Journal of Agricultural and Food Chemistry,
Год журнала:
2023,
Номер
71(37), С. 13838 - 13847
Опубликована: Сен. 5, 2023
Promoters
are
essential
for
designing
Saccharomyces
cerevisiae
cell
factories.
Identifying
novel
promoters
tuned
to
produce
specific
metabolites
under
increasingly
diverse
industrial
stresses
is
required
improve
the
economic
feasibility
of
whole
fermentation
processes.
In
this
study,
a
positively
evolved
Suc2
promoter
(SUC
2p)
with
activity
stronger
than
that
wild-type
2wtp)
was
obtained.
Quantitative
real-time
PCR,
fluorescence
analysis,
Western
blotting,
and
β-galactosidase
assay
revealed
SUC
2p
medium-strength
compared
eight
reported
at
medium
glucose
concentration
(2%
(w/v)).
Different
concentrations
modulated
strength
2p.
Low
(0.05
0.5%
(w/v))
enhanced
dramatically,
higher
strong
promoters.
Glucose
starvation
resulted
in
formation
new
Msn2/4
binding
site
on
Our
work
should
facilitate
development
fine-tuning
properties
construction
S.
factories
suitable
production
chemicals
glucose-deprived
conditions.
ACS Synthetic Biology,
Год журнала:
2024,
Номер
13(5), С. 1424 - 1433
Опубликована: Апрель 29, 2024
The
ability
to
control
cellular
processes
using
optogenetics
is
inducer-limited,
with
most
optogenetic
systems
responding
blue
light.
To
address
this
limitation,
we
leverage
an
integrated
framework
combining
Lustro,
a
powerful
high-throughput
platform,
and
machine
learning
tools
enable
multiplexed
over
light-sensitive
systems.
Specifically,
identify
light
induction
conditions
for
sequential
activation
as
well
preferential
switching
between
pairs
of
split
transcription
factors
in
the
budding
yeast,
Saccharomyces
cerevisiae.
We
use
data
generated
from
Lustro
build
Bayesian
optimization
that
incorporates
data-driven
learning,
uncertainty
quantification,
experimental
design
prediction
system
behavior
identification
optimal
control.
This
work
lays
foundation
designing
more
advanced
synthetic
biological
circuits
incorporating
optogenetics,
where
multiple
circuit
components
can
be
controlled
designer
programs,
broad
implications
biotechnology
bioengineering.
Nature Communications,
Год журнала:
2024,
Номер
15(1)
Опубликована: Авг. 2, 2024
Abstract
In
their
natural
environments,
microorganisms
mainly
operate
at
suboptimal
growth
conditions
with
fluctuations
in
nutrient
abundance.
The
resulting
cellular
adaptation
is
subject
to
conflicting
tasks:
or
survival
maximisation.
Here,
we
study
this
by
systematically
measuring
the
impact
of
a
nitrogen
downshift
24
sources
on
metabolism
single-cell
level.
Saccharomyces
lineages
grown
rich
media
and
exposed
gradually
differentiate
form
two
subpopulations
different
cell
sizes
where
one
favours
while
other
viability
an
extended
chronological
lifespan.
This
differentiation
asymmetrical
daughter
cells
representing
new
differentiated
state
increased
viability.
We
characterise
metabolic
response
using
RNA
sequencing,
biosensors
transcription
factor-tagged
GFP
library
coupled
high-throughput
microscopy,
imaging
more
than
800,000
cells.
find
that
subpopulation
associated
dormant
quiescent
displaying
differences
MAPK
signalling.
Depending
identity
source
present,
into
can
be
actively
maintained,
attenuated,
aborted.
These
results
establish
amino
acids
as
important
signalling
molecules
for
formation
genetically
identical
subpopulations,
involved
lifespan
rate
determination.
The
zinc
finger
469
gene
(ZNF469)
is
a
single-exon
predicted
to
encode
protein
of
3953
amino
acids.
Despite
pathogenic
ZNF469
variants
being
associated
with
Brittle
Cornea
Syndrome
(BCS),
relatively
little
known
about
beyond
its
participation
in
regulating
the
expression
genes
encoding
extracellular
matrix
proteins.
In
this
study,
we
examined
and
intracellular
localization
different
cell
lines.
level
mRNA
varied
from
low
levels
HEK293
cells
high
HeLa
primary
fibroblasts.
Antibodies
against
reacted
among
others
approximately
400
kDa
immunoblot
analysis,
which
was
mainly
present
insoluble
fraction
cytoplasm.
Immunofluorescence
analysis
interphase
showed
small
cytoplasmic
puncta
weak
nuclear
staining.
dividing
cells,
antibodies
recognized
foci
that
also
stained
for
proteasomes.
transfected
observed
resembling
speckles
at
midbody
during
mitosis.
overlapping
staining
live
imaging,
liquid-like
properties
were
recorded
as
they
changed
shape
position
occasionally
fused
each
other.
During
stress
granule
formation,
G3BP1.
Finally,
silico
revealed
large
intrinsically
disordered
regions
multiple
complexity
domains
ZNF469.
Our
data
indicate
forms
aggregates
possibly
biomolecular
condensates
when
overexpressed.
However,
care
must
be
taken
analyzing
distribution
due
discrepancy
endogenous
overexpressed
cells.
Microbial Biotechnology,
Год журнала:
2025,
Номер
18(4)
Опубликована: Апрель 1, 2025
ABSTRACT
In
many
microbial
biotechnology
processes,
biomass
itself
is
not
the
product
of
interest,
but
rather
targeted
chemicals
or
proteins.
these
growth
should
be
limited
to
direct
more
substrate
and
increase
process
yields.
Under
growth‐limiting
conditions,
such
as
nutrient
limitation,
microorganisms,
including
yeast
Saccharomyces
cerevisiae
,
activate
a
general
stress
response
(GSR).
Different
hypotheses
have
been
formulated
for
this
activation,
preparatory
role
future
stresses
in
cellular
protein
density.
Here
we
tested
third
hypothesis:
GSR
reduces
energy
needed
maintain
homeostasis,
also
known
maintenance
requirement
(MER).
The
impact
on
MER
was
investigated
by
assessing
effect
absence
its
key
regulators,
Msn2
Msn4,
energy‐substrate
distribution
resistance.
Chemostat
fed‐batch
cultures
revealed
significant
increases
up
85%
deletion
strain
compared
parental
strain.
contrast,
maximal
yields,
rates
morphology
were
unaffected.
Our
insights
highlight
an
additional
GSR,
namely
saving
energy.
As
determinant
yields
design,
especially
low
our
findings
can
help
optimise
bioprocesses.
ACS Synthetic Biology,
Год журнала:
2023,
Номер
12(7), С. 1943 - 1951
Опубликована: Июль 11, 2023
Optogenetic
systems
use
genetically
encoded
light-sensitive
proteins
to
control
cellular
processes.
This
provides
the
potential
orthogonally
cells
with
light;
however,
these
require
many
design-build-test
cycles
achieve
a
functional
design
and
multiple
illumination
variables
need
be
laboriously
tuned
for
optimal
stimulation.
We
combine
laboratory
automation
modular
cloning
scheme
enable
high-throughput
construction
characterization
of
optogenetic
split
transcription
factors
in
Saccharomyces
cerevisiae.
expand
yeast
toolkit
include
variants
cryptochromes
enhanced
Magnets,
incorporate
dimerizers
into
factors,
automate
measurement
cultures
96-well
microplate
format
characterization.
this
approach
rationally
test
an
optimized
Magnet
factor
improved
gene
expression.
is
generalizable
across
range
biological
applications.
ABSTRACT
Defining
the
time
of
action
for
morphogens
requires
tools
capable
temporally
controlled
perturbations.
To
study
how
transcription
factor
Dorsal
affects
patterning
Drosophila
embryonic
dorsal-ventral
axis,
we
used
two
light-inducible
tags
that
trigger
either
nuclear
export
or
degradation
under
blue
light.
Nuclear
leads
to
loss
high-threshold,
ventrally
expressed
target
gene
snail
(sna),
while
low-threshold,
laterally
short-gastrulation
(sog)
is
retained.
In
contrast,
results
in
retention
sna,
sog,
and
lower
levels
compared
when
exported
from
nucleus.
understand
why
causes
sna
but
does
not,
investigated
kinetics
using
photobleaching
found
it
rapidly
re-enters
nucleus
even
blue-light
conditions
favoring
export.
The
associated
being
imported
continuously
are
likely
responsible
but,
alternatively,
can
support
sog.
Collectively,
our
indicate
this
dynamic
process
influenced
by
both
concentration
retention.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 4, 2024
Many
organisms
maintain
generalized
stress
responses
activated
by
adverse
conditions.
Although
details
vary,
a
common
theme
is
the
redirection
of
transcriptional
and
translational
capacity
away
from
growth-promoting
genes
toward
defense
genes.
Yet
precise
roles
these
coupled
programs
are
difficult
to
dissect.
Here
we
investigated
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Май 20, 2024
Defining
the
time
of
action
for
morphogens
requires
tools
capable
temporally
controlled
perturbations.
To
study
how
transcription
factor
Dorsal
affects
patterning
