Frontiers in Plant Science,
Journal Year:
2024,
Volume and Issue:
15
Published: Nov. 26, 2024
Natural
products
derived
from
medicinal
plants
are
a
class
of
compounds
with
extensive
biological
activities,
playing
crucial
role
in
the
pharmaceutical,
food,
and
cosmetics
industries.
Due
to
their
excellent
physiological
functions,
increasing
attention
is
being
paid
biosynthesis
pathways
plant
natural
(PNPs)
(Kawatra
et
al.,
2022;Halder
Jha,
2023).
However,
as
market
demand
continues
grow,
traditional
harvesting
extraction
methods
exert
immense
pressure
on
environment
(Singh,
In
recent
years,
rapid
advancement
synthetic
biology
has
offered
new
approaches
for
producing
structurally
complex
bioactive
small-molecule
using
biotechnology
(Hesami
Nevertheless,
lack
knowledge
about
biosynthetic
significantly
impedes
largescale
biomanufacturing
plants.
Unlike
microorganisms,
genes
relatively
dispersed
across
chromosomes,
often
efficient
genetic
manipulation
systems,
which
hinders
elucidation
pathways.Recently,
chemoproteomics
based
activity
probes
demonstrated
great
potential
elucidating
product
(steviol
glycosides,
camptothecin,
chalcomoracin,
etc.),
it
enables
identification
functional
proteins
interacting
substrates,
thereby
accelerating
discovery
(Li
2018;Zhou
2018;Gao
2020;Wong
2020;Zhang
2024)
(Figure
1).Traditional
have
played
advancing
our
understanding
pathways,
laying
foundation
emerging
technologies
like
chemoproteomics.
Gene
knockout
RNA
interference
(RNAi)
methods,
example,
been
widely
used
identify
involved
by
observing
phenotypic
changes
metabolite
production
when
specific
silenced
(Zhao
2016).
Additionally,
multi-omics
approaches,
such
transcriptomics,
offer
insights
gene
coexpression,
though
these
can
be
limited
need
data
analysis
do
not
directly
enzyme
activities
(Liu
2024a;Swamidatta
Lichman,
2024).
Heterologous
expression,
microbial
enabled
individual
or
clusters
recreating
outside
native
context
(Lau
Sattely,
2015;Hong
2022;Yang
biochemical
assays
verify
function
may
require
large
amounts
purified
protein,
time-intensive
process
(Tatsis
2017).
These
while
foundational,
fall
short
dissecting
within
plants,
where
chemoproteomics,
its
activity-based
annotation
capabilities,
offers
distinct
advantages.
Consequently,
applying
technology
comprehensively
analyze
only
practical
value
but
also
holds
strategic
significance
achieving
through
(Zhang
2022;Gao
2023;Liu
2023;Zhang
2023;Golubova
2024;Jiang
2024;Liu
2024b).
Affinity
specialized
chemical
tools
isolate
active
enzymes
samples,
particularly
those
biosynthesis.
typically
consist
binding
moiety
that
targets
enzyme's
site,
reactive
tag
capture
covalent
attachment
after
activation
reporter
detection.Effective
affinity
probe
design
requires
specificity
mimic
stability
conditions,
controlled
reactivity
ensure
selective
durable
(Parker
Pratt,
2020;Fang
2021)
2).
The
primary
advantage
lies
ability
selectively
target
proteomes,
bypassing
purification
manipulation.
challenges
non-specific
complexity
limit
effectiveness
(Tabana
proven
invaluable
mapping
shown
studies
synthesizing
steviol
glycosides
other
products.
Steviol
sweetening
agents
Stevia
rebaudiana,
studied
due
non-caloric
sweeteners
(Masand
Recent
research
utilizing
chemoproteomics-based
strategy
successfully
identified
UDP-glycosyltransferases
(UGTs)
SrUGT73E1,
AtUGT73C1
AtUGT73C5,
play
pivotal
catalyzing
glycosylation
form
2018;Wong
2020).
use
photoaffinity
steviol,
combined
mass
spectrometry,
allowed
researchers
profile
UGTs
responsible
final
steps.This
advances
pathway
novel
platform
glycosylation,
enabling
scalable
production.Chalcomoracin,
flavonoid
isolated
mulberry
(Morus
alba),
synthesized
highly
unique
flavin
adenine
dinucleotide
(FAD)-dependent
intermolecular
Diels-Alder
reaction.
For
this
cycloaddition
reaction
was
unknown,
despite
importance
formation
chalcomoracin's
characteristic
cyclohexene
ring.
enzyme,
Morus
alba
Diels-Alderase
(MaDA),
intermediate
(BIP)-based
(Gao
MaDA
catalyzes
the[4+2]
high
enantioselectivity,
marking
first
stand-alone
2020;Gao
characterization
had
remained
inaccessible
genomics
transcriptomics
clustering
pathways.Camptothecin,
an
alkaloid
potent
anti-cancer
properties,
Camptotheca
acuminata
Ophiorrhiza
pumila
(Yang
2021).
camptothecin
long
subject
study,
significant
gap
steps
following
strictosamide
formation.
A
breakthrough
came
OpCYP716E111,
epoxidase
conversion
epoxide.
Using
chemoproteomic
approach,
designed
diazirine-based
strictosamide,
OpCYP716E111
proteome
This
fills
critical
underscores
power
uncover
previously
unknown
metabolic
processes.The
discoveries
surrounding
highlight
broad
applicability
field
Traditional
nature
genes,
making
difficult
pinpoint
each
step.Chemoproteomics
circumvents
issue
targeting
small
molecule
probes,
allowing
even
non-model
approach
advantageous
secondary
metabolism
organized
into
clusters,
feature
common
systems
rare
Chemoproteomics
advantages
studying
sensitivity
detecting
low-abundance
without
needing
cloning
protein
expression
steps.
It
distinguish
between
closely
related
isoforms
multiple
simultaneously,
comprehensive
view
networks
systems.These
features
make
valuable
biosynthesis.Furthermore,
integration
promise
sustainable
compounds.
By
identifying
characterizing
biosynthesis,
reconstitute
hosts,
plant-derived
2023).Despite
advantages,
faces
pathways.
include
optimization
reliance
high-quality
spectrometry
accurate
identification.
arise
limitations
affect
efficiency
specificity.
Future
advancements,
improved
selectivity
omics
technologies,
hold
overcoming
obstacles
enhancing
approach's
utility
research.Chemoproteomics
indispensable
tool
camptothecin.
frontier
research,
key
facilitating
application
biology.
As
will
likely
central
unlocking
full
pharmaceutical
industrial
applications.MY:
Conceptualization,
Writing-original
draft.
MY,
QY:
Writing-review
editing.
The Plant Journal,
Journal Year:
2025,
Volume and Issue:
122(1)
Published: April 1, 2025
High-throughput
experiments
in
plants
are
hindered
by
long
generation
times
and
high
costs.
To
address
these
challenges,
we
present
an
optimized
pipeline
for
Agrobacterium
tumefaciens
transformation
a
simplified
protocol
to
obtain
stable
transgenic
lines
of
the
model
liverwort
Marchantia
polymorpha,
paving
way
efficient
high-throughput
plant
synthetic
biology
other
applications.
Our
involves
freeze-thaw
method
six-well
plates
that
can
be
adapted
robotic
automation.
Using
Opentrons
open-source
platform,
implemented
semi-automated
showing
similar
efficiency
compared
manual
manipulation.
Additionally,
have
streamlined
process
selection
M.
reducing
cost,
time,
labor
without
compromising
efficiency.
The
addition
sucrose
media
significantly
enhances
production
gemmae,
accelerating
isogenic
plants.
We
believe
protocols
potential
facilitate
screenings
diverse
species
represent
significant
step
towards
full
automation
pipelines.
This
approach
allows
testing
~100
constructs
per
month,
using
conventional
tissue
culture
facilities.
recently
demonstrated
successful
implementation
this
screening
hundreds
fluorescent
reporters
gemmae.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2025,
Volume and Issue:
unknown
Published: Jan. 29, 2025
Summary
Establishment
of
N.
benthamiana
as
a
robust
biofactory
is
complicated
by
issues
such
product
toxicity
and
proteolytic
degradation
target
proteins
/
introduced
enzymes.
Here
we
investigate
whether
biomolecular
condensates
can
be
used
to
address
these
problems.
We
engineered
in
leaves
using
transient
expression
synthetic
modular
scaffolds.
The
vivo
properties
the
that
resulted
were
consistent
with
them
being
liquid-like
bodies
thermodynamic
features
typical
multicomponent
phase-separating
systems.
show
recruitment
enzymes
led
several
fold
yield
increases
one-
three-step
metabolic
pathways
(citramalate
biosynthesis
poly-3-hydroxybutyrate
(PHB)
biosynthesis,
respectively).
This
enhanced
could
for
reasons
including
improved
enzyme
kinetics,
metabolite
channelling
or
avoidance
cytotoxicity
retention
pathway
within
condensate,
which
was
demonstrated
PHB.
However,
also
observed
several-fold
increase
amount
accumulated
when
they
targeted
condensates.
suggests
more
stable
localised
condensate
than
freely
diffusing
cytosol.
hypothesise
this
stability
likely
main
driver
increased
production.
Our
findings
provide
foundation
leveraging
plant
engineering
advance
versatile
industrial
applications.
Plant Biotechnology Journal,
Journal Year:
2025,
Volume and Issue:
unknown
Published: April 9, 2025
Summary
The
establishment
of
Nicotiana
benthamiana
as
a
robust
biofactory
is
complicated
by
issues
such
product
toxicity
and
proteolytic
degradation
target
proteins/introduced
enzymes.
Here
we
investigate
whether
biomolecular
condensates
can
be
used
to
address
these
problems.
We
engineered
in
N.
leaves
using
transient
expression
synthetic
modular
scaffolds.
vivo
properties
the
that
resulted
were
consistent
with
them
being
liquid‐like
bodies
thermodynamic
features
typical
multicomponent
phase‐separating
systems.
show
recruitment
enzymes
led
several‐fold
yield
increases
one‐
three‐step
metabolic
pathways
(citramalate
biosynthesis
poly‐3‐hydroxybutyrate
(PHB)
biosynthesis,
respectively).
This
enhanced
could
for
several
reasons
including
improved
enzyme
kinetics,
metabolite
channelling
or
avoidance
cytotoxicity
retention
pathway
within
condensate,
which
was
demonstrated
PHB.
However,
also
observed
increase
amount
accumulated
when
they
targeted
condensates.
suggests
more
stable
localised
condensate
than
freely
diffusing
cytosol.
hypothesise
this
stability
likely
main
driver
increased
production.
Our
findings
provide
foundation
leveraging
plant
engineering
advance
versatile
industrial
applications.
The Plant Journal,
Journal Year:
2025,
Volume and Issue:
122(1)
Published: April 1, 2025
SUMMARY
Plants
make
structurally
diverse
triterpenoids
for
their
physiological
needs,
which
have
shown
numerous
therapeutic
applications.
Arjuna
tree
(
Terminalia
arjuna
)
produces
bioactive
oleanane
(β‐amyrin‐derived)
arjunic
acid,
arjungenin,
and
arjunolic
the
respective
C28‐
O
‐glucopyranosyl
esters
arjunetin,
arjunglucoside
I,
II.
Arjunic
acid
arjunetin
are
major
oleananes
in
bark,
while
II
found
minor
levels.
Although
arjungenin
was
detected
at
a
considerable
level,
I
only
trace
suggesting
selective
biosynthesis
and/or
accumulation
of
triterpenoid
glucosyl
bark.
However,
enzyme
contributing
to
‐glucosylation
not
characterized.
We
mined
RNA‐sequencing
data
identified
UDP‐glucosyltransferase
(UGT)
transcripts
that
were
enriched
bark
transcriptome.
Further,
biochemical
screening
UGTs
UGT73FB1,
catalyzed
scaffold‐selective
manner.
Recombinant
UGT73FB1
produced
Escherichia
coli
or
Nicotiana
benthamiana
formed
II,
but
ester
(arjunglucoside
I).
Interestingly,
showed
better
activity
using
than
ursanes
(α‐amyrin‐derived),
it
did
show
various
lupane
(lupeol‐derived).
Overall,
spatial
patterns
transcript
expression
suggested
role
arjuna.
Moreover,
co‐expression
with
β‐amyrin
synthase
C2,
C23,
C28
hydroxylases/oxidases
led
complete
reconstruction
pathway
N.
,
utility
enzymes
rare
glucopyranosyl
heterologous
hosts.
The Plant Journal,
Journal Year:
2025,
Volume and Issue:
121(6)
Published: March 1, 2025
SUMMARY
Plants
are
a
valuable
source
of
diverse
specialized
metabolites
with
numerous
applications.
However,
these
compounds
often
produced
in
limited
quantities,
particularly
under
unfavorable
ecological
conditions.
To
achieve
sufficient
levels
target
metabolites,
alternative
strategies
such
as
pathway
engineering
heterologous
systems
like
microbes
(e.g.,
bacteria
and
fungi)
or
cell‐free
can
be
employed.
Another
approach
is
plant
engineering,
which
aims
to
either
enhance
the
native
production
original
reconstruct
model
system.
Although
increasing
metabolite
promising
strategy,
plants
exotic
pose
significant
challenges
for
genetic
manipulation.
Effective
requires
comprehensive
prior
knowledge
genes
enzymes
involved,
well
precursor,
intermediate,
branching,
final
metabolites.
Thus,
thorough
elucidation
biosynthetic
closely
linked
successful
metabolic
host
systems.
In
this
review,
we
highlight
recent
advances
engineering.
We
focus
on
efforts
engineer
complex,
multi‐step
pathways
that
require
expression
at
least
eight
transient
three
stable
transformation.
Reports
complex
stably
transformed
remain
relatively
scarce.
discuss
major
hurdles
overcoming
them,
followed
by
an
overview
achievements,
challenges,
solutions
reconstitution
through
Recent
including
computer‐based
predictions
offer
platforms
sustainable
plants.
Comprehensive Reviews in Food Science and Food Safety,
Journal Year:
2025,
Volume and Issue:
24(2)
Published: March 1, 2025
Abstract
Recently,
the
non‐intestinal
functions
of
human
milk
oligosaccharides
(HMOs)
have
been
widely
documented,
including
their
roles
in
promoting
brain
development
and
growth,
as
well
ameliorating
anxiety,
allergies,
obesity.
Understanding
mechanisms
action
is
becoming
increasingly
critical.
Furthermore,
these
effects
are
frequently
associated
with
type
structure
HMOs.
As
an
innovative
technology,
“plant
factory”
expected
to
complement
traditional
synthesis
technology.
This
study
reviews
novel
techniques.
Particular
emphasis
placed
on
processes,
advantages,
limitations
technology
can
express
genes
related
HMO
instantaneously
plant
leaves,
thereby
enabling
rapid
cost‐effective
generation
However,
remains
underdeveloped,
challenges
low
yield
unsustainable
production
must
be
addressed.
we
present
overview
most
recent
clinical
preclinical
studies
review
emphasizes
underlying
HMOs
primarily
exert
through
cleavage
beneficial
monomer
components,
metabolism
produce
advantageous
metabolites,
regulation
immune
responses.
PLoS Biology,
Journal Year:
2024,
Volume and Issue:
22(11), P. e3002886 - e3002886
Published: Nov. 5, 2024
Genomics-based
predictions
indicate
that
plants
harbor
the
ability
to
make
a
vast
array
of
as
yet
undiscovered
chemistry.
Recent
advances
open
up
potential
harness
this
capability
at
unprecedented
scale
for
discovery
and
development
new
therapeutics.
bioRxiv (Cold Spring Harbor Laboratory),
Journal Year:
2024,
Volume and Issue:
unknown
Published: Oct. 10, 2024
ABSTRACT
High-throughput
experiments
in
plants
are
hindered
by
long
generation
times
and
high
costs.
To
address
these
challenges,
we
present
an
optimized
pipeline
for
Agrobacterium
tumefaciens
transformation
simplified
a
protocol
to
obtain
stable
transgenic
lines
of
the
model
liverwort
Marchantia
polymorpha
,
paving
way
efficient
high-throughput
plant
synthetic
biology
other
applications.
Our
involves
freeze-thaw
method
6-well
plates
that
can
be
adapted
robotic
automation.
Using
Opentrons
open-source
platform,
implemented
semi-automated
showing
similar
efficiency
compared
manual
manipulation.
Additionally,
have
streamlined
process
selection
M.
reducing
cost,
time,
labour
without
compromising
efficiency.
The
addition
sucrose
media
significantly
enhances
production
gemmae,
accelerating
isogenic
plants.
We
believe
protocols
potential
facilitate
screenings
diverse
species
represent
significant
step
towards
full
automation
pipelines.
This
approach
allows
testing
∼100
constructs
per
month,
using
conventional
tissue
culture
facilities.
recently
demonstrated
successful
implementation
this
screening
hundreds
fluorescent
reporters
gemmae.
Agronomy,
Journal Year:
2024,
Volume and Issue:
14(11), P. 2460 - 2460
Published: Oct. 22, 2024
Anisodus
luridus,
a
perennial
herb
belonging
to
the
genus
of
Solanaceae
family,
is
an
important
Tibetan
medicinal
plant
that
produces
pharmaceutical
tropane
alkaloids
(TAs)
including
hyoscyamine
and
scopolamine.
Its
high
yield
makes
A.
luridus
valuable
source
for
commercially
producing
TAs.
In
this
study,
we
conduct
homologous
gene
research
across
transcriptome
data
different
tissues
together
with
functionally
tested
sequences
in
Atropa
belladonna
as
reference
identify
13
candidate
genes
TAs
biosynthesis
luridus.
The
results
show
these
identified
were
highly
conserved
terms
sequence
similarity
expression
patterns
compared
belladonna,
suggesting
two
species
may
share
same
biosynthetic
pathway
biosynthesis.
Furthermore,
scopolamine
was
detected
Nicotiana
benthamiana
leaves
when
enzymes
co-expressed
N.
benthamiana,
which
confirmed
are
involved
our
study
not
only
systematically
elucidate
alkaloid
but
also
realize
de
novo
synthesis
first
time.
It
now
possible
make
potential
production
through
synthetic
biology
techniques.