bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2023,
Volume and Issue:
unknown
Published: Nov. 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
.
Nature Communications,
Journal Year:
2024,
Volume and Issue:
15(1)
Published: March 15, 2024
Abstract
Machine
learning
applied
to
large
compendia
of
transcriptomic
data
has
enabled
the
decomposition
bacterial
transcriptomes
identify
independently
modulated
sets
genes,
such
iModulons
represent
specific
cellular
functions.
The
identification
enables
accurate
genes
necessary
and
sufficient
for
cross-species
transfer
We
demonstrate
of:
1)
biotransformation
vanillate
protocatechuate,
2)
a
malonate
catabolic
pathway,
3)
pathway
2,3-butanediol,
4)
an
antimicrobial
resistance
ampicillin
found
in
multiple
Pseudomonas
species
Escherichia
coli
.
iModulon-based
engineering
is
transformative
strategy
as
it
includes
all
comprising
transferred
function,
including
without
functional
annotation.
Adaptive
laboratory
evolution
was
deployed
optimize
function
transferred,
revealing
mutations
host.
Combining
big
analytics
thus
enhances
level
understanding
systems
biology,
synthetic
biology
strain
design
development.
PNAS Nexus,
Journal Year:
2024,
Volume and Issue:
3(2)
Published: Feb. 1, 2024
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
cholerae
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
fresh
media.
Cells
to
plasmids,
recombination
linear
DNA,
cotransformation
both
select
for
scarless
markerless
edits.
entire
simple
inexpensive,
requiring
no
capital
equipment
room
temperature
(zero
protocol,
104
cfu/μg),
just
incubator
(high-efficiency
105−6
cfu/μg).
These
retain
their
state
when
frozen
transformable
immediately
upon
thawing
like
typical
chemical
electrochemical
cell.
Since
optimized
protocol
requires
only
50
min
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
Escherichia
coli
excellent
chassis
low-cost
highly
scalable
synthetic
biology.
PLoS Computational Biology,
Journal Year:
2024,
Volume and Issue:
20(10), P. e1012546 - e1012546
Published: Oct. 23, 2024
Public
gene
expression
databases
are
a
rapidly
expanding
resource
of
organism
responses
to
diverse
perturbations,
presenting
both
an
opportunity
and
challenge
for
bioinformatics
workflows
extract
actionable
knowledge
transcription
regulatory
network
function.
Here,
we
introduce
five-step
computational
pipeline,
called
iModulonMiner,
compile,
process,
curate,
analyze,
characterize
the
totality
RNA-seq
data
given
or
cell
type.
This
workflow
is
centered
around
data-driven
computation
co-regulated
sets
using
Independent
Component
Analysis,
iModulons,
which
have
been
shown
broad
applications.
As
demonstration,
applied
this
generate
iModulon
structure
Bacillus
subtilis
all
high-quality,
publicly-available
data.
Using
structure,
predicted
interactions
multiple
factors,
identified
groups
co-expressed
genes
that
putatively
regulated
by
undiscovered
properties
recently
discovered
single-subunit
phage
RNA
polymerase.
We
also
present
Python
package,
PyModulon,
with
functions
characterize,
visualize,
explore
computed
iModulons.
The
available
at
https://github.com/SBRG/iModulonMiner
,
can
be
readily
organisms
gain
rapid
understanding
their
transcriptional
condition-specific
activity.
Microbial Biotechnology,
Journal Year:
2024,
Volume and Issue:
17(2)
Published: Feb. 1, 2024
Lactiplantibacillus
plantarum
is
a
probiotic
bacterium
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.
plantarum,
independent
component
analysis
transcriptomes
was
to
derive
45
sets
independently
modulated
genes
(iModulons).
Those
iModulons
were
annotated
for
associated
transcription
factors
functional
pathways,
active
response
different
growth
conditions
identified
characterized
detail.
Eventually,
iModulon
activities
reveals
trade-off
between
secondary
primary
metabolism
plantarum.
Metabolic Engineering,
Journal Year:
2024,
Volume and Issue:
84, P. 34 - 47
Published: May 31, 2024
Understanding
diverse
bacterial
nutritional
requirements
and
responses
is
foundational
in
microbial
research
biotechnology.
In
this
study,
we
employed
knowledge-enriched
transcriptomic
analytics
to
decipher
complex
stress
of
Vibrio
natriegens
supplied
nutrients,
aiming
enhance
engineering
efforts.
We
computed
64
independently
modulated
gene
sets
that
comprise
a
quantitative
basis
for
transcriptome
dynamics
across
comprehensive
transcriptomics
dataset
containing
broad
array
nutrient
conditions.
Our
approach
led
the
i)
identification
novel
transporter
systems
substrates,
ii)
detailed
understanding
how
trace
elements
affect
metabolism
growth,
iii)
extensive
characterization
nutrient-induced
responses,
including
osmotic
stress,
low
glycolytic
flux,
proteostasis,
altered
protein
expression.
By
clarifying
relationship
between
acetate-associated
regulon
flux
status
various
have
showcased
its
vital
role
directing
optimal
carbon
source
selection.
findings
offer
deep
insights
into
transcriptional
landscape
nutrition
underscore
significance
tailoring
strain
strategies,
thereby
facilitating
development
more
efficient
robust
biotechnological
applications.
Biotechnology Advances,
Journal Year:
2024,
Volume and Issue:
77, P. 108464 - 108464
Published: Oct. 9, 2024
Biotechnology
has
been
built
on
the
foundation
of
a
small
handful
well
characterized
and
well-engineered
organisms.
Recent
years
have
seen
breakout
performer
gain
attention
as
new
entrant
into
bioengineering
toolbox:
Vibrio
natriegens.
This
review
covers
recent
research
efforts
making
V.
natriegens
biotechnology
platform,
using
large
language
model
(LLM)
knowledge
graph
to
expedite
literature
survey
process.
Scientists
made
advancements
in
pertaining
fundamental
metabolic
characteristics
natriegens,
development
characterization
synthetic
biology
tools,
systems
analysis
modeling,
bioproduction
engineering,
microbial
ecology.
Each
these
subcategories
relevance
future
for
applications.
In
this
review,
we
cover
offer
context
impact
they
may
field,
highlighting
benefits
drawbacks
organism.
From
examining
research,
it
appears
that
is
precipice
becoming
platform
bacterium
biotechnology.
Nucleic Acids Research,
Journal Year:
2024,
Volume and Issue:
53(D1), P. D99 - D106
Published: Nov. 4, 2024
iModulons-sets
of
co-expressed
genes
identified
through
independent
component
analysis
(ICA)
high-quality
transcriptomic
datasets-provide
an
unbiased,
modular
view
organism's
transcriptional
regulatory
network.
Established
in
2020,
iModulonDB
(iModulonDB.org)
serves
as
a
centralized
repository
curated
iModulon
sets,
enabling
users
to
explore
iModulons
and
download
the
associated
data.
This
update
reflects
significant
expansion
database-19
new
ICA
decompositions
(+633%)
spanning
8
925
expression
profiles
(+1370%),
503
studies
(+2290%)
12
additional
organisms
(+400%)-and
introduces
features
help
scientists
decipher
mechanisms
governing
prokaryotic
regulation.
To
facilitate
comprehension
underlying
profiles,
updated
user-interface
displays
essential
information
about
each
data-generating
study
(e.g.
experimental
conditions
publication
abstract).
Dashboards
now
include
condition-specific
coloring
highlight
data
generated
from
genetically
perturbed
strains,
rapidly
interpret
disruptions
New
interactive
graphs
convey
omics-derived
indicators
explained
variance
decompositions,
genetic
overlap
between
regulons).
Direct
links
operon
diagrams
(BioCyc)
protein-protein
interaction
networks
(STRING)
provide
with
seamless
access
external
resources
for
further
assessment
iModulons.
Lastly,
suite
search-driven
species-wide
tools
promotes
user-engagement
iModulons,
reinforcing
iModulonDB's
role
dynamic,
knowledgebase
Microbiological Research,
Journal Year:
2024,
Volume and Issue:
284, P. 127729 - 127729
Published: April 21, 2024
Marine
bacteria
play
vital
roles
in
symbiosis,
biogeochemical
cycles
and
produce
novel
bioactive
compounds
enzymes
of
interest
for
the
pharmaceutical,
biofuel
biotechnology
industries.
At
present,
investigations
into
marine
bacterial
functions
their
products
are
primarily
based
on
phenotypic
observations,
-omic
type
approaches
heterologous
gene
expression.
To
advance
our
understanding
harness
full
potential
industry
application,
it
is
critical
that
we
have
appropriate
tools
resources
to
genetically
manipulate
them
situ.
However,
current
genetic
largely
designed
model
organisms
such
as
E.
coli,
low
transformation
efficiencies
or
no
transfer
ability
bacteria.
improve
manipulation
applications
bacteria,
need
methods
conjugation
electroporation
addition
identifying
more
broad
host
range
plasmids.
In
this
review,
aim
outline
reported
discuss
considerations
each
approach
context
improving
efficiency.
addition,
further
plasmids
future
research
areas
including
CRISPR
