bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 5, 2023
Abstract
Lactobacillus
plantarum
is
a
probiotic
bacteria
widely
used
in
food
and
health
industries,
but
its
gene
regulatory
information
limited
existing
databases,
which
impedes
the
research
of
physiology
applications.
To
obtain
better
understanding
transcriptional
network
L.
,
independent
component
analysis
(ICA)
transcriptomes
was
to
derive
45
sets
independently
modulated
genes
(iModulons).
Those
iModulons
were
annotated
for
associated
transcription
factors
(TFs)
functional
pathways,
active
response
different
growth
conditions
identified
characterized
detail.
Eventually,
iModulon
activities
reveals
trade-off
between
secondary
primary
metabolism
.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Авг. 13, 2023
Abstract
The
fast-growing
microbe
Vibrio
natriegens
is
capable
of
natural
transformation
where
it
draws
DNA
in
from
media
via
an
active
process
under
physiological
conditions.
Using
engineered
strain
with
a
genomic
copy
the
master
competence
regulator
tfoX
cholera
combination
new
minimal
(MCM)
that
uses
acetate
as
energy
source,
we
demonstrate
naturally
competent
cells
which
are
created,
transformed,
and
recovered
entirely
same
media,
without
exchange
or
addition
media.
Cells
to
plasmids,
recombination
linear
DNA,
co-transformation
both
select
for
scarless
markerless
edits.
entire
simple
inexpensive,
requiring
no
capital
equipment
room
temperature
(Zero
Capital
protocol,
10
4
cfu/
µ
g),
just
incubator
(High
Efficiency
5–6
g).
These
retain
their
state
when
frozen
transformable
immediately
upon
thawing
like
typical
chemical
electrochemical
cell.
Since
optimized
protocol
requires
only
50
minutes
hands-on
time,
V.
grows
quickly
even
on
plates,
started
at
9
AM
yields
abundant
culturable
single
colonies
by
5
PM.
Further,
because
all
stages
occur
can
be
arbitrarily
scaled
volume,
this
could
ideal
automated
directed
evolution
applications.
As
result,
compete
E.
coli
excellent
chassis
low-cost
highly
scalable
synthetic
biology.
Nucleic Acids Research,
Год журнала:
2024,
Номер
52(18), С. 11362 - 11377
Опубликована: Авг. 28, 2024
Abstract
Synthetic
biology
enables
the
reprogramming
of
cellular
functions
for
various
applications.
However,
challenges
in
scalability
and
predictability
persist
due
to
context-dependent
performance
complex
circuit-host
interactions.
This
study
introduces
an
iModulon-based
engineering
approach,
utilizing
machine
learning-defined
co-regulated
gene
groups
(iModulons)
as
design
parts
containing
essential
genes
specific
functions.
approach
identifies
necessary
components
genetic
circuits
across
different
contexts,
enhancing
genome
by
improving
target
selection
predicting
module
behavior.
We
demonstrate
several
distinct
uses
iModulons:
(i)
discovery
unknown
iModulons
increase
protein
productivity,
heat
tolerance
fructose
utilization;
(ii)
iModulon
boosting
which
amplifies
activity
iModulons,
improved
cell
growth
under
osmotic
stress
with
minimal
host
regulation
disruption;
(iii)
rebalancing
strategy,
adjusts
levels
balance
functions,
significantly
increased
oxidative
while
minimizing
trade-offs
(iv)
annotation
enabled
natural
competence
activation
predictably
rewiring
iModulons.
Comparative
experiments
traditional
methods
showed
our
offers
advantages
efficiency
strain
engineering.
demonstrates
potential
strategies
systematically
reprogram
offering
refined
adaptable
control
over
regulatory
networks.
The
composition
of
bacterial
transcriptomes
is
determined
by
the
transcriptional
regulatory
network
(TRN).
TRN
regulates
transition
from
one
physiological
state
to
another.
Here,
we
use
independent
component
analysis
monitor
transcriptome
during
exponential
growth
phase
stationary
phase.
With
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2024,
Номер
unknown
Опубликована: Дек. 31, 2024
Abstract
We
present
TXpredict,
a
transformer-based
framework
for
predicting
microbial
transcriptomes
using
annotated
genome
sequences.
By
leveraging
information
learned
from
large
protein
language
model,
TXpredict
achieves
an
average
Spearman
correlation
of
0.53
and
0.62
in
gene
expression
new
bacterial
fungal
genomes.
further
extend
this
to
predict
2,685
additional
genomes
spanning
1,744
genera,
82%
which
remain
uncharacterized
at
the
transcriptional
level.
Our
analysis
highlights
conserved
divergent
programs
across
understudied
providing
powerful
resource
uncovering
adaptation
strategies
metabolic
potential
tree
life.
bioRxiv (Cold Spring Harbor Laboratory),
Год журнала:
2023,
Номер
unknown
Опубликована: Ноя. 5, 2023
Abstract
Lactobacillus
plantarum
is
a
probiotic
bacteria
widely
used
in
food
and
health
industries,
but
its
gene
regulatory
information
limited
existing
databases,
which
impedes
the
research
of
physiology
applications.
To
obtain
better
understanding
transcriptional
network
L.
,
independent
component
analysis
(ICA)
transcriptomes
was
to
derive
45
sets
independently
modulated
genes
(iModulons).
Those
iModulons
were
annotated
for
associated
transcription
factors
(TFs)
functional
pathways,
active
response
different
growth
conditions
identified
characterized
detail.
Eventually,
iModulon
activities
reveals
trade-off
between
secondary
primary
metabolism
.
