed
the
hybrid
silico/in-cell
controller
(HISICC)
concept
combining
model-based
optimization
with
cell-based
feedback
to
address
PMM
problem.
Herein,
this
approach
was
advanced
regulate
intracellular
concentrations
of
rate-limiting
enzymes.
Advanced
HISICC
demonstrated
using
an
engineered
Escherichia
coli
strain
for
fatty
acid
production
(FA3).
This
harbors
in-cell
controller,
which
decelerates
acetyl-CoA
carboxylase
(ACC)
overexpression
response
sensing
concentration
malonyl-CoA
formed
by
enzyme.
A
mathematical
FA3
constructed
validated
experimental
data.
Simulations
assuming
various
revealed
that
effectively
mitigates
toxicity
from
excessive
ACC
robustly
adapting
braking
its
overexpression,
minimizing
yield
loss.
study
confirmed
viable
strategy
enhancing
efficiency,
especially
balancing
bottleneck
enzyme
levels.
